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Database: PDB
Entry: 5Z5T
LinkDB: 5Z5T
Original site: 5Z5T 
HEADER    TRANSCRIPTION/INHIBITOR                 20-JAN-18   5Z5T              
TITLE     THE FIRST BROMODOMAIN OF BRD4 WITH COMPOUND BDF-2141                  
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4;                          
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: FIRST BROMODOMAIN;                                         
COMPND   5 SYNONYM: PROTEIN HUNK1;                                              
COMPND   6 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: BRD4, HUNK1;                                                   
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    BRD4, INHIBITOR, COMPLEX, PROTEIN BINDING, TRANSCRIPTION-INHIBITOR    
KEYWDS   2 COMPLEX                                                              
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    H.ZHANG,C.LUO                                                         
REVDAT   3   22-NOV-23 5Z5T    1       REMARK                                   
REVDAT   2   06-MAR-19 5Z5T    1       JRNL                                     
REVDAT   1   23-JAN-19 5Z5T    0                                                
JRNL        AUTH   W.CHEN,H.ZHANG,Z.CHEN,H.JIANG,L.LIAO,S.FAN,J.XING,Y.XIE,     
JRNL        AUTH 2 S.CHEN,H.DING,K.CHEN,H.JIANG,C.LUO,M.ZHENG,Z.YAO,Y.HUANG,    
JRNL        AUTH 3 Y.ZHANG                                                      
JRNL        TITL   DEVELOPMENT AND EVALUATION OF A NOVEL SERIES OF              
JRNL        TITL 2 NITROXOLINE-DERIVED BET INHIBITORS WITH ANTITUMOR ACTIVITY   
JRNL        TITL 3 IN RENAL CELL CARCINOMA.                                     
JRNL        REF    ONCOGENESIS                   V.   7    83 2018              
JRNL        REFN                   ISSN 2157-9024                               
JRNL        PMID   30385738                                                     
JRNL        DOI    10.1038/S41389-018-0093-Z                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.99 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX (1.10.1_2155)                                 
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN            
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,           
REMARK   3               : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,            
REMARK   3               : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,              
REMARK   3               : REETAL PAI,RANDY READ,JANE RICHARDSON,               
REMARK   3               : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,           
REMARK   3               : NICHOLAS SAUTER,JACOB SMITH,LAURENT                  
REMARK   3               : STORONI,TOM TERWILLIGER,PETER ZWART                  
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : NULL                                          
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 40.48                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.340                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.6                           
REMARK   3   NUMBER OF REFLECTIONS             : 8839                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.207                           
REMARK   3   R VALUE            (WORKING SET) : 0.204                           
REMARK   3   FREE R VALUE                     : 0.244                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 6.170                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 545                             
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).                           
REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE        
REMARK   3     1 40.4931 -  3.1604    1.00     2174   144  0.1756 0.2114        
REMARK   3     2  3.1604 -  2.5086    1.00     2057   134  0.2196 0.2405        
REMARK   3     3  2.5086 -  2.1916    0.99     2041   135  0.2376 0.2874        
REMARK   3     4  2.1916 -  1.9912    1.00     2022   132  0.2563 0.3168        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : NULL                                          
REMARK   3   SOLVENT RADIUS     : 1.11                                          
REMARK   3   SHRINKAGE RADIUS   : 0.90                                          
REMARK   3   K_SOL              : NULL                                          
REMARK   3   B_SOL              : NULL                                          
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.170            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.310           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL                           
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : NULL                                                 
REMARK   3    B22 (A**2) : NULL                                                 
REMARK   3    B33 (A**2) : NULL                                                 
REMARK   3    B12 (A**2) : NULL                                                 
REMARK   3    B13 (A**2) : NULL                                                 
REMARK   3    B23 (A**2) : NULL                                                 
REMARK   3                                                                      
REMARK   3  TWINNING INFORMATION.                                               
REMARK   3   FRACTION: NULL                                                     
REMARK   3   OPERATOR: NULL                                                     
REMARK   3                                                                      
REMARK   3  DEVIATIONS FROM IDEAL VALUES.                                       
REMARK   3                 RMSD          COUNT                                  
REMARK   3   BOND      :  0.007           1086                                  
REMARK   3   ANGLE     :  0.955           1479                                  
REMARK   3   CHIRALITY :  0.045            155                                  
REMARK   3   PLANARITY :  0.005            189                                  
REMARK   3   DIHEDRAL  : 11.228            658                                  
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : NULL                                       
REMARK   3                                                                      
REMARK   3  NCS DETAILS                                                         
REMARK   3   NUMBER OF NCS GROUPS : NULL                                        
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 5Z5T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JAN-18.                  
REMARK 100 THE DEPOSITION ID IS D_1300006524.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 17-OCT-16                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : NULL                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SSRF                               
REMARK 200  BEAMLINE                       : BL19U1                             
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9785                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : DECTRIS PILATUS3 S 6M              
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : AIMLESS                            
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 8867                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.991                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 40.480                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 100.0                              
REMARK 200  DATA REDUNDANCY                : 2.000                              
REMARK 200  R MERGE                    (I) : NULL                               
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 25.2400                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.06                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHASER                                                
REMARK 200 STARTING MODEL: 5H21                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 40.18                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 10-15% GLYCEROL, 4M SODIUM FORMATE,      
REMARK 280  VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K                     
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21                       
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X+1/2,-Y,Z+1/2                                         
REMARK 290       3555   -X,Y+1/2,-Z+1/2                                         
REMARK 290       4555   X+1/2,-Y+1/2,-Z                                         
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       16.54950            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       39.06100            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       23.66850            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       39.06100            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       16.54950            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       23.66850            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                         
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465     GLU A   167                                                      
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT                     
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500   OE2  GLU A   163     O    HOH A   301              1.84            
REMARK 500   NE2  GLN A    62     O    HOH A   302              1.94            
REMARK 500   OH   TYR A    65     O    HOH A   303              1.98            
REMARK 500   O    HOH A   365     O    HOH A   373              2.01            
REMARK 500   O    HOH A   331     O    HOH A   353              2.06            
REMARK 500   O    ILE A   138     O    HOH A   304              2.07            
REMARK 500   OE1  GLU A   151     O    HOH A   305              2.11            
REMARK 500   O    HOH A   375     O    HOH A   378              2.14            
REMARK 500   O    HOH A   306     O    HOH A   345              2.19            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS                                             
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC             
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  AN ATOM LOCATED WITHIN 0.15          
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A           
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375             
REMARK 500 INSTEAD OF REMARK 500.  ATOMS WITH NON-BLANK ALTERNATE               
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.            
REMARK 500                                                                      
REMARK 500 DISTANCE CUTOFF:                                                     
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS              
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS                  
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE          
REMARK 500   O    ASN A   140     O    HOH A   301     4445     2.10            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: TORSION ANGLES                                             
REMARK 500                                                                      
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:            
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)                    
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-           
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400            
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        PSI       PHI                                   
REMARK 500    ASN A  52      108.29   -162.06                                   
REMARK 500    LEU A  94       63.23   -115.96                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue 96R A 201                 
DBREF  5Z5T A   44   167  UNP    O60885   BRD4_HUMAN      44    167             
SEQADV 5Z5T MET A   43  UNP  O60885              INITIATING METHIONINE          
SEQRES   1 A  125  MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN LYS          
SEQRES   2 A  125  PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU ARG          
SEQRES   3 A  125  VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA TRP          
SEQRES   4 A  125  PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN LEU          
SEQRES   5 A  125  PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP MET          
SEQRES   6 A  125  GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR TRP          
SEQRES   7 A  125  ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET PHE          
SEQRES   8 A  125  THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP ILE          
SEQRES   9 A  125  VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU GLN          
SEQRES  10 A  125  LYS ILE ASN GLU LEU PRO THR GLU                              
HET    96R  A 201      17                                                       
HETNAM     96R 2-AMINO-4-(1H-IMIDAZOL-1-YL)QUINOLIN-8-OL                        
FORMUL   2  96R    C12 H10 N4 O                                                 
FORMUL   3  HOH   *81(H2 O)                                                     
HELIX    1 AA1 THR A   60  VAL A   69  1                                  10    
HELIX    2 AA2 VAL A   69  TRP A   75  1                                   7    
HELIX    3 AA3 ALA A   80  GLN A   84  5                                   5    
HELIX    4 AA4 ASP A   96  ILE A  101  1                                   6    
HELIX    5 AA5 ASP A  106  ASN A  116  1                                  11    
HELIX    6 AA6 ASN A  121  ASN A  140  1                                  20    
HELIX    7 AA7 ASP A  144  ILE A  161  1                                  18    
SITE     1 AC1 11 TRP A  81  PHE A  83  VAL A  87  LEU A  92                    
SITE     2 AC1 11 TYR A  97  CYS A 136  TYR A 139  ASN A 140                    
SITE     3 AC1 11 ILE A 146  HOH A 309  HOH A 369                               
CRYST1   33.099   47.337   78.122  90.00  90.00  90.00 P 21 21 21    4          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      0.030212  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.021125  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.012800        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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