HEADER    GENE REGULATION                         14-AUG-19   6U0D              
TITLE     CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX   
TITLE    2 WITH THE INHIBITOR ZL0590                                            
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4;                          
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: PROTEIN HUNK1;                                              
COMPND   5 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 BL21(DE3);                       
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008                                      
KEYWDS    BROMODOMAIN, INHIBITOR, COMPLEX, GENE REGULATION                      
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    P.G.LEONARD,S.JOSEPH                                                  
REVDAT   3   11-OCT-23 6U0D    1       REMARK                                   
REVDAT   2   19-JAN-22 6U0D    1       SOURCE JRNL   REMARK SITE                
REVDAT   2 2                   1       ATOM                                     
REVDAT   1   19-AUG-20 6U0D    0                                                
JRNL        AUTH   Z.LIU,Y.LI,H.CHEN,H.LAI,P.WANG,S.WU,E.A.WOLD,P.G.LEONARD,    
JRNL        AUTH 2 S.JOSEPH,H.HU,C.CHIANG,A.R.BRASIER,B.TIAN,J.ZHOU             
JRNL        TITL   DISCOVERY, X-RAY CRYSTALLOGRAPHY, AND ANTI-INFLAMMATORY      
JRNL        TITL 2 ACTIVITY OF BROMODOMAIN-CONTAINING PROTEIN 4 (BRD4) BD1      
JRNL        TITL 3 INHIBITORS TARGETING A DISTINCT NEW BINDING SITE             
JRNL        REF    J. MED. CHEM.                              2022              
JRNL        REFN                   ISSN 0022-2623                               
JRNL        DOI    10.1021/ACS.JMEDCHEM.1C01851                                 
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.43 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.16-3549                                     
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) : 1.43                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 33.95                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.340                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 97.9                           
REMARK   3   NUMBER OF REFLECTIONS             : 23882                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.188                           
REMARK   3   R VALUE            (WORKING SET) : 0.185                           
REMARK   3   FREE R VALUE                     : 0.223                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 8.350                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 1995                            
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 33.9500 -  3.4430    0.93     1616   146  0.1518 0.1750        
REMARK   3     2  3.4430 -  2.7332    0.99     1623   148  0.1670 0.2163        
REMARK   3     3  2.7332 -  2.3878    1.00     1601   146  0.1835 0.2219        
REMARK   3     4  2.3878 -  2.1695    0.96     1546   142  0.1853 0.2012        
REMARK   3     5  2.1695 -  2.0140    0.98     1555   141  0.1790 0.2304        
REMARK   3     6  2.0140 -  1.8953    0.99     1578   143  0.1877 0.2134        
REMARK   3     7  1.8953 -  1.8004    0.99     1578   145  0.1997 0.2497        
REMARK   3     8  1.8004 -  1.7220    0.99     1558   142  0.1970 0.2725        
REMARK   3     9  1.7220 -  1.6557    0.98     1546   141  0.2178 0.2763        
REMARK   3    10  1.6557 -  1.5986    0.97     1552   142  0.2235 0.2662        
REMARK   3    11  1.5986 -  1.5486    0.98     1546   141  0.2297 0.2967        
REMARK   3    12  1.5486 -  1.5044    0.97     1513   138  0.2439 0.2962        
REMARK   3    13  1.5044 -  1.4648    0.98     1528   139  0.2771 0.3350        
REMARK   3    14  1.4648 -  1.4300    0.98     1547   141  0.2976 0.3287        
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) : 23.430           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 20.72                          
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      :   NULL           NULL                                  
REMARK   3   ANGLE     :   NULL           NULL                                  
REMARK   3   CHIRALITY :   NULL           NULL                                  
REMARK   3   PLANARITY :   NULL           NULL                                  
REMARK   3   DIHEDRAL  :   NULL           NULL                                  
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 6U0D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-19.                  
REMARK 100 THE DEPOSITION ID IS D_1000243587.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 09-JUL-19                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 7.5                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : APS                                
REMARK 200  BEAMLINE                       : 22-ID                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.00018                            
REMARK 200  MONOCHROMATOR                  : SI(111)                            
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : DECTRIS EIGER X 16M                
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.2.2                      
REMARK 200  DATA SCALING SOFTWARE          : AIMLESS 0.7.4                      
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 24020                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.429                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 33.954                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 98.7                               
REMARK 200  DATA REDUNDANCY                : 4.700                              
REMARK 200  R MERGE                    (I) : 0.16700                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 5.3000                             
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.45                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 99.6                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 4.70                               
REMARK 200  R MERGE FOR SHELL          (I) : 2.22500                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 1.300                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHASER 2.8.2                                          
REMARK 200 STARTING MODEL: 5KU3                                                 
REMARK 200                                                                      
REMARK 200 REMARK: ORTHORHOMBIC                                                 
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 41.73                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, 15% PEG 3350 AT PH 7.5,    
REMARK 280  VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K                     
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       18.73500            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       40.14500            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       21.19000            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       40.14500            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       18.73500            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       21.19000            
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PISA                                                  
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   168                                                      
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    VAL A  69      -62.56   -105.44                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  6U0D A   44   168  UNP    O60885   BRD4_HUMAN      44    168             
SEQADV 6U0D SER A   42  UNP  O60885              EXPRESSION TAG                 
SEQADV 6U0D MET A   43  UNP  O60885              EXPRESSION TAG                 
SEQRES   1 A  127  SER MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN          
SEQRES   2 A  127  LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU          
SEQRES   3 A  127  ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA          
SEQRES   4 A  127  TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN          
SEQRES   5 A  127  LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP          
SEQRES   6 A  127  MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR          
SEQRES   7 A  127  TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET          
SEQRES   8 A  127  PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP          
SEQRES   9 A  127  ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU          
SEQRES  10 A  127  GLN LYS ILE ASN GLU LEU PRO THR GLU GLU                      
HET    DMS  A 201       4                                                       
HET    POJ  A 202      35                                                       
HETNAM     DMS DIMETHYL SULFOXIDE                                               
HETNAM     POJ N-[4-({(2S)-2-[(MORPHOLIN-4-YL)METHYL]PYRROLIDIN-1-              
HETNAM   2 POJ  YL}SULFONYL)PHENYL]-N'-[4-(TRIFLUOROMETHYL)PHENYL]UREA          
FORMUL   2  DMS    C2 H6 O S                                                    
FORMUL   3  POJ    C23 H27 F3 N4 O4 S                                           
FORMUL   4  HOH   *185(H2 O)                                                    
HELIX    1 AA1 THR A   60  VAL A   69  1                                  10    
HELIX    2 AA2 VAL A   69  LYS A   76  1                                   8    
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  ASN A  162  1                                  19    
CRYST1   37.470   42.380   80.290  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      0.026688  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.023596  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.012455        0.00000