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