HEADER TRANSCRIPTION/TRANSCRIPTION INHIBITOR 30-JUN-14 4QR5 TITLE BRD4 BROMODOMAIN 1 COMPLEX WITH ITS NOVEL INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 44-166; 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS BRD4, BROMODOMAIN, FOUR ALPHA HELICES, TRANSCRIPTION-TRANSCRIPTION KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.XIONG,D.Y.CAO,T.T.CHEN,Y.C.XU REVDAT 2 20-MAR-24 4QR5 1 REMARK SEQADV REVDAT 1 01-JUL-15 4QR5 0 JRNL AUTH L.ZHAO,Y.WANG,D.Y.CAO,T.T.CHEN,Q.WANG,Y.LI,Y.C.XU,N.ZHANG, JRNL AUTH 2 X.WANG,D.CHEN,L.CHEN,Y.L.CHEN,G.XIA,Z.SHI,Y.C.LIU,Y.LIN, JRNL AUTH 3 Z.MIAO,J.SHEN,B.XIONG JRNL TITL FRAGMENT-BASED DRUG DISCOVERY OF 2-THIAZOLIDINONES AS BRD4 JRNL TITL 2 INHIBITORS: 2. STRUCTURE-BASED OPTIMIZATION JRNL REF J.MED.CHEM. V. 58 1281 2015 JRNL REFN ISSN 0022-2623 JRNL PMID 25559428 JRNL DOI 10.1021/JM501504K REMARK 2 REMARK 2 RESOLUTION. 1.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 23618 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.430 REMARK 3 FREE R VALUE TEST SET COUNT : 1991 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 30.3598 - 4.2264 0.98 1483 141 0.1536 0.1586 REMARK 3 2 4.2264 - 3.3560 0.99 1492 133 0.1325 0.1669 REMARK 3 3 3.3560 - 2.9322 0.99 1498 133 0.1729 0.2150 REMARK 3 4 2.9322 - 2.6642 1.00 1500 139 0.1771 0.1905 REMARK 3 5 2.6642 - 2.4734 1.00 1491 137 0.1632 0.1880 REMARK 3 6 2.4734 - 2.3276 1.00 1516 133 0.1533 0.1404 REMARK 3 7 2.3276 - 2.2111 1.00 1507 143 0.1531 0.1788 REMARK 3 8 2.2111 - 2.1148 1.00 1482 133 0.1506 0.1699 REMARK 3 9 2.1148 - 2.0335 1.00 1489 137 0.1621 0.1755 REMARK 3 10 2.0335 - 1.9633 1.00 1515 140 0.1575 0.1774 REMARK 3 11 1.9633 - 1.9019 1.00 1516 139 0.1619 0.1880 REMARK 3 12 1.9019 - 1.8476 0.99 1486 139 0.1606 0.2282 REMARK 3 13 1.8476 - 1.7989 0.99 1507 137 0.1721 0.1997 REMARK 3 14 1.7989 - 1.7550 0.99 1497 136 0.1699 0.2048 REMARK 3 15 1.7550 - 1.7151 1.00 1499 135 0.1726 0.2162 REMARK 3 16 1.7151 - 1.6787 1.00 1482 138 0.1811 0.2493 REMARK 3 17 1.6787 - 1.6451 1.00 1545 143 0.1675 0.2035 REMARK 3 18 1.6451 - 1.6140 1.00 1477 135 0.1717 0.2135 REMARK 3 19 1.6140 - 1.5852 1.00 1458 139 0.1777 0.2022 REMARK 3 20 1.5852 - 1.5583 1.00 1536 140 0.1935 0.2023 REMARK 3 21 1.5583 - 1.5332 0.99 1491 139 0.2060 0.2139 REMARK 3 22 1.5332 - 1.5096 1.00 1486 137 0.2078 0.2063 REMARK 3 23 1.5096 - 1.4874 1.00 1521 146 0.2175 0.2694 REMARK 3 24 1.4874 - 1.4665 0.99 1492 137 0.2200 0.2762 REMARK 3 25 1.4665 - 1.4466 1.00 1497 142 0.2616 0.2937 REMARK 3 26 1.4466 - 1.4279 1.00 1475 137 0.2522 0.3267 REMARK 3 27 1.4279 - 1.4100 1.00 1532 140 0.2757 0.3404 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.20 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 : 0.006 1147 REMARK 3 ANGLE : 1.164 1570 REMARK 3 CHIRALITY : 0.070 162 REMARK 3 PLANARITY : 0.005 198 REMARK 3 DIHEDRAL : 14.537 451 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 4QR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000086408. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JAN-13 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 : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59372 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.93400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.6M NAFORMATE, 10% GLYCEROL, VAPOR REMARK 280 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 15.87000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.63500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.60000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.63500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.87000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.60000 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 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 315 2.02 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 HOH A 321 O HOH A 336 3454 2.12 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 52 107.79 -163.91 REMARK 500 LEU A 94 69.45 -119.19 REMARK 500 ASN A 140 -146.08 -113.53 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 BNM A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QR3 RELATED DB: PDB REMARK 900 RELATED ID: 4QR4 RELATED DB: PDB DBREF 4QR5 A 44 166 UNP O60885 BRD4_HUMAN 44 166 SEQADV 4QR5 SER A 42 UNP O60885 EXPRESSION TAG SEQADV 4QR5 MET A 43 UNP O60885 EXPRESSION TAG SEQRES 1 A 125 SER MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN SEQRES 2 A 125 LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU SEQRES 3 A 125 ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA SEQRES 4 A 125 TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN SEQRES 5 A 125 LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP SEQRES 6 A 125 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR SEQRES 7 A 125 TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET SEQRES 8 A 125 PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP SEQRES 9 A 125 ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU SEQRES 10 A 125 GLN LYS ILE ASN GLU LEU PRO THR HET BNM A 201 54 HETNAM BNM N-[3-(CYCLOPENTYLSULFAMOYL)-5-(2-OXO-2,3-DIHYDRO-1,3- HETNAM 2 BNM THIAZOL-4-YL)PHENYL]CYCLOPROPANECARBOXAMIDE FORMUL 2 BNM C18 H21 N3 O4 S2 FORMUL 3 HOH *143(H2 O) HELIX 1 1 THR A 60 VAL A 69 1 10 HELIX 2 2 VAL A 69 TRP A 75 1 7 HELIX 3 3 ALA A 80 GLN A 84 5 5 HELIX 4 4 ASP A 96 ILE A 101 1 6 HELIX 5 5 ASP A 106 ASN A 116 1 11 HELIX 6 6 ASN A 121 ASN A 140 1 20 HELIX 7 7 ASP A 144 ASN A 162 1 19 SITE 1 AC1 14 TRP A 81 PRO A 82 GLN A 85 LEU A 92 SITE 2 AC1 14 ASP A 96 LYS A 99 ILE A 100 ASN A 140 SITE 3 AC1 14 ASP A 145 ILE A 146 HOH A 303 HOH A 311 SITE 4 AC1 14 HOH A 327 HOH A 350 CRYST1 31.740 47.200 79.270 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 0.031506 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021186 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012615 0.00000