HEADER TRANSCRIPTION/TRANSCRIPTION INHIBITOR 05-JUN-18 6DML TITLE A MULTICONFORMER LIGAND MODEL OF 3,5 DIMETHYLISOXAXOLE BOUND TO THE TITLE 2 BROMODOMAIN OF HUMAN BRD4 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, MULTICONFORMER MODEL, TRANSCRIPTION, TRANSCRIPTION- KEYWDS 2 TRANSCRIPTION INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.M.HUDSON,G.VAN ZUNDERT,D.KEEDY,R.FONSECA,A.HELIOU,P.SURESH, AUTHOR 2 K.BORRELLI,T.DAY,J.S.FRASER,H.VAN DEN BEDEM REVDAT 3 13-MAR-24 6DML 1 REMARK REVDAT 2 24-APR-19 6DML 1 JRNL REVDAT 1 19-DEC-18 6DML 0 JRNL AUTH G.C.P.VAN ZUNDERT,B.M.HUDSON,S.H.P.DE OLIVEIRA,D.A.KEEDY, JRNL AUTH 2 R.FONSECA,A.HELIOU,P.SURESH,K.BORRELLI,T.DAY,J.S.FRASER, JRNL AUTH 3 H.VAN DEN BEDEM JRNL TITL QFIT-LIGAND REVEALS WIDESPREAD CONFORMATIONAL HETEROGENEITY JRNL TITL 2 OF DRUG-LIKE MOLECULES IN X-RAY ELECTRON DENSITY MAPS. JRNL REF J. MED. CHEM. V. 61 11183 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 30457858 JRNL DOI 10.1021/ACS.JMEDCHEM.8B01292 REMARK 0 REMARK 0 THIS ENTRY 6DML REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL REMARK 0 DATA IN 4BW3, DETERMINED BY C.CHUNG,O.MIRGUET,Y.LAMOTTE, REMARK 0 P.BAMBOROUGH,D.DELANNEE,A.BOUILLOT,F.GELLIBERT,G.KRYSA,A.LEWIS, REMARK 0 J.WITHERINGTON,P.HUET,Y.DUDIT,L.TROTTET,E.NICODEME REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH O.MIRGUET,Y.LAMOTTE,C.W.CHUNG,P.BAMBOROUGH,D.DELANNEE, REMARK 1 AUTH 2 A.BOUILLOT,F.GELLIBERT,G.KRYSA,A.LEWIS,J.WITHERINGTON, REMARK 1 AUTH 3 P.HUET,Y.DUDIT,L.TROTTET,E.NICODEME REMARK 1 TITL NAPHTHYRIDINES AS NOVEL BET FAMILY BROMODOMAIN INHIBITORS. REMARK 1 REF CHEMMEDCHEM V. 9 580 2014 REMARK 1 REFN ESSN 1860-7187 REMARK 1 PMID 24000170 REMARK 1 DOI 10.1002/CMDC.201300259 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11_2558 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21405 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1098 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 38.1474 - 2.9996 0.99 2675 150 0.1492 0.1877 REMARK 3 2 2.9996 - 2.3810 1.00 2593 122 0.1497 0.1968 REMARK 3 3 2.3810 - 2.0800 1.00 2535 133 0.1307 0.1961 REMARK 3 4 2.0800 - 1.8899 1.00 2512 153 0.1365 0.1724 REMARK 3 5 1.8899 - 1.7544 1.00 2527 114 0.1387 0.2007 REMARK 3 6 1.7544 - 1.6510 1.00 2521 143 0.1449 0.2024 REMARK 3 7 1.6510 - 1.5683 1.00 2458 137 0.1529 0.1974 REMARK 3 8 1.5683 - 1.5000 1.00 2486 146 0.1688 0.2366 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.00 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.19 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 : 0.011 1190 REMARK 3 ANGLE : 1.306 1627 REMARK 3 CHIRALITY : 0.056 162 REMARK 3 PLANARITY : 0.007 204 REMARK 3 DIHEDRAL : 12.500 707 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 6DML COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234894. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21405 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 38.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 15.5 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: AUTHOR USED THE SF DATA FROM ENTRY 5CFW REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2M NANO3, 0.1M BIS-TRIS REMARK 280 -PROPANE PH8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 21.78500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.51000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.42500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.51000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.78500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.42500 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 O HOH A 306 O HOH A 321 2.11 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 EDO A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9BM A 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BW3 RELATED DB: PDB REMARK 900 THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 3,5 REMARK 900 DIMETHYLISOXAXOLE LIGAND DBREF 6DML A 44 168 UNP O60885 BRD4_HUMAN 44 168 SEQADV 6DML SER A 42 UNP O60885 EXPRESSION TAG SEQADV 6DML 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 EDO A 201 10 HET EDO A 202 10 HET EDO A 203 10 HET 9BM A 204 116 HETNAM EDO 1,2-ETHANEDIOL HETNAM 9BM 4-((2-(TERT-BUTYL)PHENYL)AMINO)-7-(3,5- HETNAM 2 9BM DIMETHYLISOXAZOL-4-YL)-6-METHOXY-1,5-NAPHTHYRIDINE-3- HETNAM 3 9BM CARBOXYLIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 3(C2 H6 O2) FORMUL 5 9BM C25 H26 N4 O4 FORMUL 6 HOH *190(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 GLU A 163 1 20 SITE 1 AC1 5 GLN A 85 EDO A 203 HOH A 306 HOH A 336 SITE 2 AC1 5 HOH A 483 SITE 1 AC2 3 GLN A 64 LYS A 155 GLN A 159 SITE 1 AC3 7 PRO A 86 GLY A 108 THR A 109 LYS A 112 SITE 2 AC3 7 EDO A 201 HOH A 306 HOH A 448 SITE 1 AC4 15 SER A 51 LYS A 57 TRP A 81 PRO A 82 SITE 2 AC4 15 PHE A 83 LEU A 92 LEU A 94 GLU A 115 SITE 3 AC4 15 ASN A 116 ASN A 140 ILE A 146 HOH A 305 SITE 4 AC4 15 HOH A 307 HOH A 322 HOH A 363 CRYST1 43.570 48.850 61.020 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 0.022952 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020471 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016388 0.00000