HEADER TRANSFERASE/TRANSFERASE INHIBITOR 07-SEP-17 6AY5 TITLE CREBBP BROMODOMAIN IN COMPLEX WITH CPD17 (5-(7-(DIFLUOROMETHYL)-6-(1- TITLE 2 METHYL-1H-PYRAZOL-4-YL)-3,4-DIHYDROQUINOLIN-1(2H)-YL)-3- TITLE 3 METHYLBENZO[D]THIAZOL-2(3H)-ONE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CREB-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BROMODOMAIN (UNP RESIDUE 1083-1197); COMPND 5 EC: 2.3.1.48; 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: CREBBP, CBP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CREBBP, BROMODOMAIN, SBDD, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.M.MURRAY REVDAT 2 04-OCT-23 6AY5 1 REMARK REVDAT 1 21-FEB-18 6AY5 0 JRNL AUTH S.M.BRONNER,J.MURRAY,F.A.ROMERO,K.W.LAI,V.TSUI,P.CYR, JRNL AUTH 2 M.H.BERESINI,G.DE LEON BOENIG,Z.CHEN,E.F.CHOO,K.R.CLARK, JRNL AUTH 3 T.D.CRAWFORD,H.JAYARAM,S.KAUFMAN,R.LI,Y.LI,J.LIAO,X.LIANG, JRNL AUTH 4 W.LIU,J.LY,J.MAHER,J.WAI,F.WANG,A.ZHENG,X.ZHU,S.MAGNUSON JRNL TITL A UNIQUE APPROACH TO DESIGN POTENT AND SELECTIVE CYCLIC JRNL TITL 2 ADENOSINE MONOPHOSPHATE RESPONSE ELEMENT BINDING PROTEIN, JRNL TITL 3 BINDING PROTEIN (CBP) INHIBITORS. JRNL REF J. MED. CHEM. V. 60 10151 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 29155580 JRNL DOI 10.1021/ACS.JMEDCHEM.7B01372 REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_2747 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 25638 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1311 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 26.2338 - 2.9828 0.98 2851 141 0.1628 0.1686 REMARK 3 2 2.9828 - 2.3680 1.00 2763 157 0.1724 0.1821 REMARK 3 3 2.3680 - 2.0688 1.00 2728 153 0.1485 0.1799 REMARK 3 4 2.0688 - 1.8797 1.00 2703 160 0.1430 0.1907 REMARK 3 5 1.8797 - 1.7450 1.00 2702 155 0.1501 0.1913 REMARK 3 6 1.7450 - 1.6421 1.00 2695 148 0.1547 0.1870 REMARK 3 7 1.6421 - 1.5599 0.99 2672 145 0.1697 0.2126 REMARK 3 8 1.5599 - 1.4920 1.00 2684 119 0.2039 0.2279 REMARK 3 9 1.4920 - 1.4346 0.94 2529 133 0.2497 0.3551 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.03 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 : 0.013 1110 REMARK 3 ANGLE : 1.335 1521 REMARK 3 CHIRALITY : 0.089 147 REMARK 3 PLANARITY : 0.010 199 REMARK 3 DIHEDRAL : 20.578 418 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 1083:1197 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.401 3.046 6.982 REMARK 3 T TENSOR REMARK 3 T11: 0.1417 T22: 0.1385 REMARK 3 T33: 0.1574 T12: 0.0188 REMARK 3 T13: 0.0010 T23: 0.0124 REMARK 3 L TENSOR REMARK 3 L11: 0.9052 L22: 0.8150 REMARK 3 L33: 1.9049 L12: 0.2048 REMARK 3 L13: 0.3487 L23: -0.0526 REMARK 3 S TENSOR REMARK 3 S11: 0.0250 S12: -0.0607 S13: -0.0346 REMARK 3 S21: 0.0710 S22: 0.0144 S23: -0.0386 REMARK 3 S31: 0.1188 S32: 0.0372 S33: -0.0102 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 1201:1201 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.278 3.189 -1.762 REMARK 3 T TENSOR REMARK 3 T11: 0.2419 T22: 0.2348 REMARK 3 T33: 0.2411 T12: -0.0052 REMARK 3 T13: -0.0135 T23: 0.0203 REMARK 3 L TENSOR REMARK 3 L11: 5.5446 L22: 1.2523 REMARK 3 L33: 4.2906 L12: -1.6165 REMARK 3 L13: -3.6441 L23: 1.8020 REMARK 3 S TENSOR REMARK 3 S11: 0.1185 S12: 0.1299 S13: 0.1415 REMARK 3 S21: -0.1277 S22: 0.0483 S23: 0.1311 REMARK 3 S31: -0.1975 S32: -0.4173 S33: -0.0125 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 6AY5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000229989. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 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 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25692 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.97800 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDBID 5I8B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MGCL2, 0.1M BIS-TRIS PH6.5, 22% REMARK 280 PEG3350, VAPOR DIFFUSION, 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 17.21750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.48250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.61600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.48250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.21750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.61600 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C3V A 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 1204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1205 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6AY3 RELATED DB: PDB REMARK 900 SAME PROTEIN DIFFERENT INHIBITOR REMARK 900 RELATED ID: 6AXQ RELATED DB: PDB DBREF 6AY5 A 1083 1197 UNP Q92793 CBP_HUMAN 1083 1197 SEQRES 1 A 115 LYS ILE PHE LYS PRO GLU GLU LEU ARG GLN ALA LEU MET SEQRES 2 A 115 PRO THR LEU GLU ALA LEU TYR ARG GLN ASP PRO GLU SER SEQRES 3 A 115 LEU PRO PHE ARG GLN PRO VAL ASP PRO GLN LEU LEU GLY SEQRES 4 A 115 ILE PRO ASP TYR PHE ASP ILE VAL LYS ASN PRO MET ASP SEQRES 5 A 115 LEU SER THR ILE LYS ARG LYS LEU ASP THR GLY GLN TYR SEQRES 6 A 115 GLN GLU PRO TRP GLN TYR VAL ASP ASP VAL TRP LEU MET SEQRES 7 A 115 PHE ASN ASN ALA TRP LEU TYR ASN ARG LYS THR SER ARG SEQRES 8 A 115 VAL TYR LYS PHE CYS SER LYS LEU ALA GLU VAL PHE GLU SEQRES 9 A 115 GLN GLU ILE ASP PRO VAL MET GLN SER LEU GLY HET C3V A1201 30 HET SO4 A1202 5 HET SO4 A1203 5 HET DMS A1204 4 HET GOL A1205 6 HETNAM C3V 5-[7-(DIFLUOROMETHYL)-6-(1-METHYL-1H-PYRAZOL-4-YL)-3,4- HETNAM 2 C3V DIHYDROQUINOLIN-1(2H)-YL]-3-METHYL-1,3-BENZOTHIAZOL- HETNAM 3 C3V 2(3H)-ONE HETNAM SO4 SULFATE ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 C3V C22 H20 F2 N4 O S FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 DMS C2 H6 O S FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *156(H2 O) HELIX 1 AA1 LYS A 1086 ARG A 1103 1 18 HELIX 2 AA2 SER A 1108 ARG A 1112 5 5 HELIX 3 AA3 ASP A 1116 GLY A 1121 1 6 HELIX 4 AA4 ASP A 1124 VAL A 1129 1 6 HELIX 5 AA5 ASP A 1134 THR A 1144 1 11 HELIX 6 AA6 GLU A 1149 ASN A 1168 1 20 HELIX 7 AA7 SER A 1172 GLY A 1197 1 26 CISPEP 1 ASP A 1105 PRO A 1106 0 5.83 SITE 1 AC1 12 LEU A1109 PRO A1110 VAL A1115 ILE A1122 SITE 2 AC1 12 TYR A1125 ASN A1168 ARG A1173 PHE A1177 SITE 3 AC1 12 GOL A1205 HOH A1310 HOH A1317 HOH A1413 SITE 1 AC2 5 TYR A1102 ARG A1112 GLN A1113 HOH A1318 SITE 2 AC2 5 HOH A1328 SITE 1 AC3 5 ARG A1169 LYS A1170 GLN A1194 HOH A1315 SITE 2 AC3 5 HOH A1326 SITE 1 AC4 3 TYR A1102 ARG A1112 HOH A1309 SITE 1 AC5 3 ARG A1173 C3V A1201 HOH A1306 CRYST1 34.435 49.232 80.965 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 0.029040 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020312 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012351 0.00000