HEADER TRANSCRIPTION 24-MAR-22 7UGL TITLE BROMODOMAIN OF CBP LIGANDED WITH BMS-536924 AND SGC-CBP30 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE ACETYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.3.1.48; 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: CREBBP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BROMODOMAIN, SMALL MOLECULE LIGAND, COMPLEX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR E.SCHONBRUNN,M.BIKOWITZ REVDAT 2 25-OCT-23 7UGL 1 REMARK REVDAT 1 12-APR-23 7UGL 0 JRNL AUTH E.SCHONBRUNN,M.BIKOWITZ JRNL TITL STRUCTURAL BASIS OF CBP AND EP300 INTERACTION WITH KINASE JRNL TITL 2 INHIBITORS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 43711 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1747 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 40.5400 - 3.4300 1.00 3593 149 0.1570 0.1790 REMARK 3 2 3.4300 - 2.7300 1.00 3507 146 0.1590 0.1772 REMARK 3 3 2.7200 - 2.3800 1.00 3495 146 0.1444 0.1598 REMARK 3 4 2.3800 - 2.1600 1.00 3506 146 0.1378 0.1651 REMARK 3 5 2.1600 - 2.0100 1.00 3512 146 0.1480 0.1723 REMARK 3 6 2.0100 - 1.8900 1.00 3494 146 0.1591 0.2093 REMARK 3 7 1.8900 - 1.8000 1.00 3461 144 0.1741 0.1793 REMARK 3 8 1.8000 - 1.7200 1.00 3507 146 0.1676 0.1770 REMARK 3 9 1.7200 - 1.6500 1.00 3473 145 0.1708 0.2000 REMARK 3 10 1.6500 - 1.5900 1.00 3454 144 0.1824 0.2017 REMARK 3 11 1.5900 - 1.5400 1.00 3504 146 0.2146 0.2122 REMARK 3 12 1.5400 - 1.5000 0.99 3458 143 0.2699 0.2668 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.48 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -16.3893 14.4327 -20.5116 REMARK 3 T TENSOR REMARK 3 T11: 0.1193 T22: 0.0940 REMARK 3 T33: 0.1373 T12: -0.0053 REMARK 3 T13: 0.0089 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 1.0920 L22: 0.2164 REMARK 3 L33: 0.6412 L12: -0.0552 REMARK 3 L13: 0.3968 L23: -0.0762 REMARK 3 S TENSOR REMARK 3 S11: 0.0265 S12: -0.0110 S13: -0.0308 REMARK 3 S21: 0.0003 S22: -0.0099 S23: 0.0066 REMARK 3 S31: -0.0050 S32: -0.0088 S33: -0.0152 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 7UGL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000264155. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-21 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03319 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43721 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 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) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 7KPY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M DL-GLUTAMIC ACID MONOHYDRATE; REMARK 280 0.1 M DL-ALANINE; 0.1 M GLYCINE; 0.1 M DL-LYSINE REMARK 280 MONOHYDROCHLORIDE; 0.1 M DL-SERINE, 0.1 M IMIDAZOLE, 0.1 M MES REMARK 280 MONOHYDRATE (PH 6.5), 12 % (V/V) ETHYLENE GLYCOL, 6% W/V PEG REMARK 280 8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 29.74500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 LYS B 1082 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A1082 CG CD CE NZ REMARK 470 LYS B1086 CG CD CE NZ 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 N LYS B 1083 O HOH B 1301 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1450 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH B1433 DISTANCE = 5.83 ANGSTROMS REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 2LO B 1202 DBREF 7UGL A 1082 1197 UNP I3L466 I3L466_HUMAN 617 732 DBREF 7UGL B 1082 1197 UNP I3L466 I3L466_HUMAN 617 732 SEQRES 1 A 116 LYS LYS ILE PHE LYS PRO GLU GLU LEU ARG GLN ALA LEU SEQRES 2 A 116 MET PRO THR LEU GLU ALA LEU TYR ARG GLN ASP PRO GLU SEQRES 3 A 116 SER LEU PRO PHE ARG GLN PRO VAL ASP PRO GLN LEU LEU SEQRES 4 A 116 GLY ILE PRO ASP TYR PHE ASP ILE VAL LYS ASN PRO MET SEQRES 5 A 116 ASP LEU SER THR ILE LYS ARG LYS LEU ASP THR GLY GLN SEQRES 6 A 116 TYR GLN GLU PRO TRP GLN TYR VAL ASP ASP VAL TRP LEU SEQRES 7 A 116 MET PHE ASN ASN ALA TRP LEU TYR ASN ARG LYS THR SER SEQRES 8 A 116 ARG VAL TYR LYS PHE CYS SER LYS LEU ALA GLU VAL PHE SEQRES 9 A 116 GLU GLN GLU ILE ASP PRO VAL MET GLN SER LEU GLY SEQRES 1 B 116 LYS LYS ILE PHE LYS PRO GLU GLU LEU ARG GLN ALA LEU SEQRES 2 B 116 MET PRO THR LEU GLU ALA LEU TYR ARG GLN ASP PRO GLU SEQRES 3 B 116 SER LEU PRO PHE ARG GLN PRO VAL ASP PRO GLN LEU LEU SEQRES 4 B 116 GLY ILE PRO ASP TYR PHE ASP ILE VAL LYS ASN PRO MET SEQRES 5 B 116 ASP LEU SER THR ILE LYS ARG LYS LEU ASP THR GLY GLN SEQRES 6 B 116 TYR GLN GLU PRO TRP GLN TYR VAL ASP ASP VAL TRP LEU SEQRES 7 B 116 MET PHE ASN ASN ALA TRP LEU TYR ASN ARG LYS THR SER SEQRES 8 B 116 ARG VAL TYR LYS PHE CYS SER LYS LEU ALA GLU VAL PHE SEQRES 9 B 116 GLU GLN GLU ILE ASP PRO VAL MET GLN SER LEU GLY HET N6I A1201 60 HET 2LO A1202 69 HET N6I B1201 60 HET 2LO B1202 36 HETNAM N6I (3M)-4-{[(2S)-2-(3-CHLOROPHENYL)-2-HYDROXYETHYL]AMINO}- HETNAM 2 N6I 3-[4-METHYL-6-(MORPHOLIN-4-YL)-1H-BENZIMIDAZOL-2- HETNAM 3 N6I YL]PYRIDIN-2(1H)-ONE HETNAM 2LO 2-[2-(3-CHLORO-4-METHOXYPHENYL)ETHYL]-5-(3,5-DIMETHYL- HETNAM 2 2LO 1,2-OXAZOL-4-YL)-1-[(2S)-2-(MORPHOLIN-4-YL)PROPYL]-1H- HETNAM 3 2LO BENZIMIDAZOLE FORMUL 3 N6I 2(C25 H26 CL N5 O3) FORMUL 4 2LO 2(C28 H33 CL N4 O3) FORMUL 7 HOH *283(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 GLY A 1145 1 12 HELIX 6 AA6 PRO A 1150 ASN A 1168 1 19 HELIX 7 AA7 SER A 1172 GLY A 1197 1 26 HELIX 8 AA8 LYS B 1086 ARG B 1103 1 18 HELIX 9 AA9 SER B 1108 ARG B 1112 5 5 HELIX 10 AB1 ASP B 1116 GLY B 1121 1 6 HELIX 11 AB2 ASP B 1124 VAL B 1129 1 6 HELIX 12 AB3 ASP B 1134 GLY B 1145 1 12 HELIX 13 AB4 GLU B 1149 ASN B 1168 1 20 HELIX 14 AB5 SER B 1172 GLY B 1197 1 26 CISPEP 1 ASP A 1105 PRO A 1106 0 8.72 CISPEP 2 ASP B 1105 PRO B 1106 0 21.19 CRYST1 43.080 59.490 57.470 90.00 109.76 90.00 P 1 21 1 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 0.023213 0.000000 0.008338 0.00000 SCALE2 0.000000 0.016810 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018489 0.00000