HEADER TRANSCRIPTION/INHIBITOR 09-JUL-15 5CGP TITLE SELECTIVE PHARMACOLOGICAL INHIBITION OF THE CREB BINDING PROTEIN TITLE 2 BROMODOMAIN REGULATES INFLAMMATORY CYTOKINES IN MACROPHAGES AND RGS4 TITLE 3 IN NEURONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CREB-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1081-1197; 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 INHIBITOR, COMPLEX, TRANSCRIPTION-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.L.CHEKLER,L.H.JONES REVDAT 2 27-SEP-23 5CGP 1 REMARK REVDAT 1 20-APR-16 5CGP 0 JRNL AUTH E.L.CHEKLER,J.A.PELLEGRINO,T.A.LANZ,R.A.DENNY,A.C.FLICK, JRNL AUTH 2 J.COE,J.LANGILLE,A.BASAK,S.LIU,I.A.STOCK,P.SAHASRABUDHE, JRNL AUTH 3 P.D.BONIN,K.LEE,M.T.PLETCHER,L.H.JONES JRNL TITL TRANSCRIPTIONAL PROFILING OF A SELECTIVE CREB BINDING JRNL TITL 2 PROTEIN BROMODOMAIN INHIBITOR HIGHLIGHTS THERAPEUTIC JRNL TITL 3 OPPORTUNITIES. JRNL REF CHEM.BIOL. V. 22 1588 2015 JRNL REFN ISSN 1074-5521 JRNL PMID 26670081 JRNL DOI 10.1016/J.CHEMBIOL.2015.10.013 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 8701 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 865 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.19 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.55 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2375 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2147 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2132 REMARK 3 BIN R VALUE (WORKING SET) : 0.2102 REMARK 3 BIN FREE R VALUE : 0.2564 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.23 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 243 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 960 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.61730 REMARK 3 B22 (A**2) : -2.47520 REMARK 3 B33 (A**2) : 0.85800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.31640 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.283 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.202 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.170 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.202 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.170 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.895 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.865 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1057 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1466 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 360 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 29 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 175 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1057 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 121 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1247 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.07 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.85 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.75 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -13.1916 2.4761 7.5506 REMARK 3 T TENSOR REMARK 3 T11: -0.0908 T22: -0.1134 REMARK 3 T33: -0.0538 T12: 0.0140 REMARK 3 T13: 0.0184 T23: 0.0186 REMARK 3 L TENSOR REMARK 3 L11: 1.0166 L22: 1.6587 REMARK 3 L33: 2.5246 L12: 0.4080 REMARK 3 L13: 0.1297 L23: 0.0519 REMARK 3 S TENSOR REMARK 3 S11: 0.0258 S12: 0.0402 S13: 0.0270 REMARK 3 S21: 0.1010 S22: 0.0776 S23: -0.0268 REMARK 3 S31: -0.0935 S32: 0.0575 S33: -0.1034 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5CGP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211553. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9495 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 31.595 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.14100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.67500 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: BUSTER REMARK 200 STARTING MODEL: 3P1F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15-20% PEG 8000, 0.2M CAACETATE, 0.1 M REMARK 280 CACODYLATE PH 6-7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 45.04500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.87000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.04500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.87000 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 SER A 1079 REMARK 465 MET A 1080 REMARK 465 ARG A 1081 REMARK 465 LYS A 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 GLN A1118 CG CD OE1 NE2 REMARK 470 GLN A1187 CD OE1 NE2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 53W A 4000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CFW RELATED DB: PDB DBREF 5CGP A 1081 1197 UNP Q92793 CBP_HUMAN 1081 1197 SEQADV 5CGP SER A 1079 UNP Q92793 EXPRESSION TAG SEQADV 5CGP MET A 1080 UNP Q92793 EXPRESSION TAG SEQRES 1 A 119 SER MET ARG LYS LYS ILE PHE LYS PRO GLU GLU LEU ARG SEQRES 2 A 119 GLN ALA LEU MET PRO THR LEU GLU ALA LEU TYR ARG GLN SEQRES 3 A 119 ASP PRO GLU SER LEU PRO PHE ARG GLN PRO VAL ASP PRO SEQRES 4 A 119 GLN LEU LEU GLY ILE PRO ASP TYR PHE ASP ILE VAL LYS SEQRES 5 A 119 ASN PRO MET ASP LEU SER THR ILE LYS ARG LYS LEU ASP SEQRES 6 A 119 THR GLY GLN TYR GLN GLU PRO TRP GLN TYR VAL ASP ASP SEQRES 7 A 119 VAL TRP LEU MET PHE ASN ASN ALA TRP LEU TYR ASN ARG SEQRES 8 A 119 LYS THR SER ARG VAL TYR LYS PHE CYS SER LYS LEU ALA SEQRES 9 A 119 GLU VAL PHE GLU GLN GLU ILE ASP PRO VAL MET GLN SER SEQRES 10 A 119 LEU GLY HET 53W A4000 66 HETNAM 53W 5-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-2-[2-(4- HETNAM 2 53W METHOXYPHENYL)ETHYL]-1-[2-(MORPHOLIN-4-YL)ETHYL]-1H- HETNAM 3 53W BENZIMIDAZOLE FORMUL 2 53W C27 H32 N4 O3 FORMUL 3 HOH *59(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 6.98 SITE 1 AC1 12 PRO A1110 GLN A1113 VAL A1115 LEU A1120 SITE 2 AC1 12 ILE A1122 TYR A1125 ASN A1168 ARG A1173 SITE 3 AC1 12 VAL A1174 PHE A1177 HOH A4110 HOH A4127 CRYST1 90.090 33.740 40.010 90.00 92.70 90.00 C 1 2 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 0.011100 0.000000 0.000523 0.00000 SCALE2 0.000000 0.029638 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025022 0.00000