HEADER TRANSCRIPTION/TRANSCRIPTION INHIBITOR 04-OCT-18 6MOA TITLE C-TERMINAL BROMODOMAIN OF HUMAN BRD2 IN COMPLEX WITH 4-(2-CYCLOPROPYL- TITLE 2 7-(6-METHYLQUINOLIN-5-YL)-1H-BENZO[D]IMIDAZOL-5-YL)-3,5- TITLE 3 DIMETHYLISOXAZOLE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: O27.1.1,REALLY INTERESTING NEW GENE 3 PROTEIN; 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: BRD2, KIAA9001, RING3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, EPIGENETIC READER, BROMODOMAIN, TRANSCRIPTION- KEYWDS 2 TRANSCRIPTION INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR E.B.LANSDON,Z.E.R.NEWBY REVDAT 3 13-MAR-24 6MOA 1 REMARK REVDAT 2 30-JAN-19 6MOA 1 JRNL REVDAT 1 23-JAN-19 6MOA 0 JRNL AUTH D.SPERANDIO,V.AKTOUDIANAKIS,K.BABAOGLU,X.CHEN,K.ELBEL, JRNL AUTH 2 G.CHIN,B.CORKEY,J.DU,B.JIANG,T.KOBAYASHI,R.MACKMAN, JRNL AUTH 3 R.MARTINEZ,H.YANG,J.ZABLOCKI,S.KUSAM,K.JORDAN,H.WEBB, JRNL AUTH 4 J.G.BATES,L.LAD,M.MISH,A.NIEDZIELA-MAJKA,S.METOBO,A.SAPRE, JRNL AUTH 5 M.HUNG,D.JIN,W.FUNG,E.KAN,G.EISENBERG,N.LARSON,Z.E.R.NEWBY, JRNL AUTH 6 E.LANSDON,C.TAY,R.M.NEVE,S.L.SHEVICK,D.G.BRECKENRIDGE JRNL TITL STRUCTURE-GUIDED DISCOVERY OF A NOVEL, POTENT, AND ORALLY JRNL TITL 2 BIOAVAILABLE 3,5-DIMETHYLISOXAZOLE ARYL-BENZIMIDAZOLE BET JRNL TITL 3 BROMODOMAIN INHIBITOR. JRNL REF BIOORG. MED. CHEM. V. 27 457 2019 JRNL REFN ESSN 1464-3391 JRNL PMID 30606676 JRNL DOI 10.1016/J.BMC.2018.11.020 REMARK 2 REMARK 2 RESOLUTION. 1.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 31623 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.320 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 29.2092 - 3.0617 0.97 2295 154 0.1642 0.1732 REMARK 3 2 3.0617 - 2.4306 0.98 2198 149 0.1733 0.1641 REMARK 3 3 2.4306 - 2.1234 0.99 2169 146 0.1675 0.2033 REMARK 3 4 2.1234 - 1.9293 0.99 2191 148 0.1614 0.1581 REMARK 3 5 1.9293 - 1.7911 0.99 2152 146 0.1637 0.1633 REMARK 3 6 1.7911 - 1.6855 0.98 2145 144 0.1580 0.2062 REMARK 3 7 1.6855 - 1.6011 0.98 2130 145 0.1552 0.1902 REMARK 3 8 1.6011 - 1.5314 0.98 2128 143 0.1535 0.1816 REMARK 3 9 1.5314 - 1.4724 0.97 2117 143 0.1564 0.1956 REMARK 3 10 1.4724 - 1.4216 0.96 2073 140 0.1648 0.1868 REMARK 3 11 1.4216 - 1.3772 0.95 2041 138 0.1627 0.1735 REMARK 3 12 1.3772 - 1.3378 0.95 2015 136 0.1671 0.1961 REMARK 3 13 1.3378 - 1.3026 0.93 2044 138 0.1812 0.2178 REMARK 3 14 1.3026 - 1.2708 0.90 1925 130 0.2021 0.2156 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.005 963 REMARK 3 ANGLE : 0.802 1303 REMARK 3 CHIRALITY : 0.074 128 REMARK 3 PLANARITY : 0.005 164 REMARK 3 DIHEDRAL : 15.608 352 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 6MOA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1000237235. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-15 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 : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97741 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 108525 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.270 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.03200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.20900 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: EPMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 1000 100MM NATRIS-HCL PH 8.4, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.25700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.25700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.00000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 708 LIES ON A SPECIAL POSITION. 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 ASP A 455 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 LEU A 346 CG CD1 CD2 REMARK 470 LYS A 363 CD CE NZ REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JW4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 502 DBREF 6MOA A 346 455 UNP P25440 BRD2_HUMAN 346 455 SEQRES 1 A 110 LEU SER GLU GLN LEU LYS HIS CYS ASN GLY ILE LEU LYS SEQRES 2 A 110 GLU LEU LEU SER LYS LYS HIS ALA ALA TYR ALA TRP PRO SEQRES 3 A 110 PHE TYR LYS PRO VAL ASP ALA SER ALA LEU GLY LEU HIS SEQRES 4 A 110 ASP TYR HIS ASP ILE ILE LYS HIS PRO MET ASP LEU SER SEQRES 5 A 110 THR VAL LYS ARG LYS MET GLU ASN ARG ASP TYR ARG ASP SEQRES 6 A 110 ALA GLN GLU PHE ALA ALA ASP VAL ARG LEU MET PHE SER SEQRES 7 A 110 ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS ASP VAL VAL SEQRES 8 A 110 ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU PHE ARG SEQRES 9 A 110 TYR ALA LYS MET PRO ASP HET JW4 A 501 30 HET GOL A 502 6 HETNAM JW4 4-(2-CYCLOPROPYL-7-(6-METHYLQUINOLIN-5-YL)-1H- HETNAM 2 JW4 BENZO[D]IMIDAZOL-5-YL)-3,5-DIMETHYLISOXAZOLE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 JW4 C25 H22 N4 O FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *143(H2 O) HELIX 1 AA1 LEU A 346 LEU A 361 1 16 HELIX 2 AA2 SER A 362 LYS A 364 5 3 HELIX 3 AA3 HIS A 365 TRP A 370 1 6 HELIX 4 AA4 PRO A 371 TYR A 373 5 3 HELIX 5 AA5 ASP A 377 GLY A 382 1 6 HELIX 6 AA6 ASP A 385 ILE A 390 1 6 HELIX 7 AA7 ASP A 395 ASN A 405 1 11 HELIX 8 AA8 ASP A 410 ASN A 429 1 20 HELIX 9 AA9 HIS A 433 ALA A 451 1 19 SITE 1 AC1 11 TRP A 370 PRO A 371 PHE A 372 LEU A 381 SITE 2 AC1 11 LEU A 383 ASN A 429 HIS A 433 HOH A 604 SITE 3 AC1 11 HOH A 655 HOH A 657 HOH A 665 SITE 1 AC2 8 TYR A 368 LYS A 402 ASP A 407 MET A 438 SITE 2 AC2 8 LYS A 441 HOH A 601 HOH A 613 HOH A 626 CRYST1 31.947 52.514 72.000 90.00 90.00 90.00 P 2 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 0.031302 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019043 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013889 0.00000