HEADER TRANSCRIPTION/INHIBITOR 10-MAY-18 6DDJ TITLE CRYSTAL STRUCTURE OF THE HUMAN BRD2 BD2 BROMODIMAIN IN COMPLEX WITH A TITLE 2 TETRAHYDROQUINOLINE ANALOGUE 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A(+) KEYWDS BET, BRD2, BROMODOMAIN, INHIBITOR, COMPLEX, TRANSCRIPTION, KEYWDS 2 TRANSCRIPTION-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.W.WHITE,M.YUN REVDAT 3 11-OCT-23 6DDJ 1 REMARK REVDAT 2 25-NOV-20 6DDJ 1 JRNL REVDAT 1 13-NOV-19 6DDJ 0 JRNL AUTH P.J.SLAVISH,L.CHI,M.K.YUN,L.TSURKAN,N.E.MARTINEZ,B.JONCHERE, JRNL AUTH 2 S.C.CHAI,M.CONNELLY,M.B.WADDELL,S.DAS,G.NEALE,Z.LI, JRNL AUTH 3 W.R.SHADRICK,R.R.OLSEN,K.W.FREEMAN,J.A.LOW,J.E.PRICE, JRNL AUTH 4 B.M.YOUNG,N.BHARATHAM,V.A.BOYD,J.YANG,R.E.LEE,M.MORFOUACE, JRNL AUTH 5 M.F.ROUSSEL,T.CHEN,D.SAVIC,R.K.GUY,S.W.WHITE,A.A.SHELAT, JRNL AUTH 6 P.M.POTTER JRNL TITL BROMODOMAIN-SELECTIVE BET INHIBITORS ARE POTENT ANTITUMOR JRNL TITL 2 AGENTS AGAINST MYC-DRIVEN PEDIATRIC CANCER. JRNL REF CANCER RES. V. 80 3507 2020 JRNL REFN ESSN 1538-7445 JRNL PMID 32651255 JRNL DOI 10.1158/0008-5472.CAN-19-3934 REMARK 2 REMARK 2 RESOLUTION. 1.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 56521 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.116 REMARK 3 R VALUE (WORKING SET) : 0.116 REMARK 3 FREE R VALUE : 0.129 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.540 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 32.0040 - 2.5290 0.99 4190 154 0.1459 0.1526 REMARK 3 2 2.5290 - 2.0074 1.00 4032 148 0.1178 0.1192 REMARK 3 3 2.0074 - 1.7537 1.00 4005 147 0.1048 0.1343 REMARK 3 4 1.7537 - 1.5933 1.00 3986 146 0.0954 0.1117 REMARK 3 5 1.5933 - 1.4791 0.99 3946 145 0.0861 0.1001 REMARK 3 6 1.4791 - 1.3919 0.99 3920 144 0.0883 0.1101 REMARK 3 7 1.3919 - 1.3222 0.99 3902 143 0.0897 0.1254 REMARK 3 8 1.3222 - 1.2647 0.99 3889 143 0.0937 0.1043 REMARK 3 9 1.2647 - 1.2160 0.98 3840 140 0.0895 0.1238 REMARK 3 10 1.2160 - 1.1740 0.98 3866 142 0.0899 0.0914 REMARK 3 11 1.1740 - 1.1373 0.97 3797 139 0.1013 0.1184 REMARK 3 12 1.1373 - 1.1048 0.97 3798 140 0.1276 0.1458 REMARK 3 13 1.1048 - 1.0757 0.97 3773 138 0.1486 0.1658 REMARK 3 14 1.0757 - 1.0500 0.91 3577 131 0.1677 0.1808 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 10.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.42 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 : 0.009 1037 REMARK 3 ANGLE : 1.047 1395 REMARK 3 CHIRALITY : 0.079 136 REMARK 3 PLANARITY : 0.009 181 REMARK 3 DIHEDRAL : 12.291 391 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 6DDJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1000234435. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID 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 : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56564 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.049 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.57300 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: 5IG6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEHPES, PEG3000, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 26.17850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.16400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.17850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.16400 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 TOTAL BURIED SURFACE AREA: 790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 11.0 KCAL/MOL 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 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 MET A 344 SD CE REMARK 470 LYS A 363 CD CE NZ 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 A 748 DISTANCE = 5.97 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue G7V A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 DBREF 6DDJ A 348 455 UNP P25440 BRD2_HUMAN 348 455 SEQADV 6DDJ GLY A 341 UNP P25440 EXPRESSION TAG SEQADV 6DDJ SER A 342 UNP P25440 EXPRESSION TAG SEQADV 6DDJ HIS A 343 UNP P25440 EXPRESSION TAG SEQADV 6DDJ MET A 344 UNP P25440 EXPRESSION TAG SEQADV 6DDJ GLN A 345 UNP P25440 EXPRESSION TAG SEQADV 6DDJ ASP A 346 UNP P25440 EXPRESSION TAG SEQADV 6DDJ PRO A 347 UNP P25440 EXPRESSION TAG SEQRES 1 A 115 GLY SER HIS MET GLN ASP PRO GLU GLN LEU LYS HIS CYS SEQRES 2 A 115 ASN GLY ILE LEU LYS GLU LEU LEU SER LYS LYS HIS ALA SEQRES 3 A 115 ALA TYR ALA TRP PRO PHE TYR LYS PRO VAL ASP ALA SER SEQRES 4 A 115 ALA LEU GLY LEU HIS ASP TYR HIS ASP ILE ILE LYS HIS SEQRES 5 A 115 PRO MET ASP LEU SER THR VAL LYS ARG LYS MET GLU ASN SEQRES 6 A 115 ARG ASP TYR ARG ASP ALA GLN GLU PHE ALA ALA ASP VAL SEQRES 7 A 115 ARG LEU MET PHE SER ASN CYS TYR LYS TYR ASN PRO PRO SEQRES 8 A 115 ASP HIS ASP VAL VAL ALA MET ALA ARG LYS LEU GLN ASP SEQRES 9 A 115 VAL PHE GLU PHE ARG TYR ALA LYS MET PRO ASP HET G7V A 501 49 HET EDO A 502 10 HET EDO A 503 10 HET EDO A 504 10 HET EDO A 505 10 HET EDO A 506 10 HETNAM G7V 4-{[(2S,4R)-1-ACETYL-2-METHYL-6-(1H-PYRAZOL-3-YL)-1,2, HETNAM 2 G7V 3,4-TETRAHYDROQUINOLIN-4-YL]AMINO}BENZONITRILE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 G7V C22 H21 N5 O FORMUL 3 EDO 5(C2 H6 O2) FORMUL 8 HOH *148(H2 O) HELIX 1 AA1 GLN A 345 LEU A 361 1 17 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 10 TRP A 370 PRO A 371 LEU A 383 ASN A 429 SITE 2 AC1 10 HIS A 433 VAL A 435 HOH A 608 HOH A 676 SITE 3 AC1 10 HOH A 688 HOH A 706 SITE 1 AC2 7 TYR A 368 LYS A 402 ASP A 407 GLU A 413 SITE 2 AC2 7 MET A 438 LYS A 441 HOH A 614 SITE 1 AC3 6 TYR A 426 ARG A 440 GLN A 443 ASP A 444 SITE 2 AC3 6 PHE A 448 HOH A 636 SITE 1 AC4 3 LEU A 350 HOH A 603 HOH A 669 SITE 1 AC5 7 ILE A 389 ILE A 390 LYS A 391 HIS A 392 SITE 2 AC5 7 ASN A 424 LYS A 427 ASP A 455 SITE 1 AC6 5 LEU A 361 TYR A 373 HOH A 666 HOH A 690 SITE 2 AC6 5 HOH A 699 CRYST1 52.357 72.328 32.004 90.00 90.00 90.00 P 21 21 2 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 0.019100 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013826 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031246 0.00000