HEADER TRANSCRIPTION 21-APR-21 7ENZ TITLE CRYSTAL STRUCTURE OF PHENANTHREDINONE MOIETY IN COMPLEX WITH THE TITLE 2 SECOND BROMODOMAIN OF BRD2 (BRD2-BD2). COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 348-455; COMPND 5 SYNONYM: O27.1.1,REALLY INTERESTING NEW GENE 3 PROTEIN; 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: BRD2, KIAA9001, RING3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS BET FAMILY, BET INHIBITOR, BROMODOMAIN INHIBITOR, BRD2-BD1 INHIBITOR, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR B.PADMANABHAN,A.AROLE,P.DESHMUKH,S.ASHOK REVDAT 3 29-NOV-23 7ENZ 1 REMARK REVDAT 2 16-MAR-22 7ENZ 1 JRNL REVDAT 1 09-MAR-22 7ENZ 0 JRNL AUTH A.H.AROLE,P.DESHMUKH,A.SRIDHAR,B.PADMANABHAN JRNL TITL STRUCTURAL INVESTIGATION OF A PYRANO-1,3-OXAZINE DERIVATIVE JRNL TITL 2 AND THE PHENANTHRIDINONE CORE MOIETY AGAINST BRD2 JRNL TITL 3 BROMODOMAINS. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 78 119 2022 JRNL REFN ESSN 2053-230X JRNL PMID 35234137 JRNL DOI 10.1107/S2053230X22001066 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.MATHUR,P.DESHMUKH,S.TRIPATHI,P.MARIMUTHU,B.PADMANABHAN REMARK 1 TITL INSIGHTS INTO THE CRYSTAL STRUCTURE OF BRD2-BD2 - REMARK 1 TITL 2 PHENANTHRIDINONE COMPLEX AND THEORETICAL STUDIES ON REMARK 1 TITL 3 PHENANTHRIDINONE ANALOGS. REMARK 1 REF J BIOMOL STRUCT DYN V. 36 2342 2018 REMARK 1 REFN ISSN 0739-1102 REMARK 1 PMID 28696179 REMARK 1 DOI 10.1080/07391102.2017.1353441 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.DESHMUKH,S.MATHUR,G.GANGADHARAN,G.KRISHNAPPA, REMARK 1 AUTH 2 N.DALAVAIKODIHALLI NANJAIAH,B.PADMANABHAN REMARK 1 TITL NOVEL PYRANO 1,3 OXAZINE BASED LIGAND INHIBITS THE REMARK 1 TITL 2 EPIGENETIC READER HBRD2 IN GLIOBLASTOMA. REMARK 1 REF BIOCHEM.J. V. 477 2263 2020 REMARK 1 REFN ESSN 1470-8728 REMARK 1 PMID 32484211 REMARK 1 DOI 10.1042/BCJ20200339 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18_3855: ???) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 13834 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 650 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 2.9000 - 2.3100 1.00 2630 140 0.1889 0.2402 REMARK 3 2 2.3100 - 2.0200 1.00 2607 134 0.1939 0.2469 REMARK 3 3 2.0100 - 1.8300 1.00 2611 126 0.2459 0.2897 REMARK 3 4 1.8300 - 1.7000 1.00 2592 111 0.1967 0.2669 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.930 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 : 0.007 1030 REMARK 3 ANGLE : 0.813 1392 REMARK 3 CHIRALITY : 0.048 136 REMARK 3 PLANARITY : 0.005 202 REMARK 3 DIHEDRAL : 4.550 159 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 7ENZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-APR-21. REMARK 100 THE DEPOSITION ID IS D_1300021838. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54056 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13875 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 14.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35000 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: PHENIX REMARK 200 STARTING MODEL: 5XHK REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS REMARK 200 COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS PH 7.5, 50 MM NACL, 25% PEG REMARK 280 MME 2000, 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 26.33600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.82750 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.33600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.82750 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 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 936 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1016 LIES ON A SPECIAL POSITION. 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 O HOH A 801 O HOH A 952 2.09 REMARK 500 O HOH A 949 O HOH A 1005 2.14 REMARK 500 O HOH A 943 O HOH A 965 2.19 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 A1014 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A1015 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A1016 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A1017 DISTANCE = 7.28 ANGSTROMS REMARK 525 HOH A1018 DISTANCE = 8.28 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LDR A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 702 DBREF 7ENZ A 348 455 UNP P25440 BRD2_HUMAN 348 455 SEQADV 7ENZ ALA A 341 UNP P25440 EXPRESSION TAG SEQADV 7ENZ ALA A 342 UNP P25440 EXPRESSION TAG SEQADV 7ENZ HIS A 343 UNP P25440 EXPRESSION TAG SEQADV 7ENZ GLY A 344 UNP P25440 EXPRESSION TAG SEQADV 7ENZ SER A 345 UNP P25440 EXPRESSION TAG SEQADV 7ENZ ASN A 346 UNP P25440 EXPRESSION TAG SEQADV 7ENZ PRO A 347 UNP P25440 EXPRESSION TAG SEQRES 1 A 115 ALA ALA HIS GLY SER ASN 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 LDR A 701 15 HET PGE A 702 10 HETNAM LDR PHENANTHRIDIN-6(5H)-ONE HETNAM PGE TRIETHYLENE GLYCOL FORMUL 2 LDR C13 H9 N O FORMUL 3 PGE C6 H14 O4 FORMUL 4 HOH *218(H2 O) HELIX 1 AA1 SER 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 4 PRO A 371 VAL A 376 ASN A 429 HOH A 805 SITE 1 AC2 7 PRO A 347 LEU A 350 LYS A 351 MET A 403 SITE 2 AC2 7 HOH A 821 HOH A 862 HOH A 886 CRYST1 32.023 52.672 71.655 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 0.031227 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018986 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013956 0.00000