HEADER TRANSCRIPTION/INHIBITOR 25-APR-22 7USJ TITLE BRD4-BD2 IN COMPLEX WITH SF2523 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: BD2; COMPND 5 SYNONYM: PROTEIN HUNK1; 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: BRD4, HUNK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA PHAGE ECSZW-2; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 2419741 KEYWDS INHIBITOR, ACETYLLYSINE BINDING POCKET, TRANSCRIPTION-INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.D.JAYASINGHE,D.R.RONNING REVDAT 2 25-OCT-23 7USJ 1 REMARK REVDAT 1 18-JAN-23 7USJ 0 JRNL AUTH B.SETHI,V.KUMAR,T.D.JAYASINGHE,Y.DONG,D.R.RONNING,H.A.ZHONG, JRNL AUTH 2 D.W.COULTER,R.I.MAHATO JRNL TITL TARGETING BRD4 AND PI3K SIGNALING PATHWAYS FOR THE TREATMENT JRNL TITL 2 OF MEDULLOBLASTOMA. JRNL REF J CONTROL RELEASE V. 354 80 2023 JRNL REFN ISSN 1873-4995 JRNL PMID 36599397 JRNL DOI 10.1016/J.JCONREL.2022.12.055 REMARK 2 REMARK 2 RESOLUTION. 2.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 19019 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1903 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 32.8200 - 5.0100 0.99 1338 149 0.1637 0.2135 REMARK 3 2 5.0100 - 3.9800 0.99 1263 141 0.1719 0.2032 REMARK 3 3 3.9800 - 3.4800 0.97 1210 134 0.2146 0.2995 REMARK 3 4 3.4700 - 3.1600 1.00 1233 137 0.2351 0.2678 REMARK 3 5 3.1600 - 2.9300 1.00 1229 136 0.2615 0.2584 REMARK 3 6 2.9300 - 2.7600 1.00 1195 133 0.2391 0.3022 REMARK 3 7 2.7600 - 2.6200 1.00 1230 138 0.2387 0.3207 REMARK 3 8 2.6200 - 2.5100 1.00 1196 132 0.2390 0.3519 REMARK 3 9 2.5100 - 2.4100 1.00 1218 135 0.2464 0.3127 REMARK 3 10 2.4100 - 2.3300 1.00 1209 135 0.2506 0.2901 REMARK 3 11 2.3300 - 2.2500 1.00 1198 133 0.2673 0.3081 REMARK 3 12 2.2500 - 2.1900 1.00 1199 134 0.3026 0.4592 REMARK 3 13 2.1900 - 2.1300 1.00 1210 134 0.3055 0.3457 REMARK 3 14 2.1300 - 2.0800 1.00 1188 132 0.3316 0.3610 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.37 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 : 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 7USJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-22. REMARK 100 THE DEPOSITION ID IS D_1000264809. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-22 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 : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19034 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.080 REMARK 200 RESOLUTION RANGE LOW (A) : 32.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.19200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 5UF0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 28 % W/V PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 50.32250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.81250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.81250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 75.48375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.81250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.81250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.16125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.81250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.81250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 75.48375 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.81250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.81250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.16125 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 50.32250 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 358 OG REMARK 480 SER B 358 OG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 410 66.34 26.58 REMARK 500 LEU B 385 -78.71 -69.82 REMARK 500 REMARK 500 REMARK: NULL DBREF 7USJ A 352 457 UNP O60885 BRD4_HUMAN 352 457 DBREF 7USJ B 352 457 UNP O60885 BRD4_HUMAN 352 457 SEQADV 7USJ GLY A 349 UNP O60885 EXPRESSION TAG SEQADV 7USJ PRO A 350 UNP O60885 EXPRESSION TAG SEQADV 7USJ MET A 351 UNP O60885 EXPRESSION TAG SEQADV 7USJ GLY B 349 UNP O60885 EXPRESSION TAG SEQADV 7USJ PRO B 350 UNP O60885 EXPRESSION TAG SEQADV 7USJ MET B 351 UNP O60885 EXPRESSION TAG SEQRES 1 A 109 GLY PRO MET GLU GLN LEU LYS CYS CYS SER GLY ILE LEU SEQRES 2 A 109 LYS GLU MET PHE ALA LYS LYS HIS ALA ALA TYR ALA TRP SEQRES 3 A 109 PRO PHE TYR LYS PRO VAL ASP VAL GLU ALA LEU GLY LEU SEQRES 4 A 109 HIS ASP TYR CYS ASP ILE ILE LYS HIS PRO MET ASP MET SEQRES 5 A 109 SER THR ILE LYS SER LYS LEU GLU ALA ARG GLU TYR ARG SEQRES 6 A 109 ASP ALA GLN GLU PHE GLY ALA ASP VAL ARG LEU MET PHE SEQRES 7 A 109 SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS GLU VAL SEQRES 8 A 109 VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU MET SEQRES 9 A 109 ARG PHE ALA LYS MET SEQRES 1 B 109 GLY PRO MET GLU GLN LEU LYS CYS CYS SER GLY ILE LEU SEQRES 2 B 109 LYS GLU MET PHE ALA LYS LYS HIS ALA ALA TYR ALA TRP SEQRES 3 B 109 PRO PHE TYR LYS PRO VAL ASP VAL GLU ALA LEU GLY LEU SEQRES 4 B 109 HIS ASP TYR CYS ASP ILE ILE LYS HIS PRO MET ASP MET SEQRES 5 B 109 SER THR ILE LYS SER LYS LEU GLU ALA ARG GLU TYR ARG SEQRES 6 B 109 ASP ALA GLN GLU PHE GLY ALA ASP VAL ARG LEU MET PHE SEQRES 7 B 109 SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS GLU VAL SEQRES 8 B 109 VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU MET SEQRES 9 B 109 ARG PHE ALA LYS MET HET 82V A 501 26 HET 82V B 501 26 HETNAM 82V 3-(2,3-DIHYDRO-1,4-BENZODIOXIN-6-YL)-5-(MORPHOLIN-4- HETNAM 2 82V YL)-7H-THIENO[3,2-B]PYRAN-7-ONE FORMUL 3 82V 2(C19 H17 N O5 S) FORMUL 5 HOH *116(H2 O) HELIX 1 AA1 GLY A 349 ALA A 366 1 18 HELIX 2 AA2 HIS A 369 TRP A 374 1 6 HELIX 3 AA3 PRO A 375 TYR A 377 5 3 HELIX 4 AA4 ASP A 381 GLY A 386 1 6 HELIX 5 AA5 ASP A 389 ILE A 394 1 6 HELIX 6 AA6 ASP A 399 GLU A 408 1 10 HELIX 7 AA7 ASP A 414 ASN A 433 1 20 HELIX 8 AA8 HIS A 437 LYS A 456 1 20 HELIX 9 AA9 PRO B 350 PHE B 365 1 16 HELIX 10 AB1 ALA B 366 LYS B 368 5 3 HELIX 11 AB2 HIS B 369 TRP B 374 1 6 HELIX 12 AB3 PRO B 375 TYR B 377 5 3 HELIX 13 AB4 ASP B 381 GLY B 386 1 6 HELIX 14 AB5 ASP B 389 ILE B 394 1 6 HELIX 15 AB6 ASP B 399 GLU B 408 1 10 HELIX 16 AB7 ASP B 414 ASN B 433 1 20 HELIX 17 AB8 HIS B 437 LYS B 456 1 20 CRYST1 77.625 77.625 100.645 90.00 90.00 90.00 P 43 21 2 16 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 0.012882 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009936 0.00000