HEADER TRANSCRIPTION 29-MAY-20 6X7D TITLE BRD4 BROMODOMAIN 1 IN COMPLEX WITH MULTI-ACTION INHIBITOR SF2523P COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PROTEIN HUNK1; 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: BRD4, HUNK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BRD4, PI3K, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR K.R.VANN,T.G.KUTATELADZE REVDAT 2 18-OCT-23 6X7D 1 REMARK REVDAT 1 05-AUG-20 6X7D 0 JRNL AUTH K.R.VANN,D.PAL,G.A.MORALES,A.M.BURGOYNE,D.L.DURDEN, JRNL AUTH 2 T.G.KUTATELADZE JRNL TITL DESIGN OF THIENOPYRANONE-BASED BET INHIBITORS THAT BIND JRNL TITL 2 MULTIPLE SYNTHETIC LETHALITY TARGETS. JRNL REF SCI REP V. 10 12027 2020 JRNL REFN ESSN 2045-2322 JRNL PMID 32694708 JRNL DOI 10.1038/S41598-020-68964-6 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 8517 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.090 REMARK 3 FREE R VALUE TEST SET COUNT : 859 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 35.2600 - 4.5405 0.91 1321 147 0.1812 0.2073 REMARK 3 2 4.5405 - 3.6050 0.93 1299 146 0.1541 0.2430 REMARK 3 3 3.6050 - 3.1497 0.95 1318 147 0.1952 0.2774 REMARK 3 4 3.1497 - 2.8618 0.93 1287 147 0.2307 0.3103 REMARK 3 5 2.8618 - 2.6568 0.89 1227 137 0.2391 0.3296 REMARK 3 6 2.6568 - 2.5002 0.87 1206 135 0.2606 0.3794 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.40 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 6X7D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000247521. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-16 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 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8982 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 95.5 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.34900 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: 3MXF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5 M AMMONIUM SULFATE AND 0.1 M TRIS REMARK 280 PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 19.91600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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 GLU A 168 REMARK 465 THR A 169 REMARK 465 GLU A 170 REMARK 465 ILE A 171 REMARK 465 MET A 172 REMARK 465 ILE A 173 REMARK 465 VAL A 174 REMARK 465 GLN A 175 REMARK 465 ALA A 176 REMARK 465 MET B 172 REMARK 465 ILE B 173 REMARK 465 VAL B 174 REMARK 465 GLN B 175 REMARK 465 ALA B 176 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 VAL A 69 -58.46 -120.04 REMARK 500 PRO B 56 -178.57 -61.58 REMARK 500 LYS B 57 73.24 -158.29 REMARK 500 VAL B 69 -62.57 -125.25 REMARK 500 ASP B 96 22.56 49.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UT4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UT4 B 201 DBREF 6X7D A 44 176 UNP O60885 BRD4_HUMAN 44 176 DBREF 6X7D B 44 176 UNP O60885 BRD4_HUMAN 44 176 SEQRES 1 A 133 ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN LYS PRO SEQRES 2 A 133 LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU ARG VAL SEQRES 3 A 133 VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA TRP PRO SEQRES 4 A 133 PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN LEU PRO SEQRES 5 A 133 ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP MET GLY SEQRES 6 A 133 THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR TRP ASN SEQRES 7 A 133 ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET PHE THR SEQRES 8 A 133 ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP ILE VAL SEQRES 9 A 133 LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU GLN LYS SEQRES 10 A 133 ILE ASN GLU LEU PRO THR GLU GLU THR GLU ILE MET ILE SEQRES 11 A 133 VAL GLN ALA SEQRES 1 B 133 ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN LYS PRO SEQRES 2 B 133 LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU ARG VAL SEQRES 3 B 133 VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA TRP PRO SEQRES 4 B 133 PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN LEU PRO SEQRES 5 B 133 ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP MET GLY SEQRES 6 B 133 THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR TRP ASN SEQRES 7 B 133 ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET PHE THR SEQRES 8 B 133 ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP ILE VAL SEQRES 9 B 133 LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU GLN LYS SEQRES 10 B 133 ILE ASN GLU LEU PRO THR GLU GLU THR GLU ILE MET ILE SEQRES 11 B 133 VAL GLN ALA HET UT4 A 201 26 HET UT4 B 201 26 HETNAM UT4 3-(2,3-DIHYDRO-1,4-BENZODIOXIN-6-YL)-5-(PIPERAZIN-1- HETNAM 2 UT4 YL)-7H-THIENO[3,2-B]PYRAN-7-ONE FORMUL 3 UT4 2(C19 H18 N2 O4 S) FORMUL 5 HOH *116(H2 O) HELIX 1 AA1 THR A 60 VAL A 69 1 10 HELIX 2 AA2 VAL A 69 HIS A 77 1 9 HELIX 3 AA3 ALA A 80 GLN A 84 5 5 HELIX 4 AA4 ASP A 88 ASN A 93 1 6 HELIX 5 AA5 ASP A 96 ILE A 101 1 6 HELIX 6 AA6 ASP A 106 ASN A 116 1 11 HELIX 7 AA7 ASN A 121 ASN A 140 1 20 HELIX 8 AA8 ASP A 144 GLU A 163 1 20 HELIX 9 AA9 THR B 60 VAL B 69 1 10 HELIX 10 AB1 VAL B 69 LYS B 76 1 8 HELIX 11 AB2 ALA B 80 GLN B 84 5 5 HELIX 12 AB3 ASP B 96 ILE B 101 1 6 HELIX 13 AB4 ASP B 106 ASN B 116 1 11 HELIX 14 AB5 ASN B 121 ASN B 140 1 20 HELIX 15 AB6 ASP B 144 ASN B 162 1 19 SITE 1 AC1 9 TRP A 81 PRO A 82 GLN A 85 VAL A 87 SITE 2 AC1 9 LEU A 92 LEU A 94 ASN A 140 ILE A 146 SITE 3 AC1 9 HOH A 318 SITE 1 AC2 5 PRO B 82 GLN B 85 LEU B 94 ASN B 140 SITE 2 AC2 5 HOH B 301 CRYST1 56.147 39.832 62.035 90.00 106.45 90.00 P 1 21 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 0.017810 0.000000 0.005260 0.00000 SCALE2 0.000000 0.025105 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016808 0.00000