HEADER TRANSCRIPTION 04-JUL-19 6KEC TITLE CRYSTAL STRUCTURE OF BRD4 BROMODOMAIN 1 (BD1) IN COMPLEX WITH 4- TITLE 2 ETHOXY-5,16-DIMETHOXY-11-METHYL-2-OXA-11-AZATETRACYCLO[8.6.1.03, TITLE 3 8.013,17]HEPTADECA-1(17),3,5,7,9,13,15-HEPTAEN-12-ONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN HUNK1; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: SF FILE CONTAINS FRIEDEL PAIRS. 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET28B(+) KEYWDS BRD4, BROMODOMAIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR B.I.LEE,T.H.PARK REVDAT 4 22-NOV-23 6KEC 1 REMARK REVDAT 3 21-APR-21 6KEC 1 JRNL REVDAT 2 31-MAR-21 6KEC 1 JRNL REVDAT 1 08-JUL-20 6KEC 0 JRNL AUTH M.YOO,T.H.PARK,M.YOO,Y.KIM,J.Y.LEE,K.M.LEE,S.E.RYU,B.I.LEE, JRNL AUTH 2 K.Y.JUNG,C.H.PARK JRNL TITL SYNTHESIS AND STRUCTURE-ACTIVITY RELATIONSHIPS OF JRNL TITL 2 ARISTOYAGONINE DERIVATIVES AS BRD4 BROMODOMAIN INHIBITORS JRNL TITL 3 WITH X-RAY CO-CRYSTAL RESEARCH. JRNL REF MOLECULES V. 26 2021 JRNL REFN ESSN 1420-3049 JRNL PMID 33802888 JRNL DOI 10.3390/MOLECULES26061686 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 3 NUMBER OF REFLECTIONS : 24812 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1993 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 40.0000 - 3.7226 0.99 2245 191 0.1563 0.1632 REMARK 3 2 3.7226 - 2.9550 1.00 2254 193 0.1609 0.2179 REMARK 3 3 2.9550 - 2.5815 1.00 2293 199 0.1752 0.1957 REMARK 3 4 2.5815 - 2.3455 0.99 2239 191 0.1747 0.1888 REMARK 3 5 2.3455 - 2.1774 0.99 2252 189 0.1786 0.1936 REMARK 3 6 2.1774 - 2.0491 1.00 2244 200 0.1915 0.1783 REMARK 3 7 2.0491 - 1.9464 0.98 2251 195 0.1885 0.2031 REMARK 3 8 1.9464 - 1.8617 0.93 2110 175 0.1869 0.2163 REMARK 3 9 1.8617 - 1.7900 0.87 1929 172 0.1991 0.2257 REMARK 3 10 1.7900 - 1.7283 0.81 1889 161 0.2156 0.2246 REMARK 3 11 1.7283 - 1.6742 0.78 1739 148 0.2163 0.2455 REMARK 3 12 1.6742 - 1.6264 0.73 1659 143 0.2198 0.2372 REMARK 3 13 1.6264 - 1.5836 0.65 1476 125 0.2172 0.2596 REMARK 3 14 1.5836 - 1.5449 0.60 1344 114 0.2225 0.2371 REMARK 3 15 1.5449 - 1.5098 0.51 1177 103 0.2226 0.2627 REMARK 3 16 1.5098 - 1.4777 0.46 1018 86 0.2339 0.2587 REMARK 3 17 1.4777 - 1.4481 0.39 905 81 0.2371 0.2275 REMARK 3 18 1.4481 - 1.4208 0.36 806 70 0.2325 0.3036 REMARK 3 19 1.4208 - 1.3954 0.33 747 67 0.2492 0.2633 REMARK 3 20 1.3954 - 1.3717 0.31 702 63 0.2393 0.2491 REMARK 3 21 1.3717 - 1.3500 0.28 645 54 0.2519 0.3253 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.30 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 6KEC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300012788. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 11C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97942 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27116 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 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 : 6.000 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.66400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 2OSS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6 M SODIUM FORMATE, 10% GLYCEROL, PH REMARK 280 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 16.15150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.54400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.76450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.54400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.15150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.76450 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: 160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 GLY A 42 REMARK 465 SER A 43 REMARK 465 GLU A 167 REMARK 465 GLU A 168 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 ASN A 52 106.20 -161.50 REMARK 500 ASN A 140 -149.34 -110.69 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 D9C A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 405 DBREF 6KEC A 44 168 UNP O60885 BRD4_HUMAN 44 168 SEQADV 6KEC GLY A 42 UNP O60885 EXPRESSION TAG SEQADV 6KEC SER A 43 UNP O60885 EXPRESSION TAG SEQRES 1 A 127 GLY SER ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN SEQRES 2 A 127 LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU SEQRES 3 A 127 ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA SEQRES 4 A 127 TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN SEQRES 5 A 127 LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP SEQRES 6 A 127 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR SEQRES 7 A 127 TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET SEQRES 8 A 127 PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP SEQRES 9 A 127 ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU SEQRES 10 A 127 GLN LYS ILE ASN GLU LEU PRO THR GLU GLU HET D9C A 401 26 HET FMT A 402 3 HET FMT A 403 3 HET FMT A 404 3 HET FMT A 405 3 HETNAM D9C 4-ETHOXY-5,16-DIMETHOXY-11-METHYL-2-OXA-11- HETNAM 2 D9C AZATETRACYCLO[8.6.1.03,8.013,17]HEPTADECA-1(17),3,5,7, HETNAM 3 D9C 9,13,15-HEPTAEN-12-ONE HETNAM FMT FORMIC ACID FORMUL 2 D9C C20 H19 N O5 FORMUL 3 FMT 4(C H2 O2) FORMUL 7 HOH *111(H2 O) HELIX 1 AA1 THR A 60 VAL A 69 1 10 HELIX 2 AA2 VAL A 69 TRP A 75 1 7 HELIX 3 AA3 ALA A 80 GLN A 84 5 5 HELIX 4 AA4 ASP A 96 ILE A 101 1 6 HELIX 5 AA5 ASP A 106 ASN A 117 1 12 HELIX 6 AA6 ASN A 121 ASN A 140 1 20 HELIX 7 AA7 ASP A 144 ASN A 162 1 19 SITE 1 AC1 12 TRP A 81 PRO A 82 VAL A 87 LEU A 92 SITE 2 AC1 12 ASP A 96 LYS A 99 ASN A 140 ILE A 146 SITE 3 AC1 12 FMT A 404 HOH A 516 HOH A 535 HOH A 593 SITE 1 AC2 5 THR A 60 GLN A 62 ASN A 121 ALA A 122 SITE 2 AC2 5 HOH A 554 SITE 1 AC3 5 PRO A 56 LYS A 57 LYS A 99 LYS A 102 SITE 2 AC3 5 HOH A 506 SITE 1 AC4 6 GLN A 85 D9C A 401 HOH A 509 HOH A 528 SITE 2 AC4 6 HOH A 547 HOH A 587 SITE 1 AC5 3 TYR A 137 GLU A 163 HOH A 538 CRYST1 32.303 47.529 79.088 90.00 90.00 90.00 P 21 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 0.030957 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012644 0.00000