HEADER GENE REGULATION 31-MAR-21 7EIL TITLE BRD4-BD1 IN COMPLEX WITH LT-909-110 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; 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 INHIBITOR, BRD4, BD1, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR W.ZHENG,B.KONG,W.TANG,J.ZHU,Y.CHEN REVDAT 3 29-NOV-23 7EIL 1 REMARK REVDAT 2 26-OCT-22 7EIL 1 JRNL REVDAT 1 06-APR-22 7EIL 0 JRNL AUTH B.KONG,Z.ZHU,H.LI,Q.HONG,C.WANG,Y.MA,W.ZHENG,F.JIANG, JRNL AUTH 2 Z.ZHANG,T.RAN,Y.BIAN,N.YANG,T.LU,J.ZHU,W.TANG,Y.CHEN JRNL TITL DISCOVERY OF JRNL TITL 2 1-(5-(1H-BENZO[D]IMIDAZOLE-2-YL)-2, JRNL TITL 3 4-DIMETHYL-1H-PYRROL-3-YL)ETHAN-1-ONE DERIVATIVES AS NOVEL JRNL TITL 4 AND POTENT BROMODOMAIN AND EXTRA-TERMINAL (BET) INHIBITORS JRNL TITL 5 WITH ANTICANCER EFFICACY JRNL REF EUR.J.MED.CHEM. V. 227 13953 2022 JRNL REFN ISSN 0223-5234 JRNL DOI 10.1016/J.EJMECH.2021.113953 REMARK 2 REMARK 2 RESOLUTION. 1.70 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 13978 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 : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1398 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 29.9200 - 3.6600 1.00 1358 150 0.1852 0.1624 REMARK 3 2 3.6600 - 2.9100 1.00 1290 144 0.1680 0.1975 REMARK 3 3 2.9100 - 2.5400 1.00 1279 142 0.1814 0.2249 REMARK 3 4 2.5400 - 2.3100 1.00 1244 138 0.1836 0.2362 REMARK 3 5 2.3100 - 2.1400 1.00 1237 139 0.1656 0.2013 REMARK 3 6 2.1400 - 2.0200 1.00 1255 139 0.1747 0.2144 REMARK 3 7 2.0200 - 1.9100 1.00 1235 137 0.1902 0.2099 REMARK 3 8 1.9100 - 1.8300 1.00 1248 139 0.2053 0.2504 REMARK 3 9 1.8300 - 1.7600 0.99 1233 137 0.2725 0.3162 REMARK 3 10 1.7600 - 1.7000 0.99 1201 133 0.3545 0.4328 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) : 0.267 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.32 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 : 0.004 1115 REMARK 3 ANGLE : 1.177 1521 REMARK 3 CHIRALITY : 0.042 157 REMARK 3 PLANARITY : 0.004 195 REMARK 3 DIHEDRAL : 10.145 675 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 10.0305 -2.8787 -8.3245 REMARK 3 T TENSOR REMARK 3 T11: 0.1049 T22: 0.1276 REMARK 3 T33: 0.1236 T12: 0.0011 REMARK 3 T13: 0.0068 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 0.7969 L22: 1.1874 REMARK 3 L33: 1.2307 L12: 0.1831 REMARK 3 L13: -0.1389 L23: -0.1370 REMARK 3 S TENSOR REMARK 3 S11: -0.0003 S12: -0.0189 S13: -0.0069 REMARK 3 S21: -0.0722 S22: 0.0125 S23: 0.0223 REMARK 3 S31: 0.0091 S32: -0.0531 S33: -0.0115 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 7EIL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-APR-21. REMARK 100 THE DEPOSITION ID IS D_1300021554. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14046 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 29.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.20500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.8000 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) : 1.10000 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: 5UFO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4M SODIUM FORMATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 295K 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 16.13000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.97500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.64500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.97500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.13000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.64500 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 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 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 OE2 GLU A 121 O HOH A 301 2.07 REMARK 500 O ARG A 16 O HOH A 302 2.08 REMARK 500 O HOH A 302 O HOH A 354 2.15 REMARK 500 O HOH A 368 O HOH A 390 2.18 REMARK 500 O HOH A 382 O HOH A 391 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 54 C6 909 A 201 4555 1.37 REMARK 500 OD2 ASP A 54 C1 909 A 201 4555 1.48 REMARK 500 REMARK 500 REMARK: NULL 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 10 102.63 -161.92 REMARK 500 ASN A 98 -150.64 -110.63 REMARK 500 REMARK 500 REMARK: NULL DBREF 7EIL A 2 125 UNP O60885 BRD4_HUMAN 44 167 SEQADV 7EIL MET A 1 UNP O60885 EXPRESSION TAG SEQRES 1 A 125 MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN LYS SEQRES 2 A 125 PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU ARG SEQRES 3 A 125 VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA TRP SEQRES 4 A 125 PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN LEU SEQRES 5 A 125 PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP MET SEQRES 6 A 125 GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR TRP SEQRES 7 A 125 ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET PHE SEQRES 8 A 125 THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP ILE SEQRES 9 A 125 VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU GLN SEQRES 10 A 125 LYS ILE ASN GLU LEU PRO THR GLU HET 909 A 201 35 HETNAM 909 N-[4-[4-ETHANOYL-5-METHYL-2-[6-(4-METHYLPIPERAZIN-1- HETNAM 2 909 YL)-1H-BENZIMIDAZOL-2-YL]-1H-PYRROL-3- HETNAM 3 909 YL]PHENYL]ETHANAMIDE FORMUL 2 909 C27 H30 N6 O2 FORMUL 3 HOH *93(H2 O) HELIX 1 AA1 THR A 18 VAL A 27 1 10 HELIX 2 AA2 VAL A 27 LYS A 34 1 8 HELIX 3 AA3 ALA A 38 GLN A 42 5 5 HELIX 4 AA4 ASP A 54 ILE A 59 1 6 HELIX 5 AA5 ASP A 64 ASN A 74 1 11 HELIX 6 AA6 ASN A 79 ASN A 98 1 20 HELIX 7 AA7 ASP A 102 ASN A 120 1 19 CRYST1 32.260 47.290 79.950 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 0.030998 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021146 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012508 0.00000 CONECT 1048 1056 1072 CONECT 1049 1050 1075 CONECT 1050 1049 1080 CONECT 1051 1075 CONECT 1052 1053 1076 1077 CONECT 1053 1052 1054 1078 CONECT 1054 1053 1055 1061 CONECT 1055 1054 1057 1059 CONECT 1056 1048 1066 1077 CONECT 1057 1055 1058 1078 CONECT 1058 1057 CONECT 1059 1055 1060 1082 CONECT 1060 1059 CONECT 1061 1054 1062 1067 CONECT 1062 1061 1063 CONECT 1063 1062 1064 CONECT 1064 1063 1065 1079 CONECT 1065 1064 1067 CONECT 1066 1056 1070 1076 CONECT 1067 1061 1065 CONECT 1068 1069 1079 1081 CONECT 1069 1068 CONECT 1070 1066 1071 CONECT 1071 1070 1072 1080 CONECT 1072 1048 1071 CONECT 1073 1074 1080 CONECT 1074 1073 1075 CONECT 1075 1049 1051 1074 CONECT 1076 1052 1066 CONECT 1077 1052 1056 CONECT 1078 1053 1057 CONECT 1079 1064 1068 CONECT 1080 1050 1071 1073 CONECT 1081 1068 CONECT 1082 1059 MASTER 264 0 1 7 0 0 0 6 1174 1 35 10 END