HEADER GENE REGULATION/INHIBITOR 28-APR-21 7MLR TITLE X-RAY CRYSTAL STRUCTURE OF HUMAN BRD4(D1) IN COMPLEX WITH 2-(4-{5-[6- TITLE 2 (3,5-DIMETHYLPHENOXY)PYRIDIN-2-YL]-4-METHYL-1H-1,2,3-TRIAZOL-1- TITLE 3 YL}PIPERIDIN-1-YL)-N,N-DIMETHYLETHAN-1-AMINE (DW34) 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS BRD4, GENE REGULATION, GENE REGULATION-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.CUI,K.SHI,H.AIHARA,W.C.K.POMERANTZ REVDAT 3 18-OCT-23 7MLR 1 REMARK REVDAT 2 04-AUG-21 7MLR 1 JRNL REVDAT 1 28-JUL-21 7MLR 0 JRNL AUTH H.CUI,A.S.CARLSON,M.A.SCHLEIFF,A.DIVAKARAN,J.A.JOHNSON, JRNL AUTH 2 C.R.BUCHHOLZ,H.ZAHID,N.R.VAIL,K.SHI,H.AIHARA,D.A.HARKI, JRNL AUTH 3 G.P.MILLER,J.J.TOPCZEWSKI,W.C.K.POMERANTZ JRNL TITL 4-METHYL-1,2,3-TRIAZOLES AS N -ACETYL-LYSINE MIMICS AFFORD JRNL TITL 2 POTENT BET BROMODOMAIN INHIBITORS WITH IMPROVED SELECTIVITY. JRNL REF J.MED.CHEM. V. 64 10497 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 34236185 JRNL DOI 10.1021/ACS.JMEDCHEM.1C00933 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 73649 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 3717 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 38.6600 - 3.6000 0.94 2572 147 0.1478 0.1867 REMARK 3 2 3.6000 - 2.8600 0.90 2503 117 0.1383 0.1306 REMARK 3 3 2.8600 - 2.5000 0.95 2632 127 0.1368 0.1453 REMARK 3 4 2.5000 - 2.2700 0.97 2701 149 0.1246 0.1504 REMARK 3 5 2.2700 - 2.1100 0.97 2695 131 0.1100 0.1296 REMARK 3 6 2.1100 - 1.9800 0.98 2687 157 0.1183 0.1423 REMARK 3 7 1.9800 - 1.8800 0.90 2495 137 0.1157 0.1641 REMARK 3 8 1.8800 - 1.8000 0.94 2602 132 0.1109 0.1451 REMARK 3 9 1.8000 - 1.7300 0.96 2634 172 0.1220 0.1602 REMARK 3 10 1.7300 - 1.6700 0.97 2706 113 0.1048 0.1433 REMARK 3 11 1.6700 - 1.6200 0.97 2710 116 0.1066 0.1722 REMARK 3 12 1.6200 - 1.5700 0.97 2714 119 0.1057 0.1365 REMARK 3 13 1.5700 - 1.5300 0.96 2643 152 0.1102 0.1411 REMARK 3 14 1.5300 - 1.4900 0.97 2716 156 0.1128 0.1316 REMARK 3 15 1.4900 - 1.4600 0.96 2635 160 0.1135 0.1565 REMARK 3 16 1.4600 - 1.4300 0.94 2572 145 0.1270 0.1914 REMARK 3 17 1.4300 - 1.4000 0.90 2540 130 0.1722 0.1901 REMARK 3 18 1.4000 - 1.3700 0.94 2557 127 0.1696 0.2451 REMARK 3 19 1.3700 - 1.3500 0.92 2598 127 0.1673 0.1989 REMARK 3 20 1.3500 - 1.3300 0.95 2632 159 0.1722 0.1961 REMARK 3 21 1.3300 - 1.3000 0.92 2534 113 0.1626 0.2067 REMARK 3 22 1.3000 - 1.2800 0.95 2605 157 0.1734 0.2115 REMARK 3 23 1.2800 - 1.2700 0.91 2567 115 0.1953 0.2183 REMARK 3 24 1.2700 - 1.2500 0.92 2581 133 0.2335 0.2336 REMARK 3 25 1.2500 - 1.2300 0.89 2380 148 0.2593 0.3107 REMARK 3 26 1.2300 - 1.2200 0.88 2446 154 0.3203 0.3481 REMARK 3 27 1.2200 - 1.2000 0.84 2275 124 0.4043 0.4390 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.79 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 7MLR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-21. REMARK 100 THE DEPOSITION ID IS D_1000256489. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-20 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 : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77580 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 44.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.55500 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6WGX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NAI, PH 8.5, BIS-TRIS PROPANE, 20% REMARK 280 (V/V) PEG 3350, ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 18.54900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.46800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.16800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.46800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.54900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.16800 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 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 SER A 42 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 91 CD CE NZ REMARK 470 GLN A 123 CD OE1 NE2 REMARK 470 GLU A 167 CG CD OE1 OE2 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 386 O HOH A 458 2.01 REMARK 500 O HOH A 475 O HOH A 476 2.08 REMARK 500 O HOH A 327 O HOH A 346 2.18 REMARK 500 N MET A 43 O HOH A 301 2.18 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 52 95.20 -167.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 207 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 124 OE1 REMARK 620 2 GLU A 124 OE2 46.5 REMARK 620 3 HOH A 461 O 147.1 127.0 REMARK 620 N 1 2 DBREF 7MLR A 44 168 UNP O60885 BRD4_HUMAN 44 168 SEQADV 7MLR SER A 42 UNP O60885 EXPRESSION TAG SEQADV 7MLR MET A 43 UNP O60885 EXPRESSION TAG SEQRES 1 A 127 SER MET 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 EDO A 201 10 HET EDO A 202 10 HET EDO A 203 10 HET EDO A 204 10 HET EDO A 205 10 HET ZHS A 206 66 HET NA A 207 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM ZHS 2-(4-{5-[6-(3,5-DIMETHYLPHENOXY)PYRIDIN-2-YL]-4-METHYL- HETNAM 2 ZHS 1H-1,2,3-TRIAZOL-1-YL}PIPERIDIN-1-YL)-N,N- HETNAM 3 ZHS DIMETHYLETHAN-1-AMINE HETNAM NA SODIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 5(C2 H6 O2) FORMUL 7 ZHS C25 H34 N6 O FORMUL 8 NA NA 1+ FORMUL 9 HOH *197(H2 O) HELIX 1 AA1 THR A 60 VAL A 69 1 10 HELIX 2 AA2 VAL A 69 LYS A 76 1 8 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 116 1 11 HELIX 6 AA6 ASN A 121 ASN A 140 1 20 HELIX 7 AA7 ASP A 144 ASN A 162 1 19 LINK OE1 GLU A 124 NA NA A 207 1555 1555 2.20 LINK OE2 GLU A 124 NA NA A 207 1555 1555 3.03 LINK NA NA A 207 O HOH A 461 1555 1555 2.34 CRYST1 37.098 44.336 78.936 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 0.026956 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022555 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012668 0.00000