HEADER TRANSCRIPTION 05-AUG-22 7YQ9 TITLE CRYSTAL STRUCTURE OF BRD4 BROMODOMAIN 1 (BD1) IN COMPLEX WITH N-[2- TITLE 2 (1H-INDOL-3-YL)ETHYL]-3-(TRIFLUOROMETHYL)[1,2,4]TRIAZOLO[4,3- TITLE 3 B]PYRIDAZIN-6-AMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: BROMODOMAIN 1; 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 COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACTERIAL EXPRESSION VECTOR; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHIS KEYWDS BRD4, BET INHIBITOR, COMPLEX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR J.H.KIM,B.I.LEE REVDAT 3 29-NOV-23 7YQ9 1 REMARK REVDAT 2 02-AUG-23 7YQ9 1 JRNL REVDAT 1 18-JAN-23 7YQ9 0 JRNL AUTH J.H.KIM,N.PANDIT,M.YOO,T.H.PARK,J.U.CHOI,C.H.PARK,K.Y.JUNG, JRNL AUTH 2 B.I.LEE JRNL TITL CRYSTAL STRUCTURE OF [1,2,4]TRIAZOLO[4,3-B]PYRIDAZINE JRNL TITL 2 DERIVATIVES AS BRD4 BROMODOMAIN INHIBITORS AND JRNL TITL 3 STRUCTURE-ACTIVITY RELATIONSHIP STUDY. JRNL REF SCI REP V. 13 10805 2023 JRNL REFN ESSN 2045-2322 JRNL PMID 37402749 JRNL DOI 10.1038/S41598-023-37527-W REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 37174 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.370 REMARK 3 FREE R VALUE TEST SET COUNT : 1995 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 47.5000 - 3.6000 0.96 2684 150 0.1847 0.2068 REMARK 3 2 3.6000 - 2.8600 0.99 2696 153 0.1918 0.2060 REMARK 3 3 2.8600 - 2.5000 0.97 2578 149 0.1819 0.2122 REMARK 3 4 2.5000 - 2.2700 0.99 2662 149 0.1894 0.2120 REMARK 3 5 2.2700 - 2.1100 0.99 2691 152 0.1650 0.1666 REMARK 3 6 2.1100 - 1.9800 0.97 2549 146 0.1618 0.1676 REMARK 3 7 1.9800 - 1.8800 0.98 2610 145 0.1627 0.1961 REMARK 3 8 1.8800 - 1.8000 0.98 2616 149 0.1717 0.1877 REMARK 3 9 1.8000 - 1.7300 0.99 2639 155 0.1683 0.2068 REMARK 3 10 1.7300 - 1.6700 0.96 2538 142 0.1752 0.1874 REMARK 3 11 1.6700 - 1.6200 0.93 2445 141 0.1756 0.2120 REMARK 3 12 1.6200 - 1.5700 0.88 2359 133 0.1808 0.2144 REMARK 3 13 1.5700 - 1.5300 0.84 2188 120 0.1827 0.2449 REMARK 3 14 1.5300 - 1.5000 0.72 1924 111 0.1827 0.2065 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.135 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.626 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.28 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 : 0.007 2250 REMARK 3 ANGLE : 0.941 3086 REMARK 3 CHIRALITY : 0.075 323 REMARK 3 PLANARITY : 0.007 395 REMARK 3 DIHEDRAL : 10.345 290 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 7YQ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031416. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0~8.0 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) : 0.979 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38524 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 97.6 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 25.8500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28900 REMARK 200 FOR SHELL : 5.400 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: 6KEK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CONCENTRATION 12 MG/ML PROTEIN REMARK 280 STORAGE BUFFER: 10 MM HEPES PH 7.5, 500 MM NACL, 5% GLYCEROL 10 REMARK 280 MM DTT RESERVOIR SOLUTION: 6M SODIUM FORMATE, 6% GLYCEROL REMARK 280 PROTEIN: RESERVOIR SOLUTION=1:1 CO-CRYSTALLIZATION: ADDED 5MM REMARK 280 CHEMICAL AND INCUBATED OVERNIGHT AT 4 CELSIUS, PH 7.8, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 287K 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 16.19900 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 TOTAL BURIED SURFACE AREA: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 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 TOTAL BURIED SURFACE AREA: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL 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 GLY A 42 REMARK 465 SER A 43 REMARK 465 GLU A 167 REMARK 465 GLU A 168 REMARK 465 GLY B 42 REMARK 465 SER B 43 REMARK 465 GLU B 167 REMARK 465 GLU B 168 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 ARG A 58 O HOH A 301 2.05 REMARK 500 O ARG B 58 O HOH B 301 2.08 REMARK 500 OE2 GLU B 163 O HOH B 302 2.08 REMARK 500 OE2 GLU A 163 O HOH A 302 2.13 REMARK 500 O HOH A 342 O HOH A 367 2.13 REMARK 500 OD1 ASN A 117 O HOH A 301 2.16 REMARK 500 O1 FMT A 203 O HOH A 301 2.16 REMARK 500 OD1 ASN B 117 O HOH B 301 2.18 REMARK 500 O HOH A 361 O HOH A 369 2.19 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 99.66 -163.35 REMARK 500 LEU A 94 71.38 -118.76 REMARK 500 ASN A 140 -149.58 -117.86 REMARK 500 ASN B 52 97.87 -164.49 REMARK 500 LEU B 94 71.96 -118.71 REMARK 500 ASN B 140 -150.33 -117.74 REMARK 500 REMARK 500 REMARK: NULL DBREF 7YQ9 A 44 168 UNP O60885 BRD4_HUMAN 44 168 DBREF 7YQ9 B 44 168 UNP O60885 BRD4_HUMAN 44 168 SEQADV 7YQ9 GLY A 42 UNP O60885 EXPRESSION TAG SEQADV 7YQ9 SER A 43 UNP O60885 EXPRESSION TAG SEQADV 7YQ9 GLY B 42 UNP O60885 EXPRESSION TAG SEQADV 7YQ9 SER B 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 SEQRES 1 B 127 GLY SER ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN SEQRES 2 B 127 LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU SEQRES 3 B 127 ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA SEQRES 4 B 127 TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN SEQRES 5 B 127 LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP SEQRES 6 B 127 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR SEQRES 7 B 127 TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET SEQRES 8 B 127 PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP SEQRES 9 B 127 ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU SEQRES 10 B 127 GLN LYS ILE ASN GLU LEU PRO THR GLU GLU HET CL A 201 1 HET JLX A 202 25 HET FMT A 203 3 HET FMT A 204 3 HET CL B 201 1 HET JLX B 202 25 HETNAM CL CHLORIDE ION HETNAM JLX N-[2-(1H-INDOL-3-YL)ETHYL]-3-(TRIFLUOROMETHYL)-[1,2, HETNAM 2 JLX 4]TRIAZOLO[4,3-B]PYRIDAZIN-6-AMINE HETNAM FMT FORMIC ACID FORMUL 3 CL 2(CL 1-) FORMUL 4 JLX 2(C16 H13 F3 N6) FORMUL 5 FMT 2(C H2 O2) FORMUL 9 HOH *134(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 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 HELIX 8 AA8 THR B 60 VAL B 69 1 10 HELIX 9 AA9 VAL B 69 LYS B 76 1 8 HELIX 10 AB1 ALA B 80 GLN B 84 5 5 HELIX 11 AB2 ASP B 96 ILE B 101 1 6 HELIX 12 AB3 ASP B 106 ASN B 116 1 11 HELIX 13 AB4 ASN B 121 ASN B 140 1 20 HELIX 14 AB5 ASP B 144 ASN B 162 1 19 CRYST1 47.498 32.398 79.474 90.00 89.99 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 0.021054 0.000000 -0.000004 0.00000 SCALE2 0.000000 0.030866 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012583 0.00000