HEADER PROTEIN BINDING 12-JUL-19 6PS9 TITLE CRYSTAL STRUCTURE OF BRD4 BROMODOMAIN 1 WITH N-METHYLPYRROLIDIN-2-ONE TITLE 2 (NMP) DERIVATIVE 17 (5-{2-[(3R)-1-METHYL-5-OXOPYRROLIDIN-3-YL]ETHYL}- TITLE 3 2,3,4,5-TETRAHYDRO-1H-PYRIDO[4,3-B]INDOL-1-ONE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 44-168; 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28(A) KEYWDS BRD4 BD1, BROMODOMAIN, OLINONE, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR O.V.ILYICHOVA,M.J.SCANLON REVDAT 3 11-OCT-23 6PS9 1 REMARK REVDAT 2 04-DEC-19 6PS9 1 JRNL REVDAT 1 27-NOV-19 6PS9 0 JRNL AUTH J.P.HILTON-PROCTOR,O.ILYICHOVA,Z.ZHENG,I.G.JENNINGS, JRNL AUTH 2 R.W.JOHNSTONE,J.SHORTT,S.J.MOUNTFORD,M.J.SCANLON, JRNL AUTH 3 P.E.THOMPSON JRNL TITL SYNTHESIS AND ELABORATION OF N-METHYLPYRROLIDONE AS AN JRNL TITL 2 ACETAMIDE FRAGMENT SUBSTITUTE IN BROMODOMAIN INHIBITION. JRNL REF BIOORG.MED.CHEM. V. 27 15157 2019 JRNL REFN ESSN 1464-3391 JRNL PMID 31727451 JRNL DOI 10.1016/J.BMC.2019.115157 REMARK 2 REMARK 2 RESOLUTION. 1.21 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 40711 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 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 38.5000 - 2.9200 1.00 2965 143 0.1469 0.1418 REMARK 3 2 2.9200 - 2.3200 1.00 2851 139 0.1456 0.1568 REMARK 3 3 2.3200 - 2.0300 0.99 2778 149 0.1382 0.1698 REMARK 3 4 2.0300 - 1.8400 0.99 2733 150 0.1493 0.1645 REMARK 3 5 1.8400 - 1.7100 1.00 2796 128 0.1301 0.1798 REMARK 3 6 1.7100 - 1.6100 1.00 2762 153 0.1177 0.1451 REMARK 3 7 1.6100 - 1.5300 1.00 2743 148 0.1141 0.1670 REMARK 3 8 1.5300 - 1.4600 1.00 2761 129 0.1145 0.1569 REMARK 3 9 1.4600 - 1.4000 1.00 2770 145 0.1259 0.1816 REMARK 3 10 1.4000 - 1.3600 1.00 2710 149 0.1367 0.1828 REMARK 3 11 1.3600 - 1.3100 1.00 2768 138 0.1475 0.1911 REMARK 3 12 1.3100 - 1.2800 1.00 2761 133 0.2017 0.2410 REMARK 3 13 1.2800 - 1.2400 1.00 2711 140 0.1745 0.2187 REMARK 3 14 1.2400 - 1.2100 0.96 2607 151 0.2288 0.2393 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) : 0.101 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.23 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 : 0.008 1188 REMARK 3 ANGLE : 0.962 1637 REMARK 3 CHIRALITY : 0.067 173 REMARK 3 PLANARITY : 0.007 214 REMARK 3 DIHEDRAL : 6.418 714 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 6PS9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000242957. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-17 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.94645 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 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40846 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.210 REMARK 200 RESOLUTION RANGE LOW (A) : 44.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.65300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 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: PDB ENTRY 5DW2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM NITRATE, 35% PEG3350, 6% REMARK 280 V/V ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277.15K 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 18.97200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.34850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.07050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.34850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.97200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.07050 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7470 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 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 ARG A 68 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 72 CE NZ REMARK 470 LYS A 141 CE NZ 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 HZ1 LYS A 91 O HOH A 301 1.51 REMARK 500 O HOH A 308 O HOH A 430 1.83 REMARK 500 NZ LYS A 91 O HOH A 301 2.06 REMARK 500 O HOH A 496 O HOH A 517 2.16 REMARK 500 O HOH A 303 O HOH A 311 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 528 DISTANCE = 6.28 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue Y17 A 201 DBREF 6PS9 A 44 168 UNP O60885 BRD4_HUMAN 44 168 SEQADV 6PS9 SER A 43 UNP O60885 EXPRESSION TAG SEQRES 1 A 126 SER ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN LYS SEQRES 2 A 126 PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU ARG SEQRES 3 A 126 VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA TRP SEQRES 4 A 126 PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN LEU SEQRES 5 A 126 PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP MET SEQRES 6 A 126 GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR TRP SEQRES 7 A 126 ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET PHE SEQRES 8 A 126 THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP ILE SEQRES 9 A 126 VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU GLN SEQRES 10 A 126 LYS ILE ASN GLU LEU PRO THR GLU GLU HET Y17 A 201 44 HETNAM Y17 5-{2-[(3R)-1-METHYL-5-OXOPYRROLIDIN-3-YL]ETHYL}-2,3,4, HETNAM 2 Y17 5-TETRAHYDRO-1H-PYRIDO[4,3-B]INDOL-1-ONE FORMUL 2 Y17 C18 H21 N3 O2 FORMUL 3 HOH *228(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 GLU A 163 1 20 SITE 1 AC1 8 TRP A 81 PHE A 83 LYS A 99 ASN A 140 SITE 2 AC1 8 ASP A 144 ASP A 145 ILE A 146 HOH A 313 CRYST1 37.944 44.141 78.697 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 0.026355 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022655 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012707 0.00000