HEADER TRANSCRIPTION REGULATOR/INHIBITOR 30-NOV-16 5U28 TITLE BRD4 FIRST BROMODOMAIN (BD1) IN COMPLEX WITH DUAL PI3 KINASE INHIBITOR TITLE 2 SF2523 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 BROMODOMAIN, TRANSCRIPTION, INHIBITOR, EPIGENETICS, TRANSCRIPTION KEYWDS 2 REGULATOR-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.H.ANDREWS,T.G.KUTATELADZE REVDAT 3 04-OCT-23 5U28 1 REMARK REVDAT 2 01-MAR-17 5U28 1 JRNL REVDAT 1 08-FEB-17 5U28 0 JRNL AUTH F.H.ANDREWS,A.R.SINGH,S.JOSHI,C.A.SMITH,G.A.MORALES, JRNL AUTH 2 J.R.GARLICH,D.L.DURDEN,T.G.KUTATELADZE JRNL TITL DUAL-ACTIVITY PI3K-BRD4 INHIBITOR FOR THE ORTHOGONAL JRNL TITL 2 INHIBITION OF MYC TO BLOCK TUMOR GROWTH AND METASTASIS. JRNL REF PROC. NATL. ACAD. SCI. V. 114 E1072 2017 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 28137841 JRNL DOI 10.1073/PNAS.1613091114 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 15802 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) : 0.179 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1571 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 28.0380 - 3.9951 0.98 1386 153 0.1571 0.1662 REMARK 3 2 3.9951 - 3.1724 0.99 1332 153 0.1627 0.2137 REMARK 3 3 3.1724 - 2.7718 1.00 1301 149 0.1985 0.2354 REMARK 3 4 2.7718 - 2.5186 1.00 1337 139 0.1917 0.2685 REMARK 3 5 2.5186 - 2.3381 1.00 1283 149 0.1935 0.2344 REMARK 3 6 2.3381 - 2.2003 1.00 1287 141 0.1896 0.2408 REMARK 3 7 2.2003 - 2.0902 0.99 1295 140 0.1850 0.2354 REMARK 3 8 2.0902 - 1.9992 1.00 1279 144 0.1755 0.2053 REMARK 3 9 1.9992 - 1.9223 1.00 1290 147 0.1844 0.2616 REMARK 3 10 1.9223 - 1.8560 1.00 1279 140 0.2024 0.2781 REMARK 3 11 1.8560 - 1.7979 0.90 1162 116 0.1779 0.2541 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.010 1200 REMARK 3 ANGLE : 1.108 1634 REMARK 3 CHIRALITY : 0.038 171 REMARK 3 PLANARITY : 0.004 211 REMARK 3 DIHEDRAL : 15.167 468 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 5U28 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1000225193. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15802 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.798 REMARK 200 RESOLUTION RANGE LOW (A) : 28.035 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 5DW2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG3350 (W/V) AND 0.2 M POTASSIUM REMARK 280 THIOCYANATE (PH 7.5), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K 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 21.98600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.83750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.57550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.83750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.98600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.57550 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 LYS A 177 REMARK 465 GLY A 178 REMARK 465 ARG A 179 REMARK 465 GLY A 180 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 82V A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SCN A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5U2F RELATED DB: PDB REMARK 900 RELATED ID: 5U2C RELATED DB: PDB REMARK 900 RELATED ID: 5U2E RELATED DB: PDB DBREF 5U28 A 44 180 UNP O60885 BRD4_HUMAN 44 180 SEQADV 5U28 ALA A 43 UNP O60885 EXPRESSION TAG SEQRES 1 A 138 ALA ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN LYS SEQRES 2 A 138 PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU ARG SEQRES 3 A 138 VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE ALA TRP SEQRES 4 A 138 PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN LEU SEQRES 5 A 138 PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP MET SEQRES 6 A 138 GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR TRP SEQRES 7 A 138 ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET PHE SEQRES 8 A 138 THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP ILE SEQRES 9 A 138 VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU GLN SEQRES 10 A 138 LYS ILE ASN GLU LEU PRO THR GLU GLU THR GLU ILE MET SEQRES 11 A 138 ILE VAL GLN ALA LYS GLY ARG GLY HET 82V A 201 26 HET PEG A 202 7 HET SCN A 203 3 HETNAM 82V 3-(2,3-DIHYDRO-1,4-BENZODIOXIN-6-YL)-5-(MORPHOLIN-4- HETNAM 2 82V YL)-7H-THIENO[3,2-B]PYRAN-7-ONE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM SCN THIOCYANATE ION FORMUL 2 82V C19 H17 N O5 S FORMUL 3 PEG C4 H10 O3 FORMUL 4 SCN C N S 1- FORMUL 5 HOH *150(H2 O) HELIX 1 AA1 ASN A 61 VAL A 69 1 9 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 SHEET 1 AA1 2 GLN A 59 THR A 60 0 SHEET 2 AA1 2 GLU A 170 ILE A 171 -1 O ILE A 171 N GLN A 59 SITE 1 AC1 15 TYR A 65 ARG A 68 VAL A 69 TRP A 81 SITE 2 AC1 15 PRO A 82 GLN A 85 VAL A 87 LEU A 92 SITE 3 AC1 15 LEU A 94 ASN A 140 PEG A 202 SCN A 203 SITE 4 AC1 15 HOH A 314 HOH A 345 HOH A 353 SITE 1 AC2 7 TRP A 81 GLN A 84 GLN A 85 PRO A 165 SITE 2 AC2 7 82V A 201 HOH A 330 HOH A 370 SITE 1 AC3 3 GLN A 64 82V A 201 HOH A 375 CRYST1 43.972 59.151 63.675 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 0.022742 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016906 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015705 0.00000