HEADER TRANSCRIPTION REGULATOR/INHIBITOR 30-NOV-16 5U2F TITLE BRD4 FIRST BROMODOMAIN (BD1) IN COMPLEX WITH DUAL PI3 KINASE (PI3K) TITLE 2 INHIBITOR SF2558HA COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A, B; 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-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS BROMODOMAIN, TRANSCRIPTION, INHIBITOR, EPIGENETICS, TRANSCRIPTION KEYWDS 2 REGULATOR-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.H.ANDREWS,T.G.KUTATELADZE REVDAT 3 06-MAR-24 5U2F 1 REMARK REVDAT 2 01-MAR-17 5U2F 1 JRNL REVDAT 1 08-FEB-17 5U2F 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. 2.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 9804 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 488 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 20.5021 - 3.6492 0.90 3105 164 0.1777 0.2076 REMARK 3 2 3.6492 - 2.8991 0.89 3043 161 0.2321 0.2679 REMARK 3 3 2.8991 - 2.5334 0.94 3134 163 0.3076 0.3947 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.330 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 : 0.003 2330 REMARK 3 ANGLE : 0.611 3178 REMARK 3 CHIRALITY : 0.035 333 REMARK 3 PLANARITY : 0.005 412 REMARK 3 DIHEDRAL : 11.437 1426 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 5U2F 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_1000225194. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 PILATUS3 R 100K-A REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9804 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.525 REMARK 200 RESOLUTION RANGE LOW (A) : 24.272 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : 31.9000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350 (W/V), 0.2 M AMMONIUM REMARK 280 CHLORIDE, 0.1 M TRIS, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 20.00900 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 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 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 41 REMARK 465 SER A 42 REMARK 465 VAL A 174 REMARK 465 GLN A 175 REMARK 465 ALA A 176 REMARK 465 LYS A 177 REMARK 465 GLY A 178 REMARK 465 ARG A 179 REMARK 465 GLY A 180 REMARK 465 MET B 172 REMARK 465 ILE B 173 REMARK 465 VAL B 174 REMARK 465 GLN B 175 REMARK 465 ALA B 176 REMARK 465 LYS B 177 REMARK 465 GLY B 178 REMARK 465 ARG B 179 REMARK 465 GLY B 180 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 360 O HOH B 314 1.97 REMARK 500 O HOH B 403 O HOH B 457 2.16 REMARK 500 O HOH B 301 O HOH B 366 2.18 REMARK 500 O HOH B 301 O HOH B 393 2.18 REMARK 500 OE1 GLU B 151 O HOH B 301 2.18 REMARK 500 OE1 GLU B 49 O HOH B 302 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 VAL A 69 -61.80 -130.86 REMARK 500 MET A 172 64.19 7.73 REMARK 500 VAL B 69 -43.32 -137.32 REMARK 500 PRO B 165 -170.90 -69.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 171 MET A 172 144.34 REMARK 500 THR B 166 GLU B 167 -144.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 82Y A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 82Y B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5U28 RELATED DB: PDB REMARK 900 RELATED ID: 5U2C RELATED DB: PDB REMARK 900 RELATED ID: 5U2E RELATED DB: PDB DBREF 5U2F A 42 180 UNP O60885 BRD4_HUMAN 42 180 DBREF 5U2F B 42 180 UNP O60885 BRD4_HUMAN 42 180 SEQADV 5U2F GLY A 41 UNP O60885 EXPRESSION TAG SEQADV 5U2F GLY B 41 UNP O60885 EXPRESSION TAG SEQRES 1 A 140 GLY SER THR ASN PRO PRO PRO PRO GLU THR SER ASN PRO SEQRES 2 A 140 ASN LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU SEQRES 3 A 140 LEU ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE SEQRES 4 A 140 ALA TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU SEQRES 5 A 140 ASN LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET SEQRES 6 A 140 ASP MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR SEQRES 7 A 140 TYR TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR SEQRES 8 A 140 MET PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP SEQRES 9 A 140 ASP ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE SEQRES 10 A 140 LEU GLN LYS ILE ASN GLU LEU PRO THR GLU GLU THR GLU SEQRES 11 A 140 ILE MET ILE VAL GLN ALA LYS GLY ARG GLY SEQRES 1 B 140 GLY SER THR ASN PRO PRO PRO PRO GLU THR SER ASN PRO SEQRES 2 B 140 ASN LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU SEQRES 3 B 140 LEU ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE SEQRES 4 B 140 ALA TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU SEQRES 5 B 140 ASN LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET SEQRES 6 B 140 ASP MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR SEQRES 7 B 140 TYR TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR SEQRES 8 B 140 MET PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP SEQRES 9 B 140 ASP ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE SEQRES 10 B 140 LEU GLN LYS ILE ASN GLU LEU PRO THR GLU GLU THR GLU SEQRES 11 B 140 ILE MET ILE VAL GLN ALA LYS GLY ARG GLY HET 82Y A 201 26 HET 82Y B 201 26 HETNAM 82Y N-HYDROXY-4-[5-(MORPHOLIN-4-YL)-7-OXO-7H-THIENO[3,2- HETNAM 2 82Y B]PYRAN-3-YL]BENZAMIDE FORMUL 3 82Y 2(C18 H16 N2 O5 S) FORMUL 5 HOH *329(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 ASP A 88 ASN A 93 1 6 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 ASN B 61 VAL B 69 1 9 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 88 ASN B 93 1 6 HELIX 12 AB3 ASP B 96 ILE B 101 1 6 HELIX 13 AB4 ASP B 106 ASN B 116 1 11 HELIX 14 AB5 ASN B 121 ASN B 140 1 20 HELIX 15 AB6 ASP B 144 ASN B 162 1 19 SHEET 1 AA1 2 GLN B 59 THR B 60 0 SHEET 2 AA1 2 THR B 169 GLU B 170 -1 O GLU B 170 N GLN B 59 SITE 1 AC1 5 PRO A 82 LEU A 92 ASN A 140 ILE A 146 SITE 2 AC1 5 HOH A 384 SITE 1 AC2 9 TRP B 81 PRO B 82 VAL B 87 LEU B 92 SITE 2 AC2 9 ASN B 140 ILE B 146 HOH B 322 HOH B 368 SITE 3 AC2 9 HOH B 387 CRYST1 62.084 40.018 62.172 90.00 100.88 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 0.016107 0.000000 0.003095 0.00000 SCALE2 0.000000 0.024989 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016379 0.00000