HEADER SIGNALING PROTEIN/INHIBITOR 03-JAN-17 5UEZ TITLE BRD4_BD2_A-1342843 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 352-457; 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-PICHIA PASTORIS SHUTTLE VECTOR SOURCE 7 PPPARG4; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 1182032 KEYWDS SIGNALING PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.H.PARK REVDAT 4 03-APR-24 5UEZ 1 REMARK REVDAT 3 06-MAR-24 5UEZ 1 REMARK REVDAT 2 24-MAY-17 5UEZ 1 JRNL REVDAT 1 10-MAY-17 5UEZ 0 JRNL AUTH L.WANG,J.K.PRATT,T.SOLTWEDEL,G.S.SHEPPARD,S.D.FIDANZE,D.LIU, JRNL AUTH 2 L.A.HASVOLD,R.A.MANTEI,J.H.HOLMS,W.J.MCCLELLAN,M.D.WENDT, JRNL AUTH 3 C.WADA,R.FREY,T.M.HANSEN,R.HUBBARD,C.H.PARK,L.LI,T.J.MAGOC, JRNL AUTH 4 D.H.ALBERT,X.LIN,S.E.WARDER,P.KOVAR,X.HUANG,D.WILCOX,R.WANG, JRNL AUTH 5 G.RAJARAMAN,A.M.PETROS,C.W.HUTCHINS,S.C.PANCHAL,C.SUN, JRNL AUTH 6 S.W.ELMORE,Y.SHEN,W.M.KATI,K.F.MCDANIEL JRNL TITL FRAGMENT-BASED, STRUCTURE-ENABLED DISCOVERY OF NOVEL JRNL TITL 2 PYRIDONES AND PYRIDONE MACROCYCLES AS POTENT BROMODOMAIN AND JRNL TITL 3 EXTRA-TERMINAL DOMAIN (BET) FAMILY BROMODOMAIN INHIBITORS. JRNL REF J. MED. CHEM. V. 60 3828 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 28368119 JRNL DOI 10.1021/ACS.JMEDCHEM.7B00017 REMARK 2 REMARK 2 RESOLUTION. 1.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.7 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 22278 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.190 REMARK 3 FREE R VALUE TEST SET COUNT : 1156 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.020 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 11 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.51 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.58 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.92 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2369 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2550 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2233 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.74 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 136 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 892 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 183 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.82350 REMARK 3 B22 (A**2) : 5.15590 REMARK 3 B33 (A**2) : 1.66760 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.200 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.078 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.076 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.069 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.069 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 946 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1268 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 337 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 21 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 143 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 946 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 110 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1254 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.97 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.11 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.59 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5UEZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000224189. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-11 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 : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22278 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 REMARK 200 RESOLUTION RANGE LOW (A) : 33.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 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: NULL REMARK 200 STARTING MODEL: APO-BRD4_BD2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN BUFFER : 10 MM HEPES PH 7.5 REMARK 280 100 MM NACL 5MM DTT CRYSTALLIZATION : 15 %(V/V) ETHANOL TRIS PH REMARK 280 7.0, VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 28.99100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.39100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.99100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.39100 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: 6920 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 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 782 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH A 783 DISTANCE = 6.36 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 89G A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5UF0 RELATED DB: PDB REMARK 900 RELATED ID: 5UEY RELATED DB: PDB REMARK 900 RELATED ID: 5UEX RELATED DB: PDB REMARK 900 RELATED ID: 5UEV RELATED DB: PDB REMARK 900 RELATED ID: 5UEP RELATED DB: PDB REMARK 900 RELATED ID: 5UET RELATED DB: PDB REMARK 900 RELATED ID: 5UES RELATED DB: PDB REMARK 900 RELATED ID: 5UER RELATED DB: PDB REMARK 900 RELATED ID: 5UEQ RELATED DB: PDB REMARK 900 RELATED ID: 5UEU RELATED DB: PDB REMARK 900 RELATED ID: 5UEO RELATED DB: PDB REMARK 900 RELATED ID: 5UEW RELATED DB: PDB DBREF 5UEZ A 352 457 UNP O60885 BRD4_HUMAN 352 457 SEQADV 5UEZ SER A 349 UNP O60885 EXPRESSION TAG SEQADV 5UEZ HIS A 350 UNP O60885 EXPRESSION TAG SEQADV 5UEZ MET A 351 UNP O60885 EXPRESSION TAG SEQRES 1 A 109 SER HIS MET GLU GLN LEU LYS CYS CYS SER GLY ILE LEU SEQRES 2 A 109 LYS GLU MET PHE ALA LYS LYS HIS ALA ALA TYR ALA TRP SEQRES 3 A 109 PRO PHE TYR LYS PRO VAL ASP VAL GLU ALA LEU GLY LEU SEQRES 4 A 109 HIS ASP TYR CYS ASP ILE ILE LYS HIS PRO MET ASP MET SEQRES 5 A 109 SER THR ILE LYS SER LYS LEU GLU ALA ARG GLU TYR ARG SEQRES 6 A 109 ASP ALA GLN GLU PHE GLY ALA ASP VAL ARG LEU MET PHE SEQRES 7 A 109 SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS GLU VAL SEQRES 8 A 109 VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU MET SEQRES 9 A 109 ARG PHE ALA LYS MET HET 89G A 501 23 HETNAM 89G 5-METHOXY-2-METHYL-6-(2-PHENOXYPHENYL)PYRIDAZIN-3(2H)- HETNAM 2 89G ONE FORMUL 2 89G C18 H16 N2 O3 FORMUL 3 HOH *183(H2 O) HELIX 1 AA1 SER A 349 PHE A 365 1 17 HELIX 2 AA2 ALA A 366 LYS A 368 5 3 HELIX 3 AA3 HIS A 369 TRP A 374 1 6 HELIX 4 AA4 PRO A 375 TYR A 377 5 3 HELIX 5 AA5 ASP A 389 ILE A 394 1 6 HELIX 6 AA6 ASP A 399 ALA A 409 1 11 HELIX 7 AA7 ASP A 414 ASN A 433 1 20 HELIX 8 AA8 HIS A 437 MET A 457 1 21 SITE 1 AC1 8 PRO A 375 VAL A 380 LEU A 387 ASN A 433 SITE 2 AC1 8 HIS A 437 GLU A 438 HOH A 607 HOH A 642 CRYST1 57.982 72.782 33.654 90.00 90.00 90.00 P 21 21 2 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 0.017247 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013740 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029714 0.00000