HEADER TRANSCRIPTION/TRANSCRIPTION INHIBITOR 23-JAN-18 6C7R TITLE BRD4 BD1 IN COMPLEX WITH COMPOUND CF53 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, TRANSCRIPTION-TRANSCRIPTION INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.L.MEAGHER,J.A.STUCKEY REVDAT 3 04-OCT-23 6C7R 1 REMARK REVDAT 2 08-AUG-18 6C7R 1 JRNL REVDAT 1 01-AUG-18 6C7R 0 JRNL AUTH Y.ZHAO,B.ZHOU,L.BAI,L.LIU,C.Y.YANG,J.L.MEAGHER,J.A.STUCKEY, JRNL AUTH 2 D.MCEACHERN,S.PRZYBRANOWSKI,M.WANG,X.RAN,A.AGUILAR,Y.HU, JRNL AUTH 3 J.W.KAMPF,X.LI,T.ZHAO,S.LI,B.WEN,D.SUN,S.WANG JRNL TITL STRUCTURE-BASED DISCOVERY OF CF53 AS A POTENT AND ORALLY JRNL TITL 2 BIOAVAILABLE BROMODOMAIN AND EXTRA-TERMINAL (BET) JRNL TITL 3 BROMODOMAIN INHIBITOR. JRNL REF J. MED. CHEM. V. 61 6110 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 30015487 JRNL DOI 10.1021/ACS.JMEDCHEM.8B00483 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 18120 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 869 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 9 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.82 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2776 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2392 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2651 REMARK 3 BIN R VALUE (WORKING SET) : 0.2387 REMARK 3 BIN FREE R VALUE : 0.2484 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 125 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 : 912 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 135 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.91660 REMARK 3 B22 (A**2) : 3.60200 REMARK 3 B33 (A**2) : -5.51870 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.97680 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.210 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.096 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.094 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.091 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.091 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 : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1008 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1384 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 349 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 31 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 185 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1008 ; 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 : 122 ; 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 : 1295 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.96 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.24 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.37 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 6C7R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000232244. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-14 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 : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0781 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18133 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 (%) : 95.1 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 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 (%) : 94.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.11400 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: 4LYI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2M POTASSIUM CHLORIDE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K 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 20.73550 REMARK 290 SMTRY3 2 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 SER A 41 REMARK 465 ASN A 42 REMARK 465 ALA A 43 REMARK 465 ASN A 44 REMARK 465 PRO A 45 REMARK 465 PRO A 46 REMARK 465 PRO A 47 REMARK 465 PRO A 48 REMARK 465 GLU A 49 REMARK 465 THR A 50 REMARK 465 SER A 51 REMARK 465 ASN A 52 REMARK 465 PRO A 53 REMARK 465 ASN A 54 REMARK 465 LYS A 55 REMARK 465 PRO A 56 REMARK 465 LYS A 57 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 LYS A 141 CG CD CE NZ 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 435 DISTANCE = 6.41 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EO4 A 201 DBREF 6C7R A 44 165 UNP O60885 BRD4_HUMAN 44 165 SEQADV 6C7R SER A 41 UNP O60885 EXPRESSION TAG SEQADV 6C7R ASN A 42 UNP O60885 EXPRESSION TAG SEQADV 6C7R ALA A 43 UNP O60885 EXPRESSION TAG SEQRES 1 A 125 SER ASN ALA ASN PRO PRO PRO PRO GLU THR SER ASN PRO SEQRES 2 A 125 ASN LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU SEQRES 3 A 125 LEU ARG VAL VAL LEU LYS THR LEU TRP LYS HIS GLN PHE SEQRES 4 A 125 ALA TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU SEQRES 5 A 125 ASN LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET SEQRES 6 A 125 ASP MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR SEQRES 7 A 125 TYR TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR SEQRES 8 A 125 MET PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP SEQRES 9 A 125 ASP ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE SEQRES 10 A 125 LEU GLN LYS ILE ASN GLU LEU PRO HET EO4 A 201 40 HETNAM EO4 N-(3-CYCLOPROPYL-1-METHYL-1H-PYRAZOL-5-YL)-7-(3,5- HETNAM 2 EO4 DIMETHYL-1,2-OXAZOL-4-YL)-6-METHOXY-2-METHYL-9H- HETNAM 3 EO4 PYRIMIDO[4,5-B]INDOL-4-AMINE FORMUL 2 EO4 C24 H25 N7 O2 FORMUL 3 HOH *135(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 GLU A 163 1 20 SITE 1 AC1 12 TRP A 81 PRO A 82 PHE A 83 LEU A 92 SITE 2 AC1 12 LEU A 94 ASN A 140 ASP A 145 ILE A 146 SITE 3 AC1 12 HOH A 301 HOH A 347 HOH A 360 HOH A 365 CRYST1 30.377 41.471 47.981 90.00 94.87 90.00 P 1 21 1 2 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 0.032920 0.000000 0.002805 0.00000 SCALE2 0.000000 0.024113 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020917 0.00000