HEADER TRANSCRIPTION/TRANSCRIPTION INHIBITOR 23-JAN-18 6C7Q TITLE BRD4 BD2 IN COMPLEX WITH COMPOUND CE277 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 03-APR-24 6C7Q 1 REMARK REVDAT 2 08-AUG-18 6C7Q 1 JRNL REVDAT 1 01-AUG-18 6C7Q 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. 1.51 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) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 20189 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1016 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.58 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.39 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2808 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1721 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2657 REMARK 3 BIN R VALUE (WORKING SET) : 0.1701 REMARK 3 BIN FREE R VALUE : 0.2088 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.38 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 151 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 : 911 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 97 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.77670 REMARK 3 B22 (A**2) : 3.79900 REMARK 3 B33 (A**2) : -0.02230 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) : 0.190 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.079 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.081 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.074 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.077 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 : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 987 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1336 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 334 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 23 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 194 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 987 ; 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 : 115 ; 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 : 1245 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.90 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.36 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.57 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 9.8914 2.5207 0.4914 REMARK 3 T TENSOR REMARK 3 T11: -0.0199 T22: -0.0148 REMARK 3 T33: -0.0344 T12: -0.0019 REMARK 3 T13: -0.0047 T23: -0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.6799 L22: 1.2439 REMARK 3 L33: 0.4750 L12: 0.0719 REMARK 3 L13: 0.0415 L23: -0.1096 REMARK 3 S TENSOR REMARK 3 S11: 0.0007 S12: 0.0243 S13: -0.0446 REMARK 3 S21: -0.0134 S22: -0.0069 S23: -0.0175 REMARK 3 S31: -0.0085 S32: 0.0295 S33: 0.0062 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6C7Q 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_1000231618. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20228 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.32400 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: PREVIOUSLY SOLVED STRUCTURE IN LAB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50-75% PEG 400, 0.1M IMIDIZOLE, PH REMARK 280 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 26.08800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.32350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.08800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.32350 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 SER A 330 REMARK 465 ASN A 331 REMARK 465 ALA A 332 REMARK 465 LYS A 333 REMARK 465 ASP A 334 REMARK 465 VAL A 335 REMARK 465 PRO A 336 REMARK 465 ASP A 337 REMARK 465 SER A 338 REMARK 465 GLN A 339 REMARK 465 GLN A 340 REMARK 465 HIS A 341 REMARK 465 PRO A 342 REMARK 465 ALA A 343 REMARK 465 PRO A 344 REMARK 465 GLU A 345 REMARK 465 LYS A 346 REMARK 465 SER A 347 REMARK 465 SER A 348 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 367 CD CE NZ REMARK 470 GLU A 383 CG CD OE1 OE2 REMARK 470 LYS A 395 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 697 DISTANCE = 6.26 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EO1 A 501 DBREF 6C7Q A 333 460 UNP O60885 BRD4_HUMAN 333 460 SEQADV 6C7Q SER A 330 UNP O60885 EXPRESSION TAG SEQADV 6C7Q ASN A 331 UNP O60885 EXPRESSION TAG SEQADV 6C7Q ALA A 332 UNP O60885 EXPRESSION TAG SEQRES 1 A 131 SER ASN ALA LYS ASP VAL PRO ASP SER GLN GLN HIS PRO SEQRES 2 A 131 ALA PRO GLU LYS SER SER LYS VAL SER GLU GLN LEU LYS SEQRES 3 A 131 CME CYS SER GLY ILE LEU LYS GLU MET PHE ALA LYS LYS SEQRES 4 A 131 HIS ALA ALA TYR ALA TRP PRO PHE TYR LYS PRO VAL ASP SEQRES 5 A 131 VAL GLU ALA LEU GLY LEU HIS ASP TYR CME ASP ILE ILE SEQRES 6 A 131 LYS HIS PRO MET ASP MET SER THR ILE LYS SER LYS LEU SEQRES 7 A 131 GLU ALA ARG GLU TYR ARG ASP ALA GLN GLU PHE GLY ALA SEQRES 8 A 131 ASP VAL ARG LEU MET PHE SER ASN CYS TYR LYS TYR ASN SEQRES 9 A 131 PRO PRO ASP HIS GLU VAL VAL ALA MET ALA ARG LYS LEU SEQRES 10 A 131 GLN ASP VAL PHE GLU MET ARG PHE ALA LYS MET PRO ASP SEQRES 11 A 131 GLU MODRES 6C7Q CME A 356 CYS MODIFIED RESIDUE MODRES 6C7Q CME A 391 CYS MODIFIED RESIDUE HET CME A 356 10 HET CME A 391 10 HET EO1 A 501 41 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM EO1 7-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-6-METHOXY-2-METHYL-N- HETNAM 2 EO1 (1-METHYL-1H-INDAZOL-3-YL)-9H-PYRIMIDO[4,5-B]INDOL-4- HETNAM 3 EO1 AMINE FORMUL 1 CME 2(C5 H11 N O3 S2) FORMUL 2 EO1 C25 H23 N7 O2 FORMUL 3 HOH *97(H2 O) HELIX 1 AA1 LYS 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 381 GLY A 386 1 6 HELIX 6 AA6 ASP A 389 ILE A 394 1 6 HELIX 7 AA7 ASP A 399 ALA A 409 1 11 HELIX 8 AA8 ASP A 414 ASN A 433 1 20 HELIX 9 AA9 HIS A 437 ALA A 455 1 19 LINK C LYS A 355 N CME A 356 1555 1555 1.37 LINK C CME A 356 N CYS A 357 1555 1555 1.34 LINK C TYR A 390 N CME A 391 1555 1555 1.33 LINK C CME A 391 N ASP A 392 1555 1555 1.35 SITE 1 AC1 11 TRP A 374 PRO A 375 PHE A 376 LEU A 385 SITE 2 AC1 11 LEU A 387 CYS A 429 TYR A 432 ASN A 433 SITE 3 AC1 11 HIS A 437 VAL A 439 HOH A 601 CRYST1 52.176 72.647 32.222 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 0.019166 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013765 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031035 0.00000