HEADER TRANSCRIPTION 09-APR-15 4Z93 TITLE BRD4 BROMODOMAIN 2 IN COMPLEX WITH GAMMA-CARBOLINE-CONTAINING TITLE 2 COMPOUND, NUMBER 18. COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BROMODOMAIN 2 (UNP RESIDUES 349-460); 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BROMODOMAIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR J.L.MEAGHER,J.A.STUCKEY REVDAT 4 30-OCT-24 4Z93 1 REMARK REVDAT 3 27-SEP-23 4Z93 1 SOURCE KEYWDS JRNL REMARK REVDAT 2 08-JUL-15 4Z93 1 KEYWDS REVDAT 1 01-JUL-15 4Z93 0 JRNL AUTH X.RAN,Y.ZHAO,L.LIU,L.BAI,C.Y.YANG,B.ZHOU,J.L.MEAGHER, JRNL AUTH 2 K.CHINNASWAMY,J.A.STUCKEY,S.WANG JRNL TITL STRUCTURE-BASED DESIGN OF GAMMA-CARBOLINE ANALOGUES AS JRNL TITL 2 POTENT AND SPECIFIC BET BROMODOMAIN INHIBITORS. JRNL REF J.MED.CHEM. V. 58 4927 2015 JRNL REFN ISSN 0022-2623 JRNL PMID 26080064 JRNL DOI 10.1021/ACS.JMEDCHEM.5B00613 REMARK 2 REMARK 2 RESOLUTION. 1.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT BUSTER 2.11.2 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) : 1.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 32482 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1649 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 : 16 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.27 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.31 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.97 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2906 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1644 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2748 REMARK 3 BIN R VALUE (WORKING SET) : 0.1627 REMARK 3 BIN FREE R VALUE : 0.1944 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.44 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 158 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 909 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.77050 REMARK 3 B22 (A**2) : 2.87810 REMARK 3 B33 (A**2) : -1.10760 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) : 0.142 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.040 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.044 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.041 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.043 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 : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1898 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3418 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 521 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 23 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 323 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1898 ; 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 : 117 ; 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 : 2139 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.98 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.04 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.75 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): 10.1121 2.5701 0.4838 REMARK 3 T TENSOR REMARK 3 T11: -0.0152 T22: -0.0194 REMARK 3 T33: -0.0246 T12: -0.0018 REMARK 3 T13: -0.0070 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.6145 L22: 1.0676 REMARK 3 L33: 0.4554 L12: -0.0107 REMARK 3 L13: 0.0829 L23: -0.0874 REMARK 3 S TENSOR REMARK 3 S11: 0.0046 S12: 0.0153 S13: -0.0335 REMARK 3 S21: -0.0257 S22: -0.0033 S23: -0.0021 REMARK 3 S31: -0.0167 S32: 0.0410 S33: -0.0013 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4Z93 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208679. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-13 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-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07820 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 : 32674 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.270 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.32600 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: 2OUO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, IMIDIZOLE, ATP, PH 8.0, VAPOR REMARK 280 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 25.93100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.34800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.93100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.34800 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 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 349 CD CE NZ REMARK 470 LYS A 367 CD CE NZ REMARK 470 GLU A 383 CG CD OE1 OE2 REMARK 470 GLN A 416 CG CD OE1 NE2 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 HD1 HIS A 369 OH TYR A 372 1.58 REMARK 500 HH TYR A 390 O HOH A 604 1.59 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 4LD A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 DBREF 4Z93 A 349 460 UNP O60885 BRD4_HUMAN 349 460 SEQRES 1 A 112 LYS VAL SER GLU GLN LEU LYS CME CYS SER GLY ILE LEU SEQRES 2 A 112 LYS GLU MET PHE ALA LYS LYS HIS ALA ALA TYR ALA TRP SEQRES 3 A 112 PRO PHE TYR LYS PRO VAL ASP VAL GLU ALA LEU GLY LEU SEQRES 4 A 112 HIS ASP TYR CME ASP ILE ILE LYS HIS PRO MET ASP MET SEQRES 5 A 112 SER THR ILE LYS SER LYS LEU GLU ALA ARG GLU TYR ARG SEQRES 6 A 112 ASP ALA GLN GLU PHE GLY ALA ASP VAL ARG LEU MET PHE SEQRES 7 A 112 SER ASN CYS TYR LYS TYR ASN PRO PRO ASP HIS GLU VAL SEQRES 8 A 112 VAL ALA MET ALA ARG LYS LEU GLN ASP VAL PHE GLU MET SEQRES 9 A 112 ARG PHE ALA LYS MET PRO ASP GLU MODRES 4Z93 CME A 356 CYS MODIFIED RESIDUE MODRES 4Z93 CME A 391 CYS MODIFIED RESIDUE HET CME A 356 10 HET CME A 391 10 HET 4LD A 501 67 HET EDO A 502 4 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM 4LD 1-(3-CYCLOPROPYL-5-METHYL-1H-PYRAZOL-4-YL)-7-(3,5- HETNAM 2 4LD DIMETHYL-1,2-OXAZOL-4-YL)-8-METHOXY-5H-PYRIDO[4,3- HETNAM 3 4LD B]INDOLE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 CME 2(C5 H11 N O3 S2) FORMUL 2 4LD C24 H23 N5 O2 FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *119(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 1.36 LINK C CME A 356 N CYS A 357 1555 1555 1.35 LINK C TYR A 390 N CME A 391 1555 1555 1.31 LINK C CME A 391 N ASP A 392 1555 1555 1.34 SITE 1 AC1 12 TRP A 374 PRO A 375 PHE A 376 LEU A 385 SITE 2 AC1 12 LEU A 387 CYS A 429 ASN A 433 HIS A 437 SITE 3 AC1 12 VAL A 439 HOH A 604 HOH A 643 HOH A 652 SITE 1 AC2 5 TYR A 430 ARG A 444 GLN A 447 ASP A 448 SITE 2 AC2 5 HOH A 673 CRYST1 51.862 72.696 32.115 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 0.019282 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013756 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031138 0.00000