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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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