HEADER TRANSCRIPTION 03-APR-15 4UIX TITLE N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 7-(3,4-DIMETHOXYPHENYL)-N- TITLE 2 (1,1-DIOXO-1-THIAN-4-YL)-5-METHYL-4-OXO-4H,5H-THIENO-3,2-C-PYRIDINE- TITLE 3 2- CARBOXAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 4; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: N-TERMINAL BROMODOMAIN, RESIDUES 44-168; COMPND 5 SYNONYM: PROTEIN HUNK1, NHUMAN BRD4; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTION, INHIBITOR, HISTONE, EPIGENETIC READER, BROMODOMAIN, KEYWDS 2 BRD4, BROMODOMAIN CONTAINING PROTEIN 4, ANTAGONIST EXPDTA X-RAY DIFFRACTION AUTHOR C.CHUNG,N.T.THEODOULOU,P.BAMBOROUGH,P.G.HUMPHREYS REVDAT 5 08-MAY-24 4UIX 1 REMARK LINK REVDAT 4 15-MAY-19 4UIX 1 REMARK REVDAT 3 27-SEP-17 4UIX 1 REMARK REVDAT 2 09-MAR-16 4UIX 1 JRNL REVDAT 1 22-APR-15 4UIX 0 JRNL AUTH N.H.THEODOULOU,P.BAMBOROUGH,A.J.BANNISTER,I.BECHER,R.A.BIT, JRNL AUTH 2 K.H.CHE,C.CHUNG,A.DITTMANN,G.DREWES,D.H.DREWRY,L.GORDON, JRNL AUTH 3 P.GRANDI,M.LEVERIDGE,M.LINDON,A.MICHON,J.MOLNAR,S.C.ROBSON, JRNL AUTH 4 N.C.O.TOMKINSON,T.KOUZARIDES,R.K.PRINJHA,P.G.HUMPHREYS JRNL TITL THE DISCOVERY OF I-BRD9, A SELECTIVE CELL ACTIVE CHEMICAL JRNL TITL 2 PROBE FOR BROMODOMAIN CONTAINING PROTEIN 9 INHIBITION. JRNL REF J.MED.CHEM. V. 59 1425 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 25856009 JRNL DOI 10.1021/ACS.JMEDCHEM.5B00256 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 55517 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2958 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3973 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 180 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3071 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 110 REMARK 3 SOLVENT ATOMS : 428 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 0.92000 REMARK 3 B33 (A**2) : -1.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.25000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.097 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.099 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.272 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3299 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2267 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4496 ; 1.127 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5574 ; 0.836 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 371 ; 5.042 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;37.913 ;25.742 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 582 ;11.220 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;18.803 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 469 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3821 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 608 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 43 A 168 REMARK 3 ORIGIN FOR THE GROUP (A): 24.9376 6.0906 28.2101 REMARK 3 T TENSOR REMARK 3 T11: 0.0485 T22: 0.0064 REMARK 3 T33: 0.0421 T12: -0.0041 REMARK 3 T13: -0.0169 T23: -0.0030 REMARK 3 L TENSOR REMARK 3 L11: 0.1746 L22: 0.4602 REMARK 3 L33: 0.6026 L12: 0.0128 REMARK 3 L13: 0.1220 L23: 0.3412 REMARK 3 S TENSOR REMARK 3 S11: -0.0411 S12: 0.0077 S13: -0.0109 REMARK 3 S21: -0.0230 S22: -0.0127 S23: 0.0356 REMARK 3 S31: -0.0674 S32: 0.0310 S33: 0.0538 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 42 B 167 REMARK 3 ORIGIN FOR THE GROUP (A): 3.6475 27.7246 23.2063 REMARK 3 T TENSOR REMARK 3 T11: 0.0327 T22: 0.0206 REMARK 3 T33: 0.0425 T12: 0.0010 REMARK 3 T13: 0.0055 T23: -0.0083 REMARK 3 L TENSOR REMARK 3 L11: 0.3147 L22: 0.1286 REMARK 3 L33: 0.8627 L12: -0.0615 REMARK 3 L13: 0.1392 L23: -0.3209 REMARK 3 S TENSOR REMARK 3 S11: -0.0177 S12: -0.0109 S13: -0.0108 REMARK 3 S21: -0.0141 S22: 0.0283 S23: -0.0144 REMARK 3 S31: 0.0274 S32: -0.0588 S33: -0.0105 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 42 C 163 REMARK 3 ORIGIN FOR THE GROUP (A): -17.4513 14.2986 7.1332 REMARK 3 T TENSOR REMARK 3 T11: 0.0229 T22: 0.0447 REMARK 3 T33: 0.0715 T12: -0.0028 REMARK 3 T13: 0.0108 T23: 0.0373 REMARK 3 L TENSOR REMARK 3 L11: 1.4118 L22: 1.3195 REMARK 3 L33: 1.5158 L12: 0.3474 REMARK 3 L13: -1.3530 L23: -0.8422 REMARK 3 S TENSOR REMARK 3 S11: -0.0719 S12: -0.0926 S13: -0.1979 REMARK 3 S21: -0.0206 S22: -0.0674 S23: 0.0971 REMARK 3 S31: 0.0604 S32: 0.1229 S33: 0.1393 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 4UIX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-APR-15. REMARK 100 THE DEPOSITION ID IS D_1290063543. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-13 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 : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58489 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 49.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M CACL2, 0.1M HEPES, PEG 6K 20C, REMARK 280 TEMPERATURE 293K 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 22.33500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 350 REMARK 350 BIOMOLECULE: 3 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: C 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 42 REMARK 465 GLU B 168 REMARK 465 SER C 51 REMARK 465 ASN C 52 REMARK 465 PRO C 53 REMARK 465 ASN C 54 REMARK 465 LYS C 55 REMARK 465 PRO C 56 REMARK 465 LYS C 57 REMARK 465 LEU C 164 REMARK 465 PRO C 165 REMARK 465 THR C 166 REMARK 465 GLU C 167 REMARK 465 GLU C 168 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 GLU C 163 CG CD OE1 OE2 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 OH TYR C 65 O HOH C 2031 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 52 114.10 -160.88 REMARK 500 LEU A 94 72.86 -119.85 REMARK 500 ASN B 52 117.26 -160.07 REMARK 500 ASN C 162 93.80 -62.63 REMARK 500 REMARK 500 REMARK: NULL 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 A2063 DISTANCE = 6.90 ANGSTROMS REMARK 525 HOH B2025 DISTANCE = 7.18 ANGSTROMS REMARK 525 HOH B2048 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH C2110 DISTANCE = 7.91 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1169 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 145 OD2 REMARK 620 2 ASP A 145 OD1 52.0 REMARK 620 3 EDO A1170 O1 79.7 71.1 REMARK 620 4 EDO A1170 O2 114.2 134.6 63.7 REMARK 620 5 HOH A2145 O 128.9 77.7 75.5 93.4 REMARK 620 6 HOH A2147 O 83.8 72.8 143.2 152.4 90.2 REMARK 620 7 HOH A2148 O 74.7 123.3 121.2 80.5 155.3 84.9 REMARK 620 8 HOH A2167 O 149.6 143.7 126.6 73.0 77.5 81.1 77.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1168 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 145 OD1 REMARK 620 2 ASP B 145 OD2 51.9 REMARK 620 3 EDO B1169 O2 71.7 83.3 REMARK 620 4 EDO B1169 O1 134.7 109.0 64.8 REMARK 620 5 HOH B2131 O 75.7 127.6 79.1 107.0 REMARK 620 6 HOH B2133 O 70.3 79.9 141.1 154.1 83.9 REMARK 620 7 HOH B2134 O 122.1 75.7 130.1 80.1 147.8 78.8 REMARK 620 8 HOH B2146 O 134.2 145.4 130.9 86.4 72.4 74.3 76.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1169 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1168 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1170 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 1164 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 1169 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TVU A 1171 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TVU B 1170 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TVU C 1165 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UIT RELATED DB: PDB REMARK 900 BROMODOMAIN OF HUMAN BRD9 WITH 7-(3,4-DIMETHOXYPHENYL )-2-(4- REMARK 900 METHANESULFONYLPIPERAZINE-1-CARBONYL)-5-METHYL- 4H,5H-THIENO-3,2-C- REMARK 900 PYRIDIN-4-ONE REMARK 900 RELATED ID: 4UIU RELATED DB: PDB REMARK 900 BROMODOMAIN OF HUMAN BRD9 WITH 7-(3,4-DIMETHOXYPHENYL )-N-(1,1- REMARK 900 DIOXO-1-THIAN-4-YL)-5-METHYL-4-OXO- 4H,5H-THIENO-3,2-C-PYRIDINE-2- REMARK 900 CARBOXAMIDE REMARK 900 RELATED ID: 4UIV RELATED DB: PDB REMARK 900 BROMODOMAIN OF HUMAN BRD9 WITH N-(1,1-DIOXO-1- THIAN-4-YL)-5-METHYL- REMARK 900 4-OXO-7-3-(TRIFLUOROMETHYL) PHENYL-4H,5H-THIENO-3,2-C-PYRIDINE-2- REMARK 900 CARBOXIMIDAMIDE REMARK 900 RELATED ID: 4UIW RELATED DB: PDB REMARK 900 BROMODOMAIN OF HUMAN BRD9 WITH N-(1,1-DIOXO-1- THIAN-4-YL)-5-ETHYL- REMARK 900 4-OXO-7-3-(TRIFLUOROMETHYL) PHENYL-4H,5H-THIENO-3,2-C-PYRIDINE-2- REMARK 900 CARBOXIMIDAMIDE REMARK 900 RELATED ID: 4UIY RELATED DB: PDB REMARK 900 N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH N-(1,1- DIOXO-1-THIAN-4- REMARK 900 YL)-5-METHYL-4-OXO-7-3-( TRIFLUOROMETHYL)PHENYL-4H,5H-THIENO-3,2-C- REMARK 900 PYRIDINE-2 -CARBOXIMIDAMIDE REMARK 900 RELATED ID: 4UIZ RELATED DB: PDB REMARK 900 N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 7-(3,4- DIMETHOXYPHENYL)- REMARK 900 2-(4-METHANESULFONYLPIPERAZINE-1-CARBONYL )-5-METHYL-4H,5H-THIENO-3, REMARK 900 2-C-PYRIDIN-4-ONE DBREF 4UIX A 44 168 UNP O60885 BRD4_HUMAN 44 168 DBREF 4UIX B 44 168 UNP O60885 BRD4_HUMAN 44 168 DBREF 4UIX C 44 168 UNP O60885 BRD4_HUMAN 44 168 SEQADV 4UIX SER A 42 UNP O60885 EXPRESSION TAG SEQADV 4UIX MET A 43 UNP O60885 EXPRESSION TAG SEQADV 4UIX LYS A 78 UNP O60885 GLN 78 CONFLICT SEQADV 4UIX SER B 42 UNP O60885 EXPRESSION TAG SEQADV 4UIX MET B 43 UNP O60885 EXPRESSION TAG SEQADV 4UIX LYS B 78 UNP O60885 GLN 78 CONFLICT SEQADV 4UIX SER C 42 UNP O60885 EXPRESSION TAG SEQADV 4UIX MET C 43 UNP O60885 EXPRESSION TAG SEQADV 4UIX LYS C 78 UNP O60885 GLN 78 CONFLICT SEQRES 1 A 127 SER MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN SEQRES 2 A 127 LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU SEQRES 3 A 127 ARG VAL VAL LEU LYS THR LEU TRP LYS HIS LYS PHE ALA SEQRES 4 A 127 TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN SEQRES 5 A 127 LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP SEQRES 6 A 127 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR SEQRES 7 A 127 TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET SEQRES 8 A 127 PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP SEQRES 9 A 127 ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU SEQRES 10 A 127 GLN LYS ILE ASN GLU LEU PRO THR GLU GLU SEQRES 1 B 127 SER MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN SEQRES 2 B 127 LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU SEQRES 3 B 127 ARG VAL VAL LEU LYS THR LEU TRP LYS HIS LYS PHE ALA SEQRES 4 B 127 TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN SEQRES 5 B 127 LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP SEQRES 6 B 127 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR SEQRES 7 B 127 TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET SEQRES 8 B 127 PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP SEQRES 9 B 127 ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU SEQRES 10 B 127 GLN LYS ILE ASN GLU LEU PRO THR GLU GLU SEQRES 1 C 127 SER MET ASN PRO PRO PRO PRO GLU THR SER ASN PRO ASN SEQRES 2 C 127 LYS PRO LYS ARG GLN THR ASN GLN LEU GLN TYR LEU LEU SEQRES 3 C 127 ARG VAL VAL LEU LYS THR LEU TRP LYS HIS LYS PHE ALA SEQRES 4 C 127 TRP PRO PHE GLN GLN PRO VAL ASP ALA VAL LYS LEU ASN SEQRES 5 C 127 LEU PRO ASP TYR TYR LYS ILE ILE LYS THR PRO MET ASP SEQRES 6 C 127 MET GLY THR ILE LYS LYS ARG LEU GLU ASN ASN TYR TYR SEQRES 7 C 127 TRP ASN ALA GLN GLU CYS ILE GLN ASP PHE ASN THR MET SEQRES 8 C 127 PHE THR ASN CYS TYR ILE TYR ASN LYS PRO GLY ASP ASP SEQRES 9 C 127 ILE VAL LEU MET ALA GLU ALA LEU GLU LYS LEU PHE LEU SEQRES 10 C 127 GLN LYS ILE ASN GLU LEU PRO THR GLU GLU HET CA A1169 1 HET EDO A1170 4 HET TVU A1171 32 HET CA B1168 1 HET EDO B1169 4 HET TVU B1170 32 HET EDO C1164 4 HET TVU C1165 32 HETNAM CA CALCIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM TVU N-[1,1-BIS(OXIDANYLIDENE)THIAN-4-YL]-7-(3,4- HETNAM 2 TVU DIMETHOXYPHENYL)-5-METHYL-4-OXIDANYLIDENE-THIENO[3,2- HETNAM 3 TVU C]PYRIDINE-2-CARBOXAMIDE HETSYN EDO ETHYLENE GLYCOL FORMUL 4 CA 2(CA 2+) FORMUL 5 EDO 3(C2 H6 O2) FORMUL 6 TVU 3(C22 H24 N2 O6 S2) FORMUL 12 HOH *428(H2 O) HELIX 1 1 THR A 60 VAL A 69 1 10 HELIX 2 2 VAL A 69 HIS A 77 1 9 HELIX 3 3 ALA A 80 GLN A 84 5 5 HELIX 4 4 ASP A 96 ILE A 101 1 6 HELIX 5 5 ASP A 106 ASN A 116 1 11 HELIX 6 6 ASN A 121 ASN A 140 1 20 HELIX 7 7 ASP A 144 ASN A 162 1 19 HELIX 8 8 THR B 60 VAL B 69 1 10 HELIX 9 9 VAL B 69 HIS B 77 1 9 HELIX 10 10 ALA B 80 GLN B 84 5 5 HELIX 11 11 ASP B 88 ASN B 93 1 6 HELIX 12 12 ASP B 96 ILE B 101 1 6 HELIX 13 13 ASP B 106 ASN B 116 1 11 HELIX 14 14 ASN B 121 ASN B 140 1 20 HELIX 15 15 ASP B 144 ASN B 162 1 19 HELIX 16 16 THR C 60 VAL C 69 1 10 HELIX 17 17 VAL C 69 LYS C 76 1 8 HELIX 18 18 ALA C 80 GLN C 84 5 5 HELIX 19 19 ASP C 96 ILE C 101 1 6 HELIX 20 20 ASP C 106 ASN C 116 1 11 HELIX 21 21 ASN C 121 ASN C 140 1 20 HELIX 22 22 ASP C 144 ASN C 162 1 19 LINK OD2 ASP A 145 CA CA A1169 1555 1555 2.49 LINK OD1 ASP A 145 CA CA A1169 1555 1555 2.50 LINK CA CA A1169 O1 EDO A1170 1555 1555 2.53 LINK CA CA A1169 O2 EDO A1170 1555 1555 2.39 LINK CA CA A1169 O HOH A2145 1555 1555 2.49 LINK CA CA A1169 O HOH A2147 1555 1555 2.41 LINK CA CA A1169 O HOH A2148 1555 1555 2.46 LINK CA CA A1169 O HOH A2167 1555 1555 2.34 LINK OD1 ASP B 145 CA CA B1168 1555 1555 2.47 LINK OD2 ASP B 145 CA CA B1168 1555 1555 2.54 LINK CA CA B1168 O2 EDO B1169 1555 1555 2.45 LINK CA CA B1168 O1 EDO B1169 1555 1555 2.54 LINK CA CA B1168 O HOH B2131 1555 1555 2.41 LINK CA CA B1168 O HOH B2133 1555 1555 2.39 LINK CA CA B1168 O HOH B2134 1555 1555 2.39 LINK CA CA B1168 O HOH B2146 1555 1555 2.49 SITE 1 AC1 6 ASP A 145 EDO A1170 HOH A2145 HOH A2147 SITE 2 AC1 6 HOH A2148 HOH A2167 SITE 1 AC2 6 ASP B 145 EDO B1169 HOH B2131 HOH B2133 SITE 2 AC2 6 HOH B2134 HOH B2146 SITE 1 AC3 7 ASP A 144 ASP A 145 CA A1169 TVU A1171 SITE 2 AC3 7 HOH A2145 HOH A2167 HOH A2168 SITE 1 AC4 6 ILE C 100 ILE C 101 LYS C 102 THR C 103 SITE 2 AC4 6 ASN C 135 HOH C2109 SITE 1 AC5 5 ASP B 144 ASP B 145 CA B1168 TVU B1170 SITE 2 AC5 5 HOH B2131 SITE 1 AC6 12 TRP A 81 PRO A 82 PHE A 83 LEU A 92 SITE 2 AC6 12 TYR A 139 ASN A 140 LYS A 141 ASP A 144 SITE 3 AC6 12 EDO A1170 HOH A2098 HOH A2107 HOH A2169 SITE 1 AC7 12 TRP B 81 PRO B 82 PHE B 83 VAL B 87 SITE 2 AC7 12 LEU B 92 TYR B 139 ASN B 140 LYS B 141 SITE 3 AC7 12 ASP B 144 EDO B1169 HOH B2090 HOH B2148 SITE 1 AC8 10 TRP C 81 PRO C 82 VAL C 87 LEU C 92 SITE 2 AC8 10 LEU C 94 TYR C 139 ASN C 140 LYS C 141 SITE 3 AC8 10 ASP C 144 HOH C2067 CRYST1 63.640 44.670 77.550 90.00 90.09 90.00 P 1 21 1 6 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 0.015713 0.000000 0.000025 0.00000 SCALE2 0.000000 0.022386 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012895 0.00000 CONECT 876 3099 CONECT 877 3099 CONECT 1944 3136 CONECT 1945 3136 CONECT 3099 876 877 3101 3103 CONECT 3099 3353 3355 3356 3375 CONECT 3100 3101 3102 CONECT 3101 3099 3100 CONECT 3102 3100 3103 CONECT 3103 3099 3102 CONECT 3104 3105 CONECT 3105 3104 3106 3107 3109 CONECT 3106 3105 CONECT 3107 3105 3108 CONECT 3108 3107 3111 CONECT 3109 3105 3110 CONECT 3110 3109 3111 CONECT 3111 3108 3110 3112 CONECT 3112 3111 3113 CONECT 3113 3112 3114 3115 CONECT 3114 3113 CONECT 3115 3113 3116 3117 CONECT 3116 3115 3119 CONECT 3117 3115 3118 CONECT 3118 3117 3119 3125 CONECT 3119 3116 3118 3120 CONECT 3120 3119 3121 3122 CONECT 3121 3120 CONECT 3122 3120 3123 3124 CONECT 3123 3122 CONECT 3124 3122 3125 CONECT 3125 3118 3124 3126 CONECT 3126 3125 3127 3129 CONECT 3127 3126 3128 CONECT 3128 3127 3133 CONECT 3129 3126 3130 CONECT 3130 3129 3131 3133 CONECT 3131 3130 3132 CONECT 3132 3131 CONECT 3133 3128 3130 3134 CONECT 3134 3133 3135 CONECT 3135 3134 CONECT 3136 1944 1945 3138 3140 CONECT 3136 3508 3510 3511 3523 CONECT 3137 3138 3139 CONECT 3138 3136 3137 CONECT 3139 3137 3140 CONECT 3140 3136 3139 CONECT 3141 3142 CONECT 3142 3141 3143 3144 3146 CONECT 3143 3142 CONECT 3144 3142 3145 CONECT 3145 3144 3148 CONECT 3146 3142 3147 CONECT 3147 3146 3148 CONECT 3148 3145 3147 3149 CONECT 3149 3148 3150 CONECT 3150 3149 3151 3152 CONECT 3151 3150 CONECT 3152 3150 3153 3154 CONECT 3153 3152 3156 CONECT 3154 3152 3155 CONECT 3155 3154 3156 3162 CONECT 3156 3153 3155 3157 CONECT 3157 3156 3158 3159 CONECT 3158 3157 CONECT 3159 3157 3160 3161 CONECT 3160 3159 CONECT 3161 3159 3162 CONECT 3162 3155 3161 3163 CONECT 3163 3162 3164 3166 CONECT 3164 3163 3165 CONECT 3165 3164 3170 CONECT 3166 3163 3167 CONECT 3167 3166 3168 3170 CONECT 3168 3167 3169 CONECT 3169 3168 CONECT 3170 3165 3167 3171 CONECT 3171 3170 3172 CONECT 3172 3171 CONECT 3173 3174 3175 CONECT 3174 3173 CONECT 3175 3173 3176 CONECT 3176 3175 CONECT 3177 3178 CONECT 3178 3177 3179 3180 3182 CONECT 3179 3178 CONECT 3180 3178 3181 CONECT 3181 3180 3184 CONECT 3182 3178 3183 CONECT 3183 3182 3184 CONECT 3184 3181 3183 3185 CONECT 3185 3184 3186 CONECT 3186 3185 3187 3188 CONECT 3187 3186 CONECT 3188 3186 3189 3190 CONECT 3189 3188 3192 CONECT 3190 3188 3191 CONECT 3191 3190 3192 3198 CONECT 3192 3189 3191 3193 CONECT 3193 3192 3194 3195 CONECT 3194 3193 CONECT 3195 3193 3196 3197 CONECT 3196 3195 CONECT 3197 3195 3198 CONECT 3198 3191 3197 3199 CONECT 3199 3198 3200 3202 CONECT 3200 3199 3201 CONECT 3201 3200 3206 CONECT 3202 3199 3203 CONECT 3203 3202 3204 3206 CONECT 3204 3203 3205 CONECT 3205 3204 CONECT 3206 3201 3203 3207 CONECT 3207 3206 3208 CONECT 3208 3207 CONECT 3353 3099 CONECT 3355 3099 CONECT 3356 3099 CONECT 3375 3099 CONECT 3508 3136 CONECT 3510 3136 CONECT 3511 3136 CONECT 3523 3136 MASTER 464 0 8 22 0 0 19 6 3609 3 124 30 END