HEADER HYDROLASE 22-MAY-15 5A2S TITLE POTENT, SELECTIVE AND CNS-PENETRANT TETRASUBSTITUTED CYCLOPROPANE TITLE 2 CLASS IIA HISTONE DEACETYLASE (HDAC) INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE 4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: HISTONE DEACETYLASE DOMAIN, RESIDUES 648-1033; COMPND 5 SYNONYM: HD4; COMPND 6 EC: 3.5.1.98; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HYDROLASE, CLASS IIA HDAC INHIBITORS, HYDROXAMIC ACID, CNS EXPOSURE, KEYWDS 2 TETRASUBSTITUTED CYCLOPROPANE, CYCLOPROPANATION, HUNTINGTON'S KEYWDS 3 DISEASE EXPDTA X-RAY DIFFRACTION AUTHOR C.A.LUCKHURST,P.BRECCIA,A.J.STOTT,O.AZIZ,H.BIRCH,R.W.BURLI,S.HUGHES, AUTHOR 2 R.E.JARVIS,M.LAMERS,P.LEONARD,K.L.MATTHEWS,G.MCALLISTER,S.POLLACK, AUTHOR 3 E.SAVILLE-STONES,G.WISHART,D.YATES,C.DOMINGUEZ REVDAT 2 10-JAN-24 5A2S 1 REMARK REVDAT 1 10-FEB-16 5A2S 0 JRNL AUTH C.A.LUCKHURST,P.BRECCIA,A.J.STOTT,O.AZIZ,H.L.BIRCH, JRNL AUTH 2 R.W.BURLI,S.J.HUGHES,R.E.JARVIS,M.LAMERS,P.M.LEONARD, JRNL AUTH 3 K.L.MATTHEWS,G.MCALLISTER,S.POLLACK,E.SAVILLE-STONES, JRNL AUTH 4 G.WISHART,D.YATES,C.DOMINGUEZ JRNL TITL POTENT, SELECTIVE, AND CNS-PENETRANT TETRASUBSTITUTED JRNL TITL 2 CYCLOPROPANE CLASS IIA HISTONE DEACETYLASE (HDAC) JRNL TITL 3 INHIBITORS. JRNL REF ACS MED.CHEM.LETT. V. 7 34 2016 JRNL REFN ISSN 1948-5875 JRNL PMID 26819662 JRNL DOI 10.1021/ACSMEDCHEMLETT.5B00302 REMARK 2 REMARK 2 RESOLUTION. 2.65 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) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 161.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 19871 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1079 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) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1175 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.3780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5636 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.95000 REMARK 3 B22 (A**2) : 3.45000 REMARK 3 B33 (A**2) : -2.50000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.375 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.257 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.401 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.873 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5842 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3793 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7936 ; 1.216 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9261 ; 0.911 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 758 ; 5.608 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 232 ;36.272 ;24.138 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 876 ;14.105 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;14.053 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 892 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6626 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1178 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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.U VALUES REFINED INDIVIDUALLY. REMARK 4 REMARK 4 5A2S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1290063841. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-12 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20994 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.18000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.72000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: PDB ENTRY 4CBY REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% W/V PEG 3350, 0.2 M AMMONIUM REMARK 280 ACETATE, 0.1 M BIS-TRIS PH 5.5, 10 MM PROLINE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.07050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 80.81300 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.07050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 80.81300 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 MET A 645 REMARK 465 GLY A 646 REMARK 465 SER A 647 REMARK 465 THR A 648 REMARK 465 LYS A 649 REMARK 465 PRO A 650 REMARK 465 ARG A 651 REMARK 465 PHE A 652 REMARK 465 ARG A 1033 REMARK 465 HIS A 1034 REMARK 465 HIS A 1035 REMARK 465 HIS A 1036 REMARK 465 HIS A 1037 REMARK 465 HIS A 1038 REMARK 465 HIS A 1039 REMARK 465 MET B 645 REMARK 465 GLY B 646 REMARK 465 SER B 647 REMARK 465 THR B 648 REMARK 465 LYS B 649 REMARK 465 PRO B 650 REMARK 465 ARG B 651 REMARK 465 PHE B 652 REMARK 465 ARG B 1033 REMARK 465 HIS B 1034 REMARK 465 HIS B 1035 REMARK 465 HIS B 1036 REMARK 465 HIS B 1037 REMARK 465 HIS B 1038 REMARK 465 HIS B 1039 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 697 NZ REMARK 470 ARG A 702 CD NE CZ NH1 NH2 REMARK 470 LYS A 732 CG CD CE NZ REMARK 470 GLU A 996 CG CD OE1 OE2 REMARK 470 GLU A1002 CG CD OE1 OE2 REMARK 470 LYS A1003 CG CD CE NZ REMARK 470 ARG A1008 CG CD NE CZ NH1 NH2 REMARK 470 ARG A1015 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1022 CG CD OE1 OE2 REMARK 470 ARG A1029 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 697 CG CD CE NZ REMARK 470 ARG B 702 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 732 CG CD CE NZ REMARK 470 LYS B 958 CG CD CE NZ REMARK 470 GLU B 996 CG CD OE1 OE2 REMARK 470 ASP B 998 CG OD1 OD2 REMARK 470 LYS B1003 CG CD CE NZ REMARK 470 ARG B1008 CG CD NE CZ NH1 NH2 REMARK 470 ARG B1015 CZ NH1 NH2 REMARK 470 GLU B1022 CG CD OE1 OE2 REMARK 470 ARG B1029 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O LYS A 737 NH2 ARG B 748 4445 2.17 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 HIS A 665 94.94 -66.14 REMARK 500 SER A 758 -9.85 -59.32 REMARK 500 ASP A 759 -8.18 -155.76 REMARK 500 ASP A 867 28.47 48.52 REMARK 500 GLU A 879 87.27 -62.84 REMARK 500 LEU A 898 49.19 -107.09 REMARK 500 ALA A 923 75.63 67.19 REMARK 500 GLU A 973 -112.71 -121.57 REMARK 500 HIS A 976 -52.91 -130.98 REMARK 500 HIS B 665 93.05 -67.21 REMARK 500 SER B 758 7.88 -63.58 REMARK 500 ASP B 759 -24.70 -159.71 REMARK 500 TYR B 814 -53.71 -123.51 REMARK 500 ASP B 866 -117.07 53.53 REMARK 500 ALA B 923 66.17 64.70 REMARK 500 ARG B 967 81.75 -69.76 REMARK 500 GLU B 973 -117.40 -111.08 REMARK 500 HIS B 976 -54.89 -137.47 REMARK 500 GLN B1006 31.48 -89.97 REMARK 500 REMARK 500 REMARK: NULL 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 ZN A 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 OTF A 1 O6 REMARK 620 2 OTF A 1 O8 81.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 OTF B 1 O8 REMARK 620 2 OTF B 1 O6 77.4 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OTF A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OTF B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 4 DBREF 5A2S A 648 1033 UNP P56524 HDAC4_HUMAN 648 1033 DBREF 5A2S B 648 1033 UNP P56524 HDAC4_HUMAN 648 1033 SEQADV 5A2S MET A 645 UNP P56524 EXPRESSION TAG SEQADV 5A2S GLY A 646 UNP P56524 EXPRESSION TAG SEQADV 5A2S SER A 647 UNP P56524 EXPRESSION TAG SEQADV 5A2S HIS A 1034 UNP P56524 EXPRESSION TAG SEQADV 5A2S HIS A 1035 UNP P56524 EXPRESSION TAG SEQADV 5A2S HIS A 1036 UNP P56524 EXPRESSION TAG SEQADV 5A2S HIS A 1037 UNP P56524 EXPRESSION TAG SEQADV 5A2S HIS A 1038 UNP P56524 EXPRESSION TAG SEQADV 5A2S HIS A 1039 UNP P56524 EXPRESSION TAG SEQADV 5A2S ALA A 728 UNP P56524 LEU 728 ENGINEERED MUTATION SEQADV 5A2S MET B 645 UNP P56524 EXPRESSION TAG SEQADV 5A2S GLY B 646 UNP P56524 EXPRESSION TAG SEQADV 5A2S SER B 647 UNP P56524 EXPRESSION TAG SEQADV 5A2S HIS B 1034 UNP P56524 EXPRESSION TAG SEQADV 5A2S HIS B 1035 UNP P56524 EXPRESSION TAG SEQADV 5A2S HIS B 1036 UNP P56524 EXPRESSION TAG SEQADV 5A2S HIS B 1037 UNP P56524 EXPRESSION TAG SEQADV 5A2S HIS B 1038 UNP P56524 EXPRESSION TAG SEQADV 5A2S HIS B 1039 UNP P56524 EXPRESSION TAG SEQADV 5A2S ALA B 728 UNP P56524 LEU 728 ENGINEERED MUTATION SEQRES 1 A 395 MET GLY SER THR LYS PRO ARG PHE THR THR GLY LEU VAL SEQRES 2 A 395 TYR ASP THR LEU MET LEU LYS HIS GLN CYS THR CYS GLY SEQRES 3 A 395 SER SER SER SER HIS PRO GLU HIS ALA GLY ARG ILE GLN SEQRES 4 A 395 SER ILE TRP SER ARG LEU GLN GLU THR GLY LEU ARG GLY SEQRES 5 A 395 LYS CYS GLU CYS ILE ARG GLY ARG LYS ALA THR LEU GLU SEQRES 6 A 395 GLU LEU GLN THR VAL HIS SER GLU ALA HIS THR LEU LEU SEQRES 7 A 395 TYR GLY THR ASN PRO ALA ASN ARG GLN LYS LEU ASP SER SEQRES 8 A 395 LYS LYS LEU LEU GLY SER LEU ALA SER VAL PHE VAL ARG SEQRES 9 A 395 LEU PRO CYS GLY GLY VAL GLY VAL ASP SER ASP THR ILE SEQRES 10 A 395 TRP ASN GLU VAL HIS SER ALA GLY ALA ALA ARG LEU ALA SEQRES 11 A 395 VAL GLY CYS VAL VAL GLU LEU VAL PHE LYS VAL ALA THR SEQRES 12 A 395 GLY GLU LEU LYS ASN GLY PHE ALA VAL VAL ARG PRO PRO SEQRES 13 A 395 GLY HIS HIS ALA GLU GLU SER THR PRO MET GLY PHE CYS SEQRES 14 A 395 TYR PHE ASN SER VAL ALA VAL ALA ALA LYS LEU LEU GLN SEQRES 15 A 395 GLN ARG LEU SER VAL SER LYS ILE LEU ILE VAL ASP TRP SEQRES 16 A 395 ASP VAL HIS HIS GLY ASN GLY THR GLN GLN ALA PHE TYR SEQRES 17 A 395 SER ASP PRO SER VAL LEU TYR MET SER LEU HIS ARG TYR SEQRES 18 A 395 ASP ASP GLY ASN PHE PHE PRO GLY SER GLY ALA PRO ASP SEQRES 19 A 395 GLU VAL GLY THR GLY PRO GLY VAL GLY PHE ASN VAL ASN SEQRES 20 A 395 MET ALA PHE THR GLY GLY LEU ASP PRO PRO MET GLY ASP SEQRES 21 A 395 ALA GLU TYR LEU ALA ALA PHE ARG THR VAL VAL MET PRO SEQRES 22 A 395 ILE ALA SER GLU PHE ALA PRO ASP VAL VAL LEU VAL SER SEQRES 23 A 395 SER GLY PHE ASP ALA VAL GLU GLY HIS PRO THR PRO LEU SEQRES 24 A 395 GLY GLY TYR ASN LEU SER ALA ARG CYS PHE GLY TYR LEU SEQRES 25 A 395 THR LYS GLN LEU MET GLY LEU ALA GLY GLY ARG ILE VAL SEQRES 26 A 395 LEU ALA LEU GLU GLY GLY HIS ASP LEU THR ALA ILE CYS SEQRES 27 A 395 ASP ALA SER GLU ALA CYS VAL SER ALA LEU LEU GLY ASN SEQRES 28 A 395 GLU LEU ASP PRO LEU PRO GLU LYS VAL LEU GLN GLN ARG SEQRES 29 A 395 PRO ASN ALA ASN ALA VAL ARG SER MET GLU LYS VAL MET SEQRES 30 A 395 GLU ILE HIS SER LYS TYR TRP ARG CYS LEU GLN ARG HIS SEQRES 31 A 395 HIS HIS HIS HIS HIS SEQRES 1 B 395 MET GLY SER THR LYS PRO ARG PHE THR THR GLY LEU VAL SEQRES 2 B 395 TYR ASP THR LEU MET LEU LYS HIS GLN CYS THR CYS GLY SEQRES 3 B 395 SER SER SER SER HIS PRO GLU HIS ALA GLY ARG ILE GLN SEQRES 4 B 395 SER ILE TRP SER ARG LEU GLN GLU THR GLY LEU ARG GLY SEQRES 5 B 395 LYS CYS GLU CYS ILE ARG GLY ARG LYS ALA THR LEU GLU SEQRES 6 B 395 GLU LEU GLN THR VAL HIS SER GLU ALA HIS THR LEU LEU SEQRES 7 B 395 TYR GLY THR ASN PRO ALA ASN ARG GLN LYS LEU ASP SER SEQRES 8 B 395 LYS LYS LEU LEU GLY SER LEU ALA SER VAL PHE VAL ARG SEQRES 9 B 395 LEU PRO CYS GLY GLY VAL GLY VAL ASP SER ASP THR ILE SEQRES 10 B 395 TRP ASN GLU VAL HIS SER ALA GLY ALA ALA ARG LEU ALA SEQRES 11 B 395 VAL GLY CYS VAL VAL GLU LEU VAL PHE LYS VAL ALA THR SEQRES 12 B 395 GLY GLU LEU LYS ASN GLY PHE ALA VAL VAL ARG PRO PRO SEQRES 13 B 395 GLY HIS HIS ALA GLU GLU SER THR PRO MET GLY PHE CYS SEQRES 14 B 395 TYR PHE ASN SER VAL ALA VAL ALA ALA LYS LEU LEU GLN SEQRES 15 B 395 GLN ARG LEU SER VAL SER LYS ILE LEU ILE VAL ASP TRP SEQRES 16 B 395 ASP VAL HIS HIS GLY ASN GLY THR GLN GLN ALA PHE TYR SEQRES 17 B 395 SER ASP PRO SER VAL LEU TYR MET SER LEU HIS ARG TYR SEQRES 18 B 395 ASP ASP GLY ASN PHE PHE PRO GLY SER GLY ALA PRO ASP SEQRES 19 B 395 GLU VAL GLY THR GLY PRO GLY VAL GLY PHE ASN VAL ASN SEQRES 20 B 395 MET ALA PHE THR GLY GLY LEU ASP PRO PRO MET GLY ASP SEQRES 21 B 395 ALA GLU TYR LEU ALA ALA PHE ARG THR VAL VAL MET PRO SEQRES 22 B 395 ILE ALA SER GLU PHE ALA PRO ASP VAL VAL LEU VAL SER SEQRES 23 B 395 SER GLY PHE ASP ALA VAL GLU GLY HIS PRO THR PRO LEU SEQRES 24 B 395 GLY GLY TYR ASN LEU SER ALA ARG CYS PHE GLY TYR LEU SEQRES 25 B 395 THR LYS GLN LEU MET GLY LEU ALA GLY GLY ARG ILE VAL SEQRES 26 B 395 LEU ALA LEU GLU GLY GLY HIS ASP LEU THR ALA ILE CYS SEQRES 27 B 395 ASP ALA SER GLU ALA CYS VAL SER ALA LEU LEU GLY ASN SEQRES 28 B 395 GLU LEU ASP PRO LEU PRO GLU LYS VAL LEU GLN GLN ARG SEQRES 29 B 395 PRO ASN ALA ASN ALA VAL ARG SER MET GLU LYS VAL MET SEQRES 30 B 395 GLU ILE HIS SER LYS TYR TRP ARG CYS LEU GLN ARG HIS SEQRES 31 B 395 HIS HIS HIS HIS HIS HET OTF A 1 27 HET ZN A 2 1 HET ZN A 3 1 HET NA A 4 1 HET OTF B 1 27 HET ZN B 2 1 HET ZN B 3 1 HET NA B 4 1 HETNAM OTF (1S,2S,3S)-1-FLUORANYL-2-[4-(5-FLUORANYLPYRIMIDIN-2- HETNAM 2 OTF YL)PHENYL]-N-OXIDANYL-3-PHENYL-CYCLOPROPANE-1- HETNAM 3 OTF CARBOXAMIDE HETNAM ZN ZINC ION HETNAM NA SODIUM ION FORMUL 3 OTF 2(C20 H15 F2 N3 O2) FORMUL 4 ZN 4(ZN 2+) FORMUL 6 NA 2(NA 1+) FORMUL 11 HOH *87(H2 O) HELIX 1 1 ASP A 659 HIS A 665 5 7 HELIX 2 2 SER A 671 HIS A 675 5 5 HELIX 3 3 ALA A 679 THR A 692 1 14 HELIX 4 4 LEU A 694 CYS A 698 5 5 HELIX 5 5 THR A 707 GLN A 712 1 6 HELIX 6 6 SER A 716 THR A 725 1 10 HELIX 7 7 ASN A 726 ASP A 734 1 9 HELIX 8 8 SER A 741 VAL A 745 5 5 HELIX 9 9 HIS A 766 THR A 787 1 22 HELIX 10 10 ASN A 816 SER A 830 1 15 HELIX 11 11 GLY A 844 TYR A 852 1 9 HELIX 12 12 THR A 882 VAL A 886 5 5 HELIX 13 13 GLY A 903 VAL A 914 1 12 HELIX 14 14 VAL A 914 ALA A 923 1 10 HELIX 15 15 ARG A 951 MET A 961 1 11 HELIX 16 16 GLY A 962 GLY A 966 5 5 HELIX 17 17 ASP A 977 LEU A 993 1 17 HELIX 18 18 PRO A 1001 GLN A 1007 1 7 HELIX 19 19 ASN A 1010 HIS A 1024 1 15 HELIX 20 20 SER A 1025 TYR A 1027 5 3 HELIX 21 21 TRP A 1028 GLN A 1032 5 5 HELIX 22 22 ASP B 659 HIS B 665 5 7 HELIX 23 23 ALA B 679 GLU B 691 1 13 HELIX 24 24 LEU B 694 CYS B 698 5 5 HELIX 25 25 THR B 707 GLN B 712 1 6 HELIX 26 26 SER B 716 TYR B 723 1 8 HELIX 27 27 ASN B 726 ASP B 734 1 9 HELIX 28 28 HIS B 766 THR B 787 1 22 HELIX 29 29 ASN B 816 SER B 830 1 15 HELIX 30 30 GLY B 844 TYR B 852 1 9 HELIX 31 31 THR B 882 VAL B 886 5 5 HELIX 32 32 GLY B 903 VAL B 914 1 12 HELIX 33 33 VAL B 914 ALA B 923 1 10 HELIX 34 34 SER B 949 MET B 961 1 13 HELIX 35 35 GLY B 962 GLY B 966 5 5 HELIX 36 36 ASP B 977 LEU B 993 1 17 HELIX 37 37 PRO B 1001 GLN B 1006 1 6 HELIX 38 38 ASN B 1010 SER B 1025 1 16 HELIX 39 39 TRP B 1028 GLN B 1032 5 5 SHEET 1 AA 8 GLU A 699 ILE A 701 0 SHEET 2 AA 8 THR A 654 VAL A 657 1 O THR A 654 N GLU A 699 SHEET 3 AA 8 ASN A 792 ALA A 795 1 O ASN A 792 N GLY A 655 SHEET 4 AA 8 ILE A 968 LEU A 972 1 O ILE A 968 N GLY A 793 SHEET 5 AA 8 VAL A 926 SER A 931 1 O VAL A 927 N VAL A 969 SHEET 6 AA 8 ILE A 834 ASP A 838 1 O LEU A 835 N LEU A 928 SHEET 7 AA 8 VAL A 857 ARG A 864 1 O LEU A 858 N ILE A 836 SHEET 8 AA 8 ASN A 889 PHE A 894 1 O VAL A 890 N SER A 861 SHEET 1 AB 2 VAL A 747 ARG A 748 0 SHEET 2 AB 2 VAL A 754 GLY A 755 -1 O GLY A 755 N VAL A 747 SHEET 1 BA 8 GLU B 699 CYS B 700 0 SHEET 2 BA 8 GLY B 655 VAL B 657 1 N LEU B 656 O GLU B 699 SHEET 3 BA 8 GLY B 793 ALA B 795 1 O PHE B 794 N VAL B 657 SHEET 4 BA 8 ILE B 968 LEU B 972 1 O ILE B 968 N GLY B 793 SHEET 5 BA 8 VAL B 926 SER B 931 1 O VAL B 927 N VAL B 969 SHEET 6 BA 8 ILE B 834 ASP B 838 1 O LEU B 835 N LEU B 928 SHEET 7 BA 8 VAL B 857 ARG B 864 1 O LEU B 858 N ILE B 836 SHEET 8 BA 8 ASN B 889 PHE B 894 1 O VAL B 890 N SER B 861 SHEET 1 BB 2 VAL B 747 ARG B 748 0 SHEET 2 BB 2 VAL B 754 GLY B 755 -1 O GLY B 755 N VAL B 747 LINK O6 OTF A 1 ZN ZN A 2 1555 1555 2.01 LINK O8 OTF A 1 ZN ZN A 2 1555 1555 2.18 LINK O8 OTF B 1 ZN ZN B 2 1555 1555 2.18 LINK O6 OTF B 1 ZN ZN B 2 1555 1555 2.01 CISPEP 1 ARG A 798 PRO A 799 0 1.06 CISPEP 2 PHE A 871 PRO A 872 0 0.37 CISPEP 3 ASP A 899 PRO A 900 0 -0.54 CISPEP 4 THR A 941 PRO A 942 0 1.13 CISPEP 5 ARG B 798 PRO B 799 0 -1.63 CISPEP 6 PHE B 871 PRO B 872 0 4.98 CISPEP 7 ASP B 899 PRO B 900 0 -1.89 CISPEP 8 THR B 941 PRO B 942 0 6.05 SITE 1 AC1 13 ZN A 2 GLU A 677 ARG A 681 GLY A 696 SITE 2 AC1 13 HIS A 802 HIS A 803 GLY A 811 PHE A 812 SITE 3 AC1 13 ASP A 840 HIS A 842 PHE A 871 ASP A 934 SITE 4 AC1 13 GLY A 975 SITE 1 AC2 4 OTF A 1 ASP A 840 HIS A 842 ASP A 934 SITE 1 AC3 4 CYS A 667 CYS A 669 HIS A 675 CYS A 751 SITE 1 AC4 5 ASP A 838 ASP A 840 HIS A 842 SER A 861 SITE 2 AC4 5 LEU A 862 SITE 1 AC5 10 ZN B 2 HIS B 802 HIS B 803 PHE B 812 SITE 2 AC5 10 ASP B 840 HIS B 842 PHE B 871 ASP B 934 SITE 3 AC5 10 GLY B 975 HOH B2001 SITE 1 AC6 4 OTF B 1 ASP B 840 HIS B 842 ASP B 934 SITE 1 AC7 4 CYS B 667 CYS B 669 HIS B 675 CYS B 751 SITE 1 AC8 5 ASP B 838 ASP B 840 HIS B 842 SER B 861 SITE 2 AC8 5 LEU B 862 CRYST1 52.948 82.141 161.626 90.00 90.00 90.00 P 2 21 21 8 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 0.018886 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012174 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006187 0.00000