HEADER HYDROLASE/HYDROLASE INHIBITOR 01-SEP-14 3WYL TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PDE10A COMPLEXED WITH 5- TITLE 2 METHOXY-3-(1-PHENYL-1H-PYRAZOL-5-YL)-1-(3-(TRIFLUOROMETHYL)PHENYL) TITLE 3 PYRIDAZIN-4(1H)-ONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAMP AND CAMP-INHIBITED CGMP 3',5'-CYCLIC PHOSPHODIESTERASE COMPND 3 10A; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: CATALYTIC DOMAIN, UNP RESIDUES 442-779; COMPND 6 EC: 3.1.4.17, 3.1.4.35; COMPND 7 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: PDE10A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2 (DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.OKI,Y.HAYANO REVDAT 4 20-MAR-24 3WYL 1 REMARK LINK REVDAT 3 25-DEC-19 3WYL 1 JRNL REVDAT 2 22-NOV-17 3WYL 1 REMARK REVDAT 1 19-NOV-14 3WYL 0 JRNL AUTH J.KUNITOMO,M.YOSHIKAWA,M.FUSHIMI,A.KAWADA,J.F.QUINN,H.OKI, JRNL AUTH 2 H.KOKUBO,M.KONDO,K.NAKASHIMA,N.KAMIGUCHI,K.SUZUKI,H.KIMURA, JRNL AUTH 3 T.TANIGUCHI JRNL TITL DISCOVERY OF JRNL TITL 2 1-[2-FLUORO-4-(1H-PYRAZOL-1-YL) JRNL TITL 3 PHENYL]-5-METHOXY-3-(1-PHENYL-1H-PYRAZOL-5-YL) JRNL TITL 4 PYRIDAZIN-4(1H)-ONE (TAK-063), A HIGHLY POTENT, SELECTIVE, JRNL TITL 5 AND ORALLY ACTIVE PHOSPHODIESTERASE 10A (PDE10A) INHIBITOR. JRNL REF J.MED.CHEM. V. 57 9627 2014 JRNL REFN ISSN 0022-2623 JRNL PMID 25384088 JRNL DOI 10.1021/JM5013648 REMARK 2 REMARK 2 RESOLUTION. 2.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REFMAC_5.8.0049 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) : 2.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 17777 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 911 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) : 2.68 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1123 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.57 REMARK 3 BIN R VALUE (WORKING SET) : 0.2970 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.3950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5097 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 34 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.24000 REMARK 3 B22 (A**2) : -2.25000 REMARK 3 B33 (A**2) : 2.00000 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): 0.000 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.389 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.326 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 34.876 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5289 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4982 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7167 ; 1.146 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11459 ; 0.712 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 626 ; 4.969 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 248 ;37.247 ;24.073 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 929 ;14.539 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;14.860 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 776 ; 0.059 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6014 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1296 ; 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): 2510 ; 1.651 ; 3.918 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2509 ; 1.650 ; 3.917 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3134 ; 2.715 ; 5.875 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 445 A 759 REMARK 3 RESIDUE RANGE : A 1001 A 1003 REMARK 3 ORIGIN FOR THE GROUP (A): 16.3311 2.3635 -12.9199 REMARK 3 T TENSOR REMARK 3 T11: 0.1537 T22: 0.0059 REMARK 3 T33: 0.0307 T12: 0.0045 REMARK 3 T13: -0.0053 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 2.0292 L22: 3.0937 REMARK 3 L33: 2.0707 L12: 0.2325 REMARK 3 L13: -0.1922 L23: 0.0253 REMARK 3 S TENSOR REMARK 3 S11: 0.0017 S12: -0.0103 S13: 0.1545 REMARK 3 S21: 0.0841 S22: -0.0113 S23: -0.2202 REMARK 3 S31: -0.2246 S32: 0.0921 S33: 0.0096 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 447 B 759 REMARK 3 RESIDUE RANGE : B 1001 B 1003 REMARK 3 ORIGIN FOR THE GROUP (A): 7.0827 -34.4187 -26.4038 REMARK 3 T TENSOR REMARK 3 T11: 0.2289 T22: 0.0175 REMARK 3 T33: 0.0254 T12: -0.0013 REMARK 3 T13: 0.0156 T23: -0.0154 REMARK 3 L TENSOR REMARK 3 L11: 2.0798 L22: 3.1290 REMARK 3 L33: 2.4575 L12: -0.2346 REMARK 3 L13: 0.0693 L23: -0.4510 REMARK 3 S TENSOR REMARK 3 S11: -0.0231 S12: -0.0290 S13: -0.0841 REMARK 3 S21: -0.0670 S22: -0.0803 S23: -0.0318 REMARK 3 S31: 0.2061 S32: -0.0708 S33: 0.1034 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 : WITH TLS ADDED REMARK 4 REMARK 4 3WYL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000096955. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.52 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18737 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.680 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 (%) : 97.7 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.81800 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 27.4% PEG3350, PH 7.52, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 24.94050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.07800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.91650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 81.07800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.94050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.91650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 THR A 442 REMARK 465 SER A 443 REMARK 465 GLU A 444 REMARK 465 GLU A 760 REMARK 465 THR A 761 REMARK 465 ALA A 762 REMARK 465 THR A 763 REMARK 465 TRP A 764 REMARK 465 ILE A 765 REMARK 465 SER A 766 REMARK 465 SER A 767 REMARK 465 PRO A 768 REMARK 465 SER A 769 REMARK 465 VAL A 770 REMARK 465 ALA A 771 REMARK 465 GLN A 772 REMARK 465 LYS A 773 REMARK 465 ALA A 774 REMARK 465 ALA A 775 REMARK 465 ALA A 776 REMARK 465 SER A 777 REMARK 465 GLU A 778 REMARK 465 ASP A 779 REMARK 465 THR B 442 REMARK 465 SER B 443 REMARK 465 GLU B 444 REMARK 465 GLU B 445 REMARK 465 TRP B 446 REMARK 465 GLU B 760 REMARK 465 THR B 761 REMARK 465 ALA B 762 REMARK 465 THR B 763 REMARK 465 TRP B 764 REMARK 465 ILE B 765 REMARK 465 SER B 766 REMARK 465 SER B 767 REMARK 465 PRO B 768 REMARK 465 SER B 769 REMARK 465 VAL B 770 REMARK 465 ALA B 771 REMARK 465 GLN B 772 REMARK 465 LYS B 773 REMARK 465 ALA B 774 REMARK 465 ALA B 775 REMARK 465 ALA B 776 REMARK 465 SER B 777 REMARK 465 GLU B 778 REMARK 465 ASP B 779 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 CYS A 488 -50.01 -131.98 REMARK 500 ARG A 511 43.50 -75.67 REMARK 500 TYR A 514 -47.68 -131.62 REMARK 500 PHE A 568 36.46 -94.46 REMARK 500 SER A 579 60.73 38.76 REMARK 500 LYS A 708 44.47 -108.72 REMARK 500 VAL A 723 -57.73 -120.46 REMARK 500 PHE B 472 53.65 -111.65 REMARK 500 CYS B 492 -62.12 -12.09 REMARK 500 VAL B 723 -66.33 -126.32 REMARK 500 ILE B 756 31.62 -94.17 REMARK 500 ARG B 757 13.38 -140.44 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 A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 519 NE2 REMARK 620 2 HIS A 553 NE2 90.3 REMARK 620 3 ASP A 554 OD2 89.0 83.2 REMARK 620 4 ASP A 664 OD1 91.7 90.5 173.7 REMARK 620 5 HOH A1107 O 172.3 96.7 88.5 91.6 REMARK 620 6 HOH A1116 O 78.5 168.5 99.1 87.2 94.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 554 OD1 REMARK 620 2 HOH A1102 O 110.7 REMARK 620 3 HOH A1103 O 86.2 162.9 REMARK 620 4 HOH A1106 O 88.0 92.5 91.1 REMARK 620 5 HOH A1107 O 96.5 84.1 91.2 175.1 REMARK 620 6 HOH A1108 O 165.6 81.9 81.0 98.7 77.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 519 NE2 REMARK 620 2 HIS B 553 NE2 91.4 REMARK 620 3 ASP B 554 OD2 76.6 90.5 REMARK 620 4 ASP B 664 OD1 89.5 92.0 165.9 REMARK 620 5 HOH B1104 O 86.7 163.2 105.3 71.3 REMARK 620 6 HOH B1112 O 149.0 114.6 86.2 105.3 73.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 554 OD1 REMARK 620 2 HOH B1103 O 149.9 REMARK 620 3 HOH B1105 O 72.3 78.7 REMARK 620 4 HOH B1110 O 79.8 103.2 80.0 REMARK 620 5 HOH B1111 O 82.5 87.8 86.3 160.3 REMARK 620 6 HOH B1112 O 80.3 129.8 149.3 81.9 103.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3KB A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3KB B 1003 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WYK RELATED DB: PDB REMARK 900 RELATED ID: 3WYM RELATED DB: PDB DBREF 3WYL A 442 779 UNP Q9Y233 PDE10_HUMAN 442 779 DBREF 3WYL B 442 779 UNP Q9Y233 PDE10_HUMAN 442 779 SEQRES 1 A 338 THR SER GLU GLU TRP GLN GLY LEU MET GLN PHE THR LEU SEQRES 2 A 338 PRO VAL ARG LEU CYS LYS GLU ILE GLU LEU PHE HIS PHE SEQRES 3 A 338 ASP ILE GLY PRO PHE GLU ASN MET TRP PRO GLY ILE PHE SEQRES 4 A 338 VAL TYR MET VAL HIS ARG SER CYS GLY THR SER CYS PHE SEQRES 5 A 338 GLU LEU GLU LYS LEU CYS ARG PHE ILE MET SER VAL LYS SEQRES 6 A 338 LYS ASN TYR ARG ARG VAL PRO TYR HIS ASN TRP LYS HIS SEQRES 7 A 338 ALA VAL THR VAL ALA HIS CYS MET TYR ALA ILE LEU GLN SEQRES 8 A 338 ASN ASN HIS THR LEU PHE THR ASP LEU GLU ARG LYS GLY SEQRES 9 A 338 LEU LEU ILE ALA CYS LEU CYS HIS ASP LEU ASP HIS ARG SEQRES 10 A 338 GLY PHE SER ASN SER TYR LEU GLN LYS PHE ASP HIS PRO SEQRES 11 A 338 LEU ALA ALA LEU TYR SER THR SER THR MET GLU GLN HIS SEQRES 12 A 338 HIS PHE SER GLN THR VAL SER ILE LEU GLN LEU GLU GLY SEQRES 13 A 338 HIS ASN ILE PHE SER THR LEU SER SER SER GLU TYR GLU SEQRES 14 A 338 GLN VAL LEU GLU ILE ILE ARG LYS ALA ILE ILE ALA THR SEQRES 15 A 338 ASP LEU ALA LEU TYR PHE GLY ASN ARG LYS GLN LEU GLU SEQRES 16 A 338 GLU MET TYR GLN THR GLY SER LEU ASN LEU ASN ASN GLN SEQRES 17 A 338 SER HIS ARG ASP ARG VAL ILE GLY LEU MET MET THR ALA SEQRES 18 A 338 CYS ASP LEU CYS SER VAL THR LYS LEU TRP PRO VAL THR SEQRES 19 A 338 LYS LEU THR ALA ASN ASP ILE TYR ALA GLU PHE TRP ALA SEQRES 20 A 338 GLU GLY ASP GLU MET LYS LYS LEU GLY ILE GLN PRO ILE SEQRES 21 A 338 PRO MET MET ASP ARG ASP LYS LYS ASP GLU VAL PRO GLN SEQRES 22 A 338 GLY GLN LEU GLY PHE TYR ASN ALA VAL ALA ILE PRO CYS SEQRES 23 A 338 TYR THR THR LEU THR GLN ILE LEU PRO PRO THR GLU PRO SEQRES 24 A 338 LEU LEU LYS ALA CYS ARG ASP ASN LEU SER GLN TRP GLU SEQRES 25 A 338 LYS VAL ILE ARG GLY GLU GLU THR ALA THR TRP ILE SER SEQRES 26 A 338 SER PRO SER VAL ALA GLN LYS ALA ALA ALA SER GLU ASP SEQRES 1 B 338 THR SER GLU GLU TRP GLN GLY LEU MET GLN PHE THR LEU SEQRES 2 B 338 PRO VAL ARG LEU CYS LYS GLU ILE GLU LEU PHE HIS PHE SEQRES 3 B 338 ASP ILE GLY PRO PHE GLU ASN MET TRP PRO GLY ILE PHE SEQRES 4 B 338 VAL TYR MET VAL HIS ARG SER CYS GLY THR SER CYS PHE SEQRES 5 B 338 GLU LEU GLU LYS LEU CYS ARG PHE ILE MET SER VAL LYS SEQRES 6 B 338 LYS ASN TYR ARG ARG VAL PRO TYR HIS ASN TRP LYS HIS SEQRES 7 B 338 ALA VAL THR VAL ALA HIS CYS MET TYR ALA ILE LEU GLN SEQRES 8 B 338 ASN ASN HIS THR LEU PHE THR ASP LEU GLU ARG LYS GLY SEQRES 9 B 338 LEU LEU ILE ALA CYS LEU CYS HIS ASP LEU ASP HIS ARG SEQRES 10 B 338 GLY PHE SER ASN SER TYR LEU GLN LYS PHE ASP HIS PRO SEQRES 11 B 338 LEU ALA ALA LEU TYR SER THR SER THR MET GLU GLN HIS SEQRES 12 B 338 HIS PHE SER GLN THR VAL SER ILE LEU GLN LEU GLU GLY SEQRES 13 B 338 HIS ASN ILE PHE SER THR LEU SER SER SER GLU TYR GLU SEQRES 14 B 338 GLN VAL LEU GLU ILE ILE ARG LYS ALA ILE ILE ALA THR SEQRES 15 B 338 ASP LEU ALA LEU TYR PHE GLY ASN ARG LYS GLN LEU GLU SEQRES 16 B 338 GLU MET TYR GLN THR GLY SER LEU ASN LEU ASN ASN GLN SEQRES 17 B 338 SER HIS ARG ASP ARG VAL ILE GLY LEU MET MET THR ALA SEQRES 18 B 338 CYS ASP LEU CYS SER VAL THR LYS LEU TRP PRO VAL THR SEQRES 19 B 338 LYS LEU THR ALA ASN ASP ILE TYR ALA GLU PHE TRP ALA SEQRES 20 B 338 GLU GLY ASP GLU MET LYS LYS LEU GLY ILE GLN PRO ILE SEQRES 21 B 338 PRO MET MET ASP ARG ASP LYS LYS ASP GLU VAL PRO GLN SEQRES 22 B 338 GLY GLN LEU GLY PHE TYR ASN ALA VAL ALA ILE PRO CYS SEQRES 23 B 338 TYR THR THR LEU THR GLN ILE LEU PRO PRO THR GLU PRO SEQRES 24 B 338 LEU LEU LYS ALA CYS ARG ASP ASN LEU SER GLN TRP GLU SEQRES 25 B 338 LYS VAL ILE ARG GLY GLU GLU THR ALA THR TRP ILE SER SEQRES 26 B 338 SER PRO SER VAL ALA GLN LYS ALA ALA ALA SER GLU ASP HET ZN A1001 1 HET MG A1002 1 HET 3KB A1003 30 HET ZN B1001 1 HET MG B1002 1 HET 3KB B1003 30 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM 3KB 5-METHOXY-3-(1-PHENYL-1H-PYRAZOL-5-YL)-1-[3- HETNAM 2 3KB (TRIFLUOROMETHYL)PHENYL]PYRIDAZIN-4(1H)-ONE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 3KB 2(C21 H15 F3 N4 O2) FORMUL 9 HOH *34(H2 O) HELIX 1 1 GLU A 445 GLN A 451 1 7 HELIX 2 2 PRO A 455 CYS A 459 5 5 HELIX 3 3 PHE A 472 ASN A 474 5 3 HELIX 4 4 MET A 475 CYS A 488 1 14 HELIX 5 5 GLU A 494 ASN A 508 1 15 HELIX 6 6 ASN A 516 ASN A 533 1 18 HELIX 7 7 THR A 539 HIS A 553 1 15 HELIX 8 8 SER A 561 PHE A 568 1 8 HELIX 9 9 HIS A 570 TYR A 576 1 7 HELIX 10 10 SER A 579 GLN A 594 1 16 HELIX 11 11 SER A 605 THR A 623 1 19 HELIX 12 12 ASP A 624 THR A 641 1 18 HELIX 13 13 ASN A 648 LEU A 665 1 18 HELIX 14 14 CYS A 666 LYS A 670 5 5 HELIX 15 15 LEU A 671 LYS A 695 1 25 HELIX 16 16 ILE A 701 ASP A 710 5 10 HELIX 17 17 GLU A 711 VAL A 723 1 13 HELIX 18 18 VAL A 723 LEU A 735 1 13 HELIX 19 19 THR A 738 ARG A 757 1 20 HELIX 20 20 GLY B 448 PHE B 452 1 5 HELIX 21 21 PRO B 455 GLU B 463 1 9 HELIX 22 22 ILE B 469 ASN B 474 5 6 HELIX 23 23 MET B 475 GLY B 489 1 15 HELIX 24 24 GLU B 494 ASN B 508 1 15 HELIX 25 25 ASN B 516 ASN B 534 1 19 HELIX 26 26 HIS B 535 PHE B 538 5 4 HELIX 27 27 THR B 539 HIS B 553 1 15 HELIX 28 28 SER B 561 PHE B 568 1 8 HELIX 29 29 HIS B 570 TYR B 576 1 7 HELIX 30 30 SER B 579 GLN B 594 1 16 HELIX 31 31 SER B 605 ALA B 622 1 18 HELIX 32 32 ASP B 624 THR B 641 1 18 HELIX 33 33 ASN B 648 LEU B 665 1 18 HELIX 34 34 CYS B 666 LYS B 670 5 5 HELIX 35 35 LEU B 671 LEU B 696 1 26 HELIX 36 36 ILE B 701 ASP B 705 5 5 HELIX 37 37 LYS B 708 ASP B 710 5 3 HELIX 38 38 GLU B 711 VAL B 723 1 13 HELIX 39 39 VAL B 723 LEU B 735 1 13 HELIX 40 40 THR B 738 ILE B 756 1 19 LINK NE2 HIS A 519 ZN ZN A1001 1555 1555 2.42 LINK NE2 HIS A 553 ZN ZN A1001 1555 1555 2.12 LINK OD2 ASP A 554 ZN ZN A1001 1555 1555 2.11 LINK OD1 ASP A 554 MG MG A1002 1555 1555 1.90 LINK OD1 ASP A 664 ZN ZN A1001 1555 1555 2.23 LINK ZN ZN A1001 O HOH A1107 1555 1555 2.16 LINK ZN ZN A1001 O HOH A1116 1555 1555 2.03 LINK MG MG A1002 O HOH A1102 1555 1555 1.95 LINK MG MG A1002 O HOH A1103 1555 1555 2.15 LINK MG MG A1002 O HOH A1106 1555 1555 2.03 LINK MG MG A1002 O HOH A1107 1555 1555 2.02 LINK MG MG A1002 O HOH A1108 1555 1555 2.04 LINK NE2 HIS B 519 ZN ZN B1001 1555 1555 2.35 LINK NE2 HIS B 553 ZN ZN B1001 1555 1555 2.14 LINK OD2 ASP B 554 ZN ZN B1001 1555 1555 2.16 LINK OD1 ASP B 554 MG MG B1002 1555 1555 2.39 LINK OD1 ASP B 664 ZN ZN B1001 1555 1555 2.28 LINK ZN ZN B1001 O HOH B1104 1555 1555 2.50 LINK ZN ZN B1001 O HOH B1112 1555 1555 2.04 LINK MG MG B1002 O HOH B1103 1555 1555 1.98 LINK MG MG B1002 O HOH B1105 1555 1555 2.10 LINK MG MG B1002 O HOH B1110 1555 1555 2.32 LINK MG MG B1002 O HOH B1111 1555 1555 2.24 LINK MG MG B1002 O HOH B1112 1555 1555 1.78 SITE 1 AC1 7 HIS A 519 HIS A 553 ASP A 554 ASP A 664 SITE 2 AC1 7 MG A1002 HOH A1107 HOH A1116 SITE 1 AC2 8 ASP A 554 GLU A 582 ZN A1001 HOH A1102 SITE 2 AC2 8 HOH A1103 HOH A1106 HOH A1107 HOH A1108 SITE 1 AC3 7 LEU A 625 LEU A 665 TYR A 683 PHE A 686 SITE 2 AC3 7 GLN A 716 PHE A 719 HOH A1109 SITE 1 AC4 7 HIS B 519 HIS B 553 ASP B 554 ASP B 664 SITE 2 AC4 7 MG B1002 HOH B1104 HOH B1112 SITE 1 AC5 7 ASP B 554 ZN B1001 HOH B1103 HOH B1105 SITE 2 AC5 7 HOH B1110 HOH B1111 HOH B1112 SITE 1 AC6 8 LEU A 696 GLY A 697 TYR B 514 LEU B 625 SITE 2 AC6 8 SER B 667 TYR B 683 GLN B 716 PHE B 719 CRYST1 49.881 81.833 162.156 90.00 90.00 90.00 P 21 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 0.020048 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012220 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006167 0.00000