HEADER HYDROLASE 18-NOV-22 8BPY TITLE X-RAY STRUCTURE OF PDE9A IN COMPLEX WITH INHIBITOR 13A COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH AFFINITY CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE COMPND 3 9A; COMPND 4 CHAIN: A, B; COMPND 5 EC: 3.1.4.35; 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: PDE9A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PDE9A, INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.STEUBER REVDAT 4 01-MAY-24 8BPY 1 REMARK REVDAT 3 11-JAN-23 8BPY 1 CAVEAT COMPND HETNAM FORMUL REVDAT 2 04-JAN-23 8BPY 1 JRNL REVDAT 1 28-DEC-22 8BPY 0 JRNL AUTH D.MEIBOM,S.MICUS,A.L.ANDREEVSKI,S.ANLAUF,P.BOGNER, JRNL AUTH 2 C.J.VON BUEHLER,A.P.DIESKAU,J.DREHER,F.EITNER,D.FLIEGNER, JRNL AUTH 3 M.FOLLMANN,K.M.GERICKE,S.MAASSEN,J.MEYER,K.H.SCHLEMMER, JRNL AUTH 4 H.STEUBER,A.TERSTEEGEN,F.WUNDER JRNL TITL BAY-7081: A POTENT, SELECTIVE, AND ORALLY BIOAVAILABLE JRNL TITL 2 CYANOPYRIDONE-BASED PDE9A INHIBITOR. JRNL REF J.MED.CHEM. V. 65 16420 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 36475653 JRNL DOI 10.1021/ACS.JMEDCHEM.2C01267 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0123 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) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 21832 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) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.312 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1149 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.38 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1557 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.4040 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.4660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5160 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 131.9 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.01000 REMARK 3 B22 (A**2) : 4.01000 REMARK 3 B33 (A**2) : -8.01000 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): 1.839 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.511 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.525 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 35.017 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5331 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4978 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7232 ; 1.563 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11431 ; 1.019 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 628 ; 7.051 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 264 ;35.885 ;24.242 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 932 ;16.146 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;14.198 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 786 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5948 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1235 ; 0.002 ; 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): 2518 ; 9.763 ;13.141 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2517 ; 9.765 ;13.138 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3143 ;15.420 ;19.660 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3144 ;15.417 ;19.664 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2813 ; 8.043 ;13.481 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2814 ; 8.042 ;13.479 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4087 ;13.002 ;20.073 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 REMARK 4 REMARK 4 8BPY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126854. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-15 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918409 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22982 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.49 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: INHOUSE STRUCTURE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PP 5/4, 0.2 M KCL, 50 MM HEPES PH REMARK 280 7.25, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 111.21150 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 111.21150 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 60.12850 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 111.21150 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 111.21150 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 60.12850 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 111.21150 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 111.21150 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 60.12850 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 111.21150 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 111.21150 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 60.12850 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 111.21150 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 111.21150 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 60.12850 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 111.21150 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 111.21150 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 60.12850 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 111.21150 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 111.21150 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 60.12850 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 111.21150 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 111.21150 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 60.12850 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 350 CG CD CE NZ REMARK 470 GLN A 354 CG CD OE1 NE2 REMARK 470 GLU A 411 CG CD OE1 OE2 REMARK 470 LYS A 501 CG CD CE NZ REMARK 470 LYS B 350 CG CD CE NZ REMARK 470 GLN B 354 CG CD OE1 NE2 REMARK 470 GLU B 411 CG CD OE1 OE2 REMARK 470 LYS B 501 CG CD CE NZ 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 OD1 ASP B 293 MG MG B 2002 1.36 REMARK 500 OD1 ASP B 402 ZN ZN B 2001 1.36 REMARK 500 OD2 ASP B 293 ZN ZN B 2001 1.54 REMARK 500 NE2 HIS B 292 ZN ZN B 2001 1.68 REMARK 500 OD1 ASP A 293 ZN ZN A 2001 1.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP B 402 CB ASP B 402 CG 0.127 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 187 CB - CG - CD1 ANGL. DEV. = -15.0 DEGREES REMARK 500 ARG A 353 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP B 402 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES 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 THR A 200 -76.46 -57.65 REMARK 500 PHE A 201 113.53 12.13 REMARK 500 SER A 229 57.18 33.59 REMARK 500 ASN A 248 59.14 -93.18 REMARK 500 ASN A 300 -173.57 -63.88 REMARK 500 ILE A 305 -70.85 -64.60 REMARK 500 ASP A 317 9.43 48.97 REMARK 500 SER A 319 68.45 22.38 REMARK 500 ASP A 402 -7.76 -53.11 REMARK 500 ILE A 403 42.64 -156.00 REMARK 500 ASN A 405 -61.59 -21.27 REMARK 500 PRO A 437 150.79 -44.00 REMARK 500 PRO B 190 17.85 -69.04 REMARK 500 PHE B 201 116.74 -14.86 REMARK 500 ASP B 227 -71.37 -71.50 REMARK 500 ASN B 245 33.87 -99.43 REMARK 500 PHE B 251 -65.83 -126.81 REMARK 500 SER B 319 68.37 24.72 REMARK 500 ASN B 339 88.84 -67.19 REMARK 500 ARG B 353 -77.95 -67.50 REMARK 500 GLN B 354 5.50 -61.72 REMARK 500 ILE B 357 -76.99 -53.19 REMARK 500 MET B 410 0.59 -65.80 REMARK 500 LYS B 449 -58.16 -22.01 REMARK 500 VAL B 460 -62.76 -125.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 447 THR A 448 149.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 LIGAND ISOPROPYL GROUP NOT FULLY DEFINED BY REMARK 600 ELECTRON DENSITY. NO LIGAND BOUND TO CHAIN B. REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 ZN A 2001 REMARK 615 MG A 2002 REMARK 615 NA A 2003 REMARK 615 ZN B 2001 REMARK 615 MG B 2002 REMARK 615 NA B 2003 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 NA A2003 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 244 O REMARK 620 2 TYR A 246 O 86.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 256 NE2 REMARK 620 2 HIS A 292 NE2 131.5 REMARK 620 3 ASP A 402 OD2 108.5 72.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A2002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 293 OD1 REMARK 620 2 ASP A 293 OD2 51.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B2003 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 244 O REMARK 620 2 TYR B 246 O 99.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B2001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 256 NE2 REMARK 620 2 ASP B 402 OD2 143.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B2002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 293 OD2 REMARK 620 2 THR B 363 OG1 106.3 REMARK 620 N 1 DBREF 8BPY A 187 501 UNP O76083 PDE9A_HUMAN 247 561 DBREF 8BPY B 187 501 UNP O76083 PDE9A_HUMAN 247 561 SEQRES 1 A 315 LEU LEU SER PRO GLU THR ILE GLU ALA LEU ARG LYS PRO SEQRES 2 A 315 THR PHE ASP VAL TRP LEU TRP GLU PRO ASN GLU MET LEU SEQRES 3 A 315 SER CYS LEU GLU HIS MET TYR HIS ASP LEU GLY LEU VAL SEQRES 4 A 315 ARG ASP PHE SER ILE ASN PRO VAL THR LEU ARG ARG TRP SEQRES 5 A 315 LEU PHE CYS VAL HIS ASP ASN TYR ARG ASN ASN PRO PHE SEQRES 6 A 315 HIS ASN PHE ARG HIS CYS PHE CYS VAL ALA GLN MET MET SEQRES 7 A 315 TYR SER MET VAL TRP LEU CYS SER LEU GLN GLU LYS PHE SEQRES 8 A 315 SER GLN THR ASP ILE LEU ILE LEU MET THR ALA ALA ILE SEQRES 9 A 315 CYS HIS ASP LEU ASP HIS PRO GLY TYR ASN ASN THR TYR SEQRES 10 A 315 GLN ILE ASN ALA ARG THR GLU LEU ALA VAL ARG TYR ASN SEQRES 11 A 315 ASP ILE SER PRO LEU GLU ASN HIS HIS CYS ALA VAL ALA SEQRES 12 A 315 PHE GLN ILE LEU ALA GLU PRO GLU CYS ASN ILE PHE SER SEQRES 13 A 315 ASN ILE PRO PRO ASP GLY PHE LYS GLN ILE ARG GLN GLY SEQRES 14 A 315 MET ILE THR LEU ILE LEU ALA THR ASP MET ALA ARG HIS SEQRES 15 A 315 ALA GLU ILE MET ASP SER PHE LYS GLU LYS MET GLU ASN SEQRES 16 A 315 PHE ASP TYR SER ASN GLU GLU HIS MET THR LEU LEU LYS SEQRES 17 A 315 MET ILE LEU ILE LYS CYS CYS ASP ILE SER ASN GLU VAL SEQRES 18 A 315 ARG PRO MET GLU VAL ALA GLU PRO TRP VAL ASP CYS LEU SEQRES 19 A 315 LEU GLU GLU TYR PHE MET GLN SER ASP ARG GLU LYS SER SEQRES 20 A 315 GLU GLY LEU PRO VAL ALA PRO PHE MET ASP ARG ASP LYS SEQRES 21 A 315 VAL THR LYS ALA THR ALA GLN ILE GLY PHE ILE LYS PHE SEQRES 22 A 315 VAL LEU ILE PRO MET PHE GLU THR VAL THR LYS LEU PHE SEQRES 23 A 315 PRO MET VAL GLU GLU ILE MET LEU GLN PRO LEU TRP GLU SEQRES 24 A 315 SER ARG ASP ARG TYR GLU GLU LEU LYS ARG ILE ASP ASP SEQRES 25 A 315 ALA MET LYS SEQRES 1 B 315 LEU LEU SER PRO GLU THR ILE GLU ALA LEU ARG LYS PRO SEQRES 2 B 315 THR PHE ASP VAL TRP LEU TRP GLU PRO ASN GLU MET LEU SEQRES 3 B 315 SER CYS LEU GLU HIS MET TYR HIS ASP LEU GLY LEU VAL SEQRES 4 B 315 ARG ASP PHE SER ILE ASN PRO VAL THR LEU ARG ARG TRP SEQRES 5 B 315 LEU PHE CYS VAL HIS ASP ASN TYR ARG ASN ASN PRO PHE SEQRES 6 B 315 HIS ASN PHE ARG HIS CYS PHE CYS VAL ALA GLN MET MET SEQRES 7 B 315 TYR SER MET VAL TRP LEU CYS SER LEU GLN GLU LYS PHE SEQRES 8 B 315 SER GLN THR ASP ILE LEU ILE LEU MET THR ALA ALA ILE SEQRES 9 B 315 CYS HIS ASP LEU ASP HIS PRO GLY TYR ASN ASN THR TYR SEQRES 10 B 315 GLN ILE ASN ALA ARG THR GLU LEU ALA VAL ARG TYR ASN SEQRES 11 B 315 ASP ILE SER PRO LEU GLU ASN HIS HIS CYS ALA VAL ALA SEQRES 12 B 315 PHE GLN ILE LEU ALA GLU PRO GLU CYS ASN ILE PHE SER SEQRES 13 B 315 ASN ILE PRO PRO ASP GLY PHE LYS GLN ILE ARG GLN GLY SEQRES 14 B 315 MET ILE THR LEU ILE LEU ALA THR ASP MET ALA ARG HIS SEQRES 15 B 315 ALA GLU ILE MET ASP SER PHE LYS GLU LYS MET GLU ASN SEQRES 16 B 315 PHE ASP TYR SER ASN GLU GLU HIS MET THR LEU LEU LYS SEQRES 17 B 315 MET ILE LEU ILE LYS CYS CYS ASP ILE SER ASN GLU VAL SEQRES 18 B 315 ARG PRO MET GLU VAL ALA GLU PRO TRP VAL ASP CYS LEU SEQRES 19 B 315 LEU GLU GLU TYR PHE MET GLN SER ASP ARG GLU LYS SER SEQRES 20 B 315 GLU GLY LEU PRO VAL ALA PRO PHE MET ASP ARG ASP LYS SEQRES 21 B 315 VAL THR LYS ALA THR ALA GLN ILE GLY PHE ILE LYS PHE SEQRES 22 B 315 VAL LEU ILE PRO MET PHE GLU THR VAL THR LYS LEU PHE SEQRES 23 B 315 PRO MET VAL GLU GLU ILE MET LEU GLN PRO LEU TRP GLU SEQRES 24 B 315 SER ARG ASP ARG TYR GLU GLU LEU LYS ARG ILE ASP ASP SEQRES 25 B 315 ALA MET LYS HET ZN A2001 1 HET MG A2002 1 HET NA A2003 1 HET R4I A2004 35 HET ZN B2001 1 HET MG B2002 1 HET NA B2003 1 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM R4I (8~{S})-6-[2-(2,3-DIHYDROINDOL-1-YL)-2-OXIDANYLIDENE- HETNAM 2 R4I ETHYL]-4-(4-METHYLPHENYL)-2-OXIDANYLIDENE-8-PROPYL-1, HETNAM 3 R4I 5,7,8-TETRAHYDRO-1,6-NAPHTHYRIDINE-3-CARBONITRILE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 NA 2(NA 1+) FORMUL 6 R4I C29 H30 N4 O2 HELIX 1 AA1 SER A 189 LEU A 196 1 8 HELIX 2 AA2 ASP A 202 TRP A 206 5 5 HELIX 3 AA3 GLU A 207 LEU A 222 1 16 HELIX 4 AA4 GLY A 223 PHE A 228 1 6 HELIX 5 AA5 ASN A 231 TYR A 246 1 16 HELIX 6 AA6 ASN A 253 CYS A 271 1 19 HELIX 7 AA7 SER A 272 PHE A 277 1 6 HELIX 8 AA8 SER A 278 HIS A 292 1 15 HELIX 9 AA9 ASN A 300 ALA A 307 1 8 HELIX 10 AB1 THR A 309 TYR A 315 1 7 HELIX 11 AB2 SER A 319 GLU A 335 1 17 HELIX 12 AB3 PRO A 336 ASN A 339 5 4 HELIX 13 AB4 PRO A 345 ALA A 362 1 18 HELIX 14 AB5 ARG A 367 GLU A 380 1 14 HELIX 15 AB6 ASN A 386 ASP A 402 1 17 HELIX 16 AB7 ILE A 403 ARG A 408 5 6 HELIX 17 AB8 PRO A 409 GLY A 435 1 27 HELIX 18 AB9 ALA A 439 ASP A 443 5 5 HELIX 19 AC1 THR A 448 VAL A 460 1 13 HELIX 20 AC2 VAL A 460 PHE A 472 1 13 HELIX 21 AC3 PRO A 473 LEU A 480 1 8 HELIX 22 AC4 LEU A 480 LYS A 501 1 22 HELIX 23 AC5 GLU B 191 LEU B 196 1 6 HELIX 24 AC6 GLU B 207 LEU B 222 1 16 HELIX 25 AC7 GLY B 223 SER B 229 1 7 HELIX 26 AC8 VAL B 233 ASN B 245 1 13 HELIX 27 AC9 ASN B 253 SER B 272 1 20 HELIX 28 AD1 SER B 272 PHE B 277 1 6 HELIX 29 AD2 SER B 278 HIS B 292 1 15 HELIX 30 AD3 ASN B 300 ALA B 307 1 8 HELIX 31 AD4 THR B 309 ASN B 316 1 8 HELIX 32 AD5 SER B 319 LEU B 333 1 15 HELIX 33 AD6 ASN B 339 ILE B 344 5 6 HELIX 34 AD7 PRO B 345 LEU B 361 1 17 HELIX 35 AD8 ALA B 362 THR B 363 5 2 HELIX 36 AD9 ASP B 364 ALA B 366 5 3 HELIX 37 AE1 ARG B 367 GLU B 380 1 14 HELIX 38 AE2 ASN B 386 ILE B 403 1 18 HELIX 39 AE3 PRO B 415 GLU B 434 1 20 HELIX 40 AE4 ASP B 443 VAL B 447 5 5 HELIX 41 AE5 THR B 448 PHE B 459 1 12 HELIX 42 AE6 VAL B 460 LYS B 470 1 11 HELIX 43 AE7 PRO B 473 MET B 479 1 7 HELIX 44 AE8 MET B 479 LYS B 501 1 23 SSBOND 1 CYS A 241 CYS A 338 1555 1555 2.76 LINK O ASP A 244 NA NA A2003 1555 1555 2.34 LINK O TYR A 246 NA NA A2003 1555 1555 2.70 LINK NE2 HIS A 256 ZN ZN A2001 1555 1555 2.38 LINK NE2 HIS A 292 ZN ZN A2001 1555 1555 1.93 LINK OD1 ASP A 293 MG MG A2002 1555 1555 2.81 LINK OD2 ASP A 293 MG MG A2002 1555 1555 1.98 LINK OD2 ASP A 402 ZN ZN A2001 1555 1555 2.27 LINK O ASP B 244 NA NA B2003 1555 1555 2.06 LINK O TYR B 246 NA NA B2003 1555 1555 2.21 LINK NE2 HIS B 256 ZN ZN B2001 1555 1555 2.00 LINK OD2 ASP B 293 MG MG B2002 1555 1555 2.85 LINK OG1 THR B 363 MG MG B2002 1555 1555 2.72 LINK OD2 ASP B 402 ZN ZN B2001 1555 1555 2.57 CRYST1 222.423 222.423 120.257 90.00 90.00 90.00 I 4 2 2 32 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 0.004496 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004496 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008316 0.00000