HEADER HYDROLASE 15-JUN-18 6A3N TITLE CRYSTAL STRUCTURE OF THE PDE9 CATALYTIC DOMAIN IN COMPLEX WITH TITLE 2 INHIBITOR 2 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 BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS PDE9 INHIBITOR COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.N.WU,Q.ZHOU,Y.P.CHEN,H.B.LUO REVDAT 3 22-NOV-23 6A3N 1 LINK REVDAT 2 08-MAY-19 6A3N 1 JRNL REVDAT 1 10-APR-19 6A3N 0 JRNL AUTH Y.WU,Q.ZHOU,T.ZHANG,Z.LI,Y.P.CHEN,P.ZHANG,Y.F.YU,H.GENG, JRNL AUTH 2 Y.J.TIAN,C.ZHANG,Y.WANG,J.W.CHEN,Y.CHEN,H.B.LUO JRNL TITL DISCOVERY OF POTENT, SELECTIVE, AND ORALLY BIOAVAILABLE JRNL TITL 2 INHIBITORS AGAINST PHOSPHODIESTERASE-9, A NOVEL TARGET FOR JRNL TITL 3 THE TREATMENT OF VASCULAR DEMENTIA. JRNL REF J. MED. CHEM. V. 62 4218 2019 JRNL REFN ISSN 1520-4804 JRNL PMID 30916555 JRNL DOI 10.1021/ACS.JMEDCHEM.8B01041 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 44160 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) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2292 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3225 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.3750 REMARK 3 BIN FREE R VALUE SET COUNT : 155 REMARK 3 BIN FREE R VALUE : 0.3810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5322 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 193 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.01000 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): 0.330 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.263 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.297 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.751 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.882 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.842 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5539 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5194 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7470 ; 1.249 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11992 ; 0.929 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 642 ; 5.818 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 274 ;36.186 ;24.380 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 994 ;15.734 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;12.904 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 804 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6238 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1270 ; 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): 2574 ; 1.236 ; 3.165 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2573 ; 1.224 ; 3.164 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3214 ; 2.151 ; 4.739 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3215 ; 2.151 ; 4.741 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2965 ; 1.495 ; 3.349 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2966 ; 1.495 ; 3.349 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4257 ; 2.129 ; 4.949 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6359 ; 4.124 ;24.847 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6324 ; 4.098 ;24.874 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 : NULL 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 6A3N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1300008105. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OXFORD DIFFRACTION ENHANCE ULTRA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD ONYX CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO 38.41 REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO 38.41 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46482 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 25.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.17300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.55100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.10 REMARK 200 STARTING MODEL: 4QGE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5M NA FORMATE, 0.1M HEPES (PH 7.5), REMARK 280 5% XYLITOL, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 134.53950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 52.05500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.05500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.26975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.05500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.05500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 201.80925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.05500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.05500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.26975 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.05500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.05500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 201.80925 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 134.53950 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 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 O HOH B 702 O HOH B 707 1.93 REMARK 500 O HOH A 702 O HOH A 737 1.94 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 LEU A 187 92.12 71.02 REMARK 500 SER A 319 62.34 28.49 REMARK 500 ASN A 381 83.32 -156.08 REMARK 500 LEU B 187 114.19 77.27 REMARK 500 SER B 229 38.12 38.59 REMARK 500 ASN B 248 46.59 -83.74 REMARK 500 SER B 319 55.69 30.42 REMARK 500 ASN B 381 84.48 -151.79 REMARK 500 VAL B 460 -64.60 -124.14 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 B 795 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH B 796 DISTANCE = 7.49 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 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 256 NE2 REMARK 620 2 HIS A 292 NE2 102.8 REMARK 620 3 ASP A 293 OD2 94.9 77.9 REMARK 620 4 ASP A 402 OD1 101.0 85.7 159.4 REMARK 620 5 HOH A 701 O 161.3 90.3 74.7 93.2 REMARK 620 6 HOH A 703 O 94.0 158.9 113.5 78.6 76.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 293 OD1 REMARK 620 2 HOH A 701 O 80.7 REMARK 620 3 HOH A 702 O 69.8 75.4 REMARK 620 4 HOH A 707 O 87.0 152.8 77.7 REMARK 620 5 HOH A 737 O 119.8 70.1 52.6 95.9 REMARK 620 6 HOH A 772 O 123.8 118.6 160.3 88.3 116.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 256 NE2 REMARK 620 2 HIS B 292 NE2 102.8 REMARK 620 3 ASP B 293 OD2 93.9 82.7 REMARK 620 4 ASP B 402 OD1 100.3 86.1 163.6 REMARK 620 5 HOH B 702 O 156.1 97.7 76.5 93.2 REMARK 620 6 HOH B 707 O 104.2 152.5 100.9 83.7 57.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 293 OD1 REMARK 620 2 HOH B 701 O 68.7 REMARK 620 3 HOH B 702 O 82.9 82.5 REMARK 620 4 HOH B 705 O 79.2 76.6 156.3 REMARK 620 5 HOH B 733 O 143.3 75.6 84.4 100.8 REMARK 620 6 HOH B 738 O 114.6 168.1 109.1 92.6 102.0 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 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9Q9 A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9Q9 B 603 DBREF 6A3N A 185 506 UNP O76083 PDE9A_HUMAN 245 566 DBREF 6A3N B 185 506 UNP O76083 PDE9A_HUMAN 245 566 SEQRES 1 A 322 LYS TYR LEU LEU SER PRO GLU THR ILE GLU ALA LEU ARG SEQRES 2 A 322 LYS PRO THR PHE ASP VAL TRP LEU TRP GLU PRO ASN GLU SEQRES 3 A 322 MET LEU SER CYS LEU GLU HIS MET TYR HIS ASP LEU GLY SEQRES 4 A 322 LEU VAL ARG ASP PHE SER ILE ASN PRO VAL THR LEU ARG SEQRES 5 A 322 ARG TRP LEU PHE CYS VAL HIS ASP ASN TYR ARG ASN ASN SEQRES 6 A 322 PRO PHE HIS ASN PHE ARG HIS CYS PHE CYS VAL ALA GLN SEQRES 7 A 322 MET MET TYR SER MET VAL TRP LEU CYS SER LEU GLN GLU SEQRES 8 A 322 LYS PHE SER GLN THR ASP ILE LEU ILE LEU MET THR ALA SEQRES 9 A 322 ALA ILE CYS HIS ASP LEU ASP HIS PRO GLY TYR ASN ASN SEQRES 10 A 322 THR TYR GLN ILE ASN ALA ARG THR GLU LEU ALA VAL ARG SEQRES 11 A 322 TYR ASN ASP ILE SER PRO LEU GLU ASN HIS HIS CYS ALA SEQRES 12 A 322 VAL ALA PHE GLN ILE LEU ALA GLU PRO GLU CYS ASN ILE SEQRES 13 A 322 PHE SER ASN ILE PRO PRO ASP GLY PHE LYS GLN ILE ARG SEQRES 14 A 322 GLN GLY MET ILE THR LEU ILE LEU ALA THR ASP MET ALA SEQRES 15 A 322 ARG HIS ALA GLU ILE MET ASP SER PHE LYS GLU LYS MET SEQRES 16 A 322 GLU ASN PHE ASP TYR SER ASN GLU GLU HIS MET THR LEU SEQRES 17 A 322 LEU LYS MET ILE LEU ILE LYS CYS CYS ASP ILE SER ASN SEQRES 18 A 322 GLU VAL ARG PRO MET GLU VAL ALA GLU PRO TRP VAL ASP SEQRES 19 A 322 CYS LEU LEU GLU GLU TYR PHE MET GLN SER ASP ARG GLU SEQRES 20 A 322 LYS SER GLU GLY LEU PRO VAL ALA PRO PHE MET ASP ARG SEQRES 21 A 322 ASP LYS VAL THR LYS ALA THR ALA GLN ILE GLY PHE ILE SEQRES 22 A 322 LYS PHE VAL LEU ILE PRO MET PHE GLU THR VAL THR LYS SEQRES 23 A 322 LEU PHE PRO MET VAL GLU GLU ILE MET LEU GLN PRO LEU SEQRES 24 A 322 TRP GLU SER ARG ASP ARG TYR GLU GLU LEU LYS ARG ILE SEQRES 25 A 322 ASP ASP ALA MET LYS GLU LEU GLN LYS LYS SEQRES 1 B 322 LYS TYR LEU LEU SER PRO GLU THR ILE GLU ALA LEU ARG SEQRES 2 B 322 LYS PRO THR PHE ASP VAL TRP LEU TRP GLU PRO ASN GLU SEQRES 3 B 322 MET LEU SER CYS LEU GLU HIS MET TYR HIS ASP LEU GLY SEQRES 4 B 322 LEU VAL ARG ASP PHE SER ILE ASN PRO VAL THR LEU ARG SEQRES 5 B 322 ARG TRP LEU PHE CYS VAL HIS ASP ASN TYR ARG ASN ASN SEQRES 6 B 322 PRO PHE HIS ASN PHE ARG HIS CYS PHE CYS VAL ALA GLN SEQRES 7 B 322 MET MET TYR SER MET VAL TRP LEU CYS SER LEU GLN GLU SEQRES 8 B 322 LYS PHE SER GLN THR ASP ILE LEU ILE LEU MET THR ALA SEQRES 9 B 322 ALA ILE CYS HIS ASP LEU ASP HIS PRO GLY TYR ASN ASN SEQRES 10 B 322 THR TYR GLN ILE ASN ALA ARG THR GLU LEU ALA VAL ARG SEQRES 11 B 322 TYR ASN ASP ILE SER PRO LEU GLU ASN HIS HIS CYS ALA SEQRES 12 B 322 VAL ALA PHE GLN ILE LEU ALA GLU PRO GLU CYS ASN ILE SEQRES 13 B 322 PHE SER ASN ILE PRO PRO ASP GLY PHE LYS GLN ILE ARG SEQRES 14 B 322 GLN GLY MET ILE THR LEU ILE LEU ALA THR ASP MET ALA SEQRES 15 B 322 ARG HIS ALA GLU ILE MET ASP SER PHE LYS GLU LYS MET SEQRES 16 B 322 GLU ASN PHE ASP TYR SER ASN GLU GLU HIS MET THR LEU SEQRES 17 B 322 LEU LYS MET ILE LEU ILE LYS CYS CYS ASP ILE SER ASN SEQRES 18 B 322 GLU VAL ARG PRO MET GLU VAL ALA GLU PRO TRP VAL ASP SEQRES 19 B 322 CYS LEU LEU GLU GLU TYR PHE MET GLN SER ASP ARG GLU SEQRES 20 B 322 LYS SER GLU GLY LEU PRO VAL ALA PRO PHE MET ASP ARG SEQRES 21 B 322 ASP LYS VAL THR LYS ALA THR ALA GLN ILE GLY PHE ILE SEQRES 22 B 322 LYS PHE VAL LEU ILE PRO MET PHE GLU THR VAL THR LYS SEQRES 23 B 322 LEU PHE PRO MET VAL GLU GLU ILE MET LEU GLN PRO LEU SEQRES 24 B 322 TRP GLU SER ARG ASP ARG TYR GLU GLU LEU LYS ARG ILE SEQRES 25 B 322 ASP ASP ALA MET LYS GLU LEU GLN LYS LYS HET ZN A 601 1 HET MG A 602 1 HET 9Q9 A 603 26 HET ZN B 601 1 HET MG B 602 1 HET 9Q9 B 603 26 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM 9Q9 1-CYCLOPENTYL-6-({(2R)-1-[(3S)-3-FLUOROPYRROLIDIN-1- HETNAM 2 9Q9 YL]-1-OXOPROPAN-2-YL}AMINO)-1,5-DIHYDRO-4H-PYRAZOLO[3, HETNAM 3 9Q9 4-D]PYRIMIDIN-4-ONE HETSYN 9Q9 1-CYCLOPENTYL-6-(((R)-1-((S)-3-FLUOROPYRROLIDIN-1-YL)- HETSYN 2 9Q9 1-OXOPROPAN-2-YL)AMINO)-1H-PYRAZOLO[3,4-D]PYRIMIDIN- HETSYN 3 9Q9 4(5H)-ONE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 9Q9 2(C17 H23 F N6 O2) FORMUL 9 HOH *193(H2 O) 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 ASN A 245 1 15 HELIX 6 AA6 ASN A 253 SER A 272 1 20 HELIX 7 AA7 LEU A 273 LYS A 276 5 4 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 THR A 363 1 19 HELIX 14 AB5 ASP A 364 ALA A 366 5 3 HELIX 15 AB6 ARG A 367 GLU A 380 1 14 HELIX 16 AB7 ASN A 386 ILE A 403 1 18 HELIX 17 AB8 SER A 404 ARG A 408 5 5 HELIX 18 AB9 PRO A 409 GLU A 434 1 26 HELIX 19 AC1 ALA A 439 ASP A 443 5 5 HELIX 20 AC2 THR A 448 VAL A 460 1 13 HELIX 21 AC3 VAL A 460 PHE A 472 1 13 HELIX 22 AC4 MET A 474 MET A 479 1 6 HELIX 23 AC5 MET A 479 LYS A 505 1 27 HELIX 24 AC6 SER B 189 LEU B 196 1 8 HELIX 25 AC7 ASP B 202 TRP B 206 5 5 HELIX 26 AC8 GLU B 207 LEU B 222 1 16 HELIX 27 AC9 GLY B 223 PHE B 228 1 6 HELIX 28 AD1 ASN B 231 ASN B 245 1 15 HELIX 29 AD2 ASN B 253 SER B 272 1 20 HELIX 30 AD3 LEU B 273 LYS B 276 5 4 HELIX 31 AD4 SER B 278 HIS B 292 1 15 HELIX 32 AD5 ASN B 300 ARG B 308 1 9 HELIX 33 AD6 THR B 309 TYR B 315 1 7 HELIX 34 AD7 SER B 319 ALA B 334 1 16 HELIX 35 AD8 GLU B 335 ASN B 339 5 5 HELIX 36 AD9 PRO B 345 THR B 363 1 19 HELIX 37 AE1 ASP B 364 ALA B 366 5 3 HELIX 38 AE2 ARG B 367 GLU B 380 1 14 HELIX 39 AE3 ASN B 386 ILE B 403 1 18 HELIX 40 AE4 SER B 404 ARG B 408 5 5 HELIX 41 AE5 PRO B 409 GLU B 414 1 6 HELIX 42 AE6 GLU B 414 GLY B 435 1 22 HELIX 43 AE7 ALA B 439 ASP B 443 5 5 HELIX 44 AE8 THR B 448 VAL B 460 1 13 HELIX 45 AE9 VAL B 460 PHE B 472 1 13 HELIX 46 AF1 MET B 474 MET B 479 1 6 HELIX 47 AF2 MET B 479 GLU B 502 1 24 SSBOND 1 CYS B 241 CYS B 338 1555 1555 2.08 LINK NE2 HIS A 256 ZN ZN A 601 1555 1555 2.16 LINK NE2 HIS A 292 ZN ZN A 601 1555 1555 2.11 LINK OD2 ASP A 293 ZN ZN A 601 1555 1555 2.03 LINK OD1 ASP A 293 MG MG A 602 1555 1555 2.18 LINK OD1 ASP A 402 ZN ZN A 601 1555 1555 2.03 LINK ZN ZN A 601 O HOH A 701 1555 1555 2.02 LINK ZN ZN A 601 O HOH A 703 1555 1555 2.01 LINK MG MG A 602 O HOH A 701 1555 1555 2.19 LINK MG MG A 602 O HOH A 702 1555 1555 2.19 LINK MG MG A 602 O HOH A 707 1555 1555 2.18 LINK MG MG A 602 O HOH A 737 1555 1555 2.18 LINK MG MG A 602 O HOH A 772 1555 1555 2.20 LINK NE2 HIS B 256 ZN ZN B 601 1555 1555 2.13 LINK NE2 HIS B 292 ZN ZN B 601 1555 1555 2.12 LINK OD2 ASP B 293 ZN ZN B 601 1555 1555 2.01 LINK OD1 ASP B 293 MG MG B 602 1555 1555 2.19 LINK OD1 ASP B 402 ZN ZN B 601 1555 1555 2.03 LINK ZN ZN B 601 O HOH B 702 1555 1555 2.01 LINK ZN ZN B 601 O HOH B 707 1555 1555 2.01 LINK MG MG B 602 O HOH B 701 1555 1555 2.18 LINK MG MG B 602 O HOH B 702 1555 1555 2.17 LINK MG MG B 602 O HOH B 705 1555 1555 2.19 LINK MG MG B 602 O HOH B 733 1555 1555 2.18 LINK MG MG B 602 O HOH B 738 1555 1555 2.18 SITE 1 AC1 6 HIS A 256 HIS A 292 ASP A 293 ASP A 402 SITE 2 AC1 6 HOH A 701 HOH A 703 SITE 1 AC2 6 ASP A 293 HOH A 701 HOH A 702 HOH A 707 SITE 2 AC2 6 HOH A 737 HOH A 772 SITE 1 AC3 10 LEU A 420 TYR A 424 ALA A 452 GLN A 453 SITE 2 AC3 10 PHE A 456 HOH A 705 HOH A 720 HOH A 761 SITE 3 AC3 10 MET B 500 LEU B 503 SITE 1 AC4 6 HIS B 256 HIS B 292 ASP B 293 ASP B 402 SITE 2 AC4 6 HOH B 702 HOH B 707 SITE 1 AC5 6 ASP B 293 HOH B 701 HOH B 702 HOH B 705 SITE 2 AC5 6 HOH B 733 HOH B 738 SITE 1 AC6 9 LEU B 420 TYR B 424 ALA B 452 GLN B 453 SITE 2 AC6 9 PHE B 456 HOH B 722 HOH B 723 HOH B 724 SITE 3 AC6 9 HOH B 745 CRYST1 104.110 104.110 269.079 90.00 90.00 90.00 P 41 21 2 16 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 0.009605 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009605 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003716 0.00000