HEADER HYDROLASE 06-JUL-20 6ZND TITLE [1,2,4]TRIAZOLO[1,5-A]PYRIMIDINE PHOSPHODIESTERASE 2 INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CGMP-DEPENDENT 3',5'-CYCLIC PHOSPHODIESTERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CYCLIC GMP-STIMULATED PHOSPHODIESTERASE,CGSPDE; COMPND 5 EC: 3.1.4.17; 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: PDE2A; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF9 KEYWDS PDE2A INHIBITOR, FEP, SBDD, FREE ENERGY PERTURBATION, MOLECULAR KEYWDS 2 DYNAMICS, ALZHEIMERS DISEASE, PHOSPHODIESTERASE, MOLECULAR DESIGN, KEYWDS 3 BINDING FREE ENERGY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.TRESADERN,P.M.LEONARD REVDAT 4 31-JAN-24 6ZND 1 REMARK REVDAT 3 25-NOV-20 6ZND 1 JRNL REVDAT 2 18-NOV-20 6ZND 1 JRNL LINK REVDAT 1 22-JUL-20 6ZND 0 JRNL AUTH G.TRESADERN,I.VELTER,A.A.TRABANCO,F.VAN DEN KEYBUS, JRNL AUTH 2 G.J.MACDONALD,M.V.F.SOMERS,G.VANHOOF,P.M.LEONARD, JRNL AUTH 3 M.B.A.C.LAMERS,Y.E.M.VAN ROOSBROECK,P.J.J.A.BUIJNSTERS JRNL TITL [1,2,4]TRIAZOLO[1,5- A ]PYRIMIDINE PHOSPHODIESTERASE 2A JRNL TITL 2 INHIBITORS: STRUCTURE AND FREE-ENERGY PERTURBATION-GUIDED JRNL TITL 3 EXPLORATION. JRNL REF J.MED.CHEM. V. 63 12887 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 33105987 JRNL DOI 10.1021/ACS.JMEDCHEM.0C01272 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 85.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 25640 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) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.291 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1355 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) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1834 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 123 REMARK 3 BIN FREE R VALUE : 0.3900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5274 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.52000 REMARK 3 B22 (A**2) : 0.69000 REMARK 3 B33 (A**2) : -1.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.83000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.647 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.323 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.250 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.445 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.872 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5467 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3611 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7402 ; 1.257 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8781 ; 0.886 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 653 ; 5.686 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 261 ;36.677 ;23.870 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 913 ;17.225 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;18.213 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 806 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6051 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1152 ; 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 : 1.40 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 6ZND COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1292109787. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26995 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 85.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.12500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.51100 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: 1Z1L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MGCL2, 0.1 M TRIS-HCL PH 8.0 AND REMARK 280 20 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 85.53000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.76000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 85.53000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.76000 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 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 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 576 REMARK 465 GLY A 577 REMARK 465 SER A 578 REMARK 465 ASP A 579 REMARK 465 ASP A 580 REMARK 465 GLU A 581 REMARK 465 TYR A 582 REMARK 465 THR A 583 REMARK 465 LYS A 584 REMARK 465 LEU A 585 REMARK 465 LEU A 586 REMARK 465 HIS A 587 REMARK 465 ASP A 588 REMARK 465 GLY A 589 REMARK 465 ILE A 590 REMARK 465 ALA A 594 REMARK 465 SER A 909 REMARK 465 ASP A 917 REMARK 465 GLU A 918 REMARK 465 GLU A 919 REMARK 465 TYR A 920 REMARK 465 GLU A 921 REMARK 465 ARG A 922 REMARK 465 HIS A 923 REMARK 465 HIS A 924 REMARK 465 HIS A 925 REMARK 465 HIS A 926 REMARK 465 HIS A 927 REMARK 465 HIS A 928 REMARK 465 MET B 576 REMARK 465 GLY B 577 REMARK 465 SER B 578 REMARK 465 ASP B 579 REMARK 465 GLY B 841 REMARK 465 ASN B 842 REMARK 465 ARG B 843 REMARK 465 ASP B 917 REMARK 465 GLU B 918 REMARK 465 GLU B 919 REMARK 465 TYR B 920 REMARK 465 GLU B 921 REMARK 465 ARG B 922 REMARK 465 HIS B 923 REMARK 465 HIS B 924 REMARK 465 HIS B 925 REMARK 465 HIS B 926 REMARK 465 HIS B 927 REMARK 465 HIS B 928 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 648 CD CE NZ REMARK 470 GLU A 682 CG CD OE1 OE2 REMARK 470 LYS A 752 CG CD CE NZ REMARK 470 ARG A 790 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 793 CG CD CE NZ REMARK 470 GLN A 794 CG CD OE1 NE2 REMARK 470 ARG A 797 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 817 CG CD CE NZ REMARK 470 ARG A 843 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 857 CG CD OE1 OE2 REMARK 470 GLU A 886 CG CD OE1 OE2 REMARK 470 GLU A 893 CG CD OE1 OE2 REMARK 470 LYS A 897 CG CD CE NZ REMARK 470 LYS A 901 CG CD CE NZ REMARK 470 LYS B 633 CG CD CE NZ REMARK 470 ARG B 641 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 648 CD CE NZ REMARK 470 ASP B 747 CG OD1 OD2 REMARK 470 LYS B 752 CG CD CE NZ REMARK 470 ARG B 790 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 793 CG CD CE NZ REMARK 470 GLN B 794 CG CD OE1 NE2 REMARK 470 ARG B 797 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 817 CG CD CE NZ REMARK 470 MET B 840 CG SD CE REMARK 470 MET B 845 CG SD CE REMARK 470 GLU B 857 CG CD OE1 OE2 REMARK 470 LYS B 897 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 O TYR B 655 O HOH B 1101 2.11 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 ASP A 597 146.53 -175.45 REMARK 500 LEU A 677 -45.14 69.93 REMARK 500 ARG A 790 -17.35 -48.21 REMARK 500 ILE A 866 -61.82 -108.09 REMARK 500 ASN B 630 -72.72 -74.16 REMARK 500 SER B 720 -55.02 13.63 REMARK 500 ALA B 839 39.42 -76.86 REMARK 500 SER B 909 -53.35 -18.78 REMARK 500 ASN B 911 -0.35 76.79 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 660 NE2 REMARK 620 2 HIS A 696 NE2 95.4 REMARK 620 3 ASP A 697 OD2 82.5 89.0 REMARK 620 4 ASP A 808 OD1 93.1 94.4 174.7 REMARK 620 5 HOH A1126 O 149.5 114.0 89.9 92.4 REMARK 620 N 1 2 3 4 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 697 OD1 REMARK 620 2 HOH A1114 O 81.2 REMARK 620 3 HOH A1126 O 93.2 107.5 REMARK 620 4 HOH A1142 O 88.9 82.5 170.0 REMARK 620 5 HOH A1150 O 160.5 83.1 102.6 77.5 REMARK 620 6 HOH A1173 O 107.6 156.8 93.7 76.4 83.0 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 660 NE2 REMARK 620 2 HIS B 696 NE2 99.0 REMARK 620 3 ASP B 697 OD2 88.1 83.4 REMARK 620 4 ASP B 808 OD1 88.4 93.3 174.7 REMARK 620 5 HOH B1135 O 155.8 103.7 86.2 98.5 REMARK 620 6 HOH B1151 O 97.6 162.8 101.8 82.6 60.8 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 697 OD1 REMARK 620 2 HOH B1112 O 169.2 REMARK 620 3 HOH B1113 O 78.0 91.4 REMARK 620 4 HOH B1133 O 102.0 88.6 178.5 REMARK 620 5 HOH B1135 O 87.8 90.4 90.7 87.8 REMARK 620 6 HOH B1146 O 95.3 87.4 94.7 86.8 174.2 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 QMZ 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 QMZ B 1003 DBREF 6ZND A 578 921 UNP O00408 PDE2A_HUMAN 578 921 DBREF 6ZND B 578 921 UNP O00408 PDE2A_HUMAN 578 921 SEQADV 6ZND MET A 576 UNP O00408 INITIATING METHIONINE SEQADV 6ZND GLY A 577 UNP O00408 EXPRESSION TAG SEQADV 6ZND ARG A 922 UNP O00408 EXPRESSION TAG SEQADV 6ZND HIS A 923 UNP O00408 EXPRESSION TAG SEQADV 6ZND HIS A 924 UNP O00408 EXPRESSION TAG SEQADV 6ZND HIS A 925 UNP O00408 EXPRESSION TAG SEQADV 6ZND HIS A 926 UNP O00408 EXPRESSION TAG SEQADV 6ZND HIS A 927 UNP O00408 EXPRESSION TAG SEQADV 6ZND HIS A 928 UNP O00408 EXPRESSION TAG SEQADV 6ZND MET B 576 UNP O00408 INITIATING METHIONINE SEQADV 6ZND GLY B 577 UNP O00408 EXPRESSION TAG SEQADV 6ZND ARG B 922 UNP O00408 EXPRESSION TAG SEQADV 6ZND HIS B 923 UNP O00408 EXPRESSION TAG SEQADV 6ZND HIS B 924 UNP O00408 EXPRESSION TAG SEQADV 6ZND HIS B 925 UNP O00408 EXPRESSION TAG SEQADV 6ZND HIS B 926 UNP O00408 EXPRESSION TAG SEQADV 6ZND HIS B 927 UNP O00408 EXPRESSION TAG SEQADV 6ZND HIS B 928 UNP O00408 EXPRESSION TAG SEQRES 1 A 353 MET GLY SER ASP ASP GLU TYR THR LYS LEU LEU HIS ASP SEQRES 2 A 353 GLY ILE GLN PRO VAL ALA ALA ILE ASP SER ASN PHE ALA SEQRES 3 A 353 SER PHE THR TYR THR PRO ARG SER LEU PRO GLU ASP ASP SEQRES 4 A 353 THR SER MET ALA ILE LEU SER MET LEU GLN ASP MET ASN SEQRES 5 A 353 PHE ILE ASN ASN TYR LYS ILE ASP CYS PRO THR LEU ALA SEQRES 6 A 353 ARG PHE CYS LEU MET VAL LYS LYS GLY TYR ARG ASP PRO SEQRES 7 A 353 PRO TYR HIS ASN TRP MET HIS ALA PHE SER VAL SER HIS SEQRES 8 A 353 PHE CYS TYR LEU LEU TYR LYS ASN LEU GLU LEU THR ASN SEQRES 9 A 353 TYR LEU GLU ASP ILE GLU ILE PHE ALA LEU PHE ILE SER SEQRES 10 A 353 CYS MET CYS HIS ASP LEU ASP HIS ARG GLY THR ASN ASN SEQRES 11 A 353 SER PHE GLN VAL ALA SER LYS SER VAL LEU ALA ALA LEU SEQRES 12 A 353 TYR SER SER GLU GLY SER VAL MET GLU ARG HIS HIS PHE SEQRES 13 A 353 ALA GLN ALA ILE ALA ILE LEU ASN THR HIS GLY CYS ASN SEQRES 14 A 353 ILE PHE ASP HIS PHE SER ARG LYS ASP TYR GLN ARG MET SEQRES 15 A 353 LEU ASP LEU MET ARG ASP ILE ILE LEU ALA THR ASP LEU SEQRES 16 A 353 ALA HIS HIS LEU ARG ILE PHE LYS ASP LEU GLN LYS MET SEQRES 17 A 353 ALA GLU VAL GLY TYR ASP ARG ASN ASN LYS GLN HIS HIS SEQRES 18 A 353 ARG LEU LEU LEU CYS LEU LEU MET THR SER CYS ASP LEU SEQRES 19 A 353 SER ASP GLN THR LYS GLY TRP LYS THR THR ARG LYS ILE SEQRES 20 A 353 ALA GLU LEU ILE TYR LYS GLU PHE PHE SER GLN GLY ASP SEQRES 21 A 353 LEU GLU LYS ALA MET GLY ASN ARG PRO MET GLU MET MET SEQRES 22 A 353 ASP ARG GLU LYS ALA TYR ILE PRO GLU LEU GLN ILE SER SEQRES 23 A 353 PHE MET GLU HIS ILE ALA MET PRO ILE TYR LYS LEU LEU SEQRES 24 A 353 GLN ASP LEU PHE PRO LYS ALA ALA GLU LEU TYR GLU ARG SEQRES 25 A 353 VAL ALA SER ASN ARG GLU HIS TRP THR LYS VAL SER HIS SEQRES 26 A 353 LYS PHE THR ILE ARG GLY LEU PRO SER ASN ASN SER LEU SEQRES 27 A 353 ASP PHE LEU ASP GLU GLU TYR GLU ARG HIS HIS HIS HIS SEQRES 28 A 353 HIS HIS SEQRES 1 B 353 MET GLY SER ASP ASP GLU TYR THR LYS LEU LEU HIS ASP SEQRES 2 B 353 GLY ILE GLN PRO VAL ALA ALA ILE ASP SER ASN PHE ALA SEQRES 3 B 353 SER PHE THR TYR THR PRO ARG SER LEU PRO GLU ASP ASP SEQRES 4 B 353 THR SER MET ALA ILE LEU SER MET LEU GLN ASP MET ASN SEQRES 5 B 353 PHE ILE ASN ASN TYR LYS ILE ASP CYS PRO THR LEU ALA SEQRES 6 B 353 ARG PHE CYS LEU MET VAL LYS LYS GLY TYR ARG ASP PRO SEQRES 7 B 353 PRO TYR HIS ASN TRP MET HIS ALA PHE SER VAL SER HIS SEQRES 8 B 353 PHE CYS TYR LEU LEU TYR LYS ASN LEU GLU LEU THR ASN SEQRES 9 B 353 TYR LEU GLU ASP ILE GLU ILE PHE ALA LEU PHE ILE SER SEQRES 10 B 353 CYS MET CYS HIS ASP LEU ASP HIS ARG GLY THR ASN ASN SEQRES 11 B 353 SER PHE GLN VAL ALA SER LYS SER VAL LEU ALA ALA LEU SEQRES 12 B 353 TYR SER SER GLU GLY SER VAL MET GLU ARG HIS HIS PHE SEQRES 13 B 353 ALA GLN ALA ILE ALA ILE LEU ASN THR HIS GLY CYS ASN SEQRES 14 B 353 ILE PHE ASP HIS PHE SER ARG LYS ASP TYR GLN ARG MET SEQRES 15 B 353 LEU ASP LEU MET ARG ASP ILE ILE LEU ALA THR ASP LEU SEQRES 16 B 353 ALA HIS HIS LEU ARG ILE PHE LYS ASP LEU GLN LYS MET SEQRES 17 B 353 ALA GLU VAL GLY TYR ASP ARG ASN ASN LYS GLN HIS HIS SEQRES 18 B 353 ARG LEU LEU LEU CYS LEU LEU MET THR SER CYS ASP LEU SEQRES 19 B 353 SER ASP GLN THR LYS GLY TRP LYS THR THR ARG LYS ILE SEQRES 20 B 353 ALA GLU LEU ILE TYR LYS GLU PHE PHE SER GLN GLY ASP SEQRES 21 B 353 LEU GLU LYS ALA MET GLY ASN ARG PRO MET GLU MET MET SEQRES 22 B 353 ASP ARG GLU LYS ALA TYR ILE PRO GLU LEU GLN ILE SER SEQRES 23 B 353 PHE MET GLU HIS ILE ALA MET PRO ILE TYR LYS LEU LEU SEQRES 24 B 353 GLN ASP LEU PHE PRO LYS ALA ALA GLU LEU TYR GLU ARG SEQRES 25 B 353 VAL ALA SER ASN ARG GLU HIS TRP THR LYS VAL SER HIS SEQRES 26 B 353 LYS PHE THR ILE ARG GLY LEU PRO SER ASN ASN SER LEU SEQRES 27 B 353 ASP PHE LEU ASP GLU GLU TYR GLU ARG HIS HIS HIS HIS SEQRES 28 B 353 HIS HIS HET ZN A1001 1 HET MG A1002 1 HET QMZ A1003 29 HET ZN B1001 1 HET MG B1002 1 HET QMZ B1003 29 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM QMZ [(3~{S})-3-([1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL) HETNAM 2 QMZ PIPERIDIN-1-YL]-(3,4,5-TRIMETHOXYPHENYL)METHANONE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 QMZ 2(C20 H23 N5 O4) FORMUL 9 HOH *201(H2 O) HELIX 1 AA1 PRO A 592 VAL A 593 5 2 HELIX 2 AA2 ALA A 595 ASP A 597 5 3 HELIX 3 AA3 THR A 606 LEU A 610 5 5 HELIX 4 AA4 PRO A 611 ASP A 613 5 3 HELIX 5 AA5 ASP A 614 MET A 626 1 13 HELIX 6 AA6 ASN A 627 TYR A 632 1 6 HELIX 7 AA7 ASP A 635 TYR A 650 1 16 HELIX 8 AA8 ASN A 657 LEU A 675 1 19 HELIX 9 AA9 GLU A 682 HIS A 696 1 15 HELIX 10 AB1 ASN A 704 SER A 711 1 8 HELIX 11 AB2 SER A 713 SER A 720 1 8 HELIX 12 AB3 SER A 724 ASN A 739 1 16 HELIX 13 AB4 SER A 750 THR A 768 1 19 HELIX 14 AB5 ASP A 769 VAL A 786 1 18 HELIX 15 AB6 ASN A 792 LEU A 809 1 18 HELIX 16 AB7 SER A 810 LYS A 814 5 5 HELIX 17 AB8 GLY A 815 MET A 840 1 26 HELIX 18 AB9 MET A 845 ASP A 849 5 5 HELIX 19 AC1 TYR A 854 ILE A 866 1 13 HELIX 20 AC2 ILE A 866 PHE A 878 1 13 HELIX 21 AC3 ALA A 881 HIS A 900 1 20 HELIX 22 AC4 LYS A 901 THR A 903 5 3 HELIX 23 AC5 GLU B 581 ASP B 588 1 8 HELIX 24 AC6 PRO B 592 ASP B 597 1 6 HELIX 25 AC7 THR B 606 LEU B 610 5 5 HELIX 26 AC8 PRO B 611 ASP B 613 5 3 HELIX 27 AC9 ASP B 614 MET B 626 1 13 HELIX 28 AD1 ASN B 627 LYS B 633 1 7 HELIX 29 AD2 ASP B 635 GLY B 649 1 15 HELIX 30 AD3 ASN B 657 LEU B 675 1 19 HELIX 31 AD4 GLU B 676 TYR B 680 5 5 HELIX 32 AD5 GLU B 682 HIS B 696 1 15 HELIX 33 AD6 ASN B 704 LYS B 712 1 9 HELIX 34 AD7 SER B 713 SER B 720 1 8 HELIX 35 AD8 SER B 721 GLY B 723 5 3 HELIX 36 AD9 SER B 724 ASN B 739 1 16 HELIX 37 AE1 SER B 750 ALA B 767 1 18 HELIX 38 AE2 ASP B 769 GLY B 787 1 19 HELIX 39 AE3 ASN B 792 LEU B 809 1 18 HELIX 40 AE4 SER B 810 LYS B 814 5 5 HELIX 41 AE5 GLY B 815 ALA B 839 1 25 HELIX 42 AE6 MET B 845 ASP B 849 5 5 HELIX 43 AE7 TYR B 854 ILE B 866 1 13 HELIX 44 AE8 ILE B 866 PHE B 878 1 13 HELIX 45 AE9 ALA B 881 SER B 899 1 19 HELIX 46 AF1 HIS B 900 THR B 903 5 4 LINK NE2 HIS A 660 ZN ZN A1001 1555 1555 2.20 LINK NE2 HIS A 696 ZN ZN A1001 1555 1555 2.01 LINK OD2 ASP A 697 ZN ZN A1001 1555 1555 1.97 LINK OD1 ASP A 697 MG MG A1002 1555 1555 1.91 LINK OD1 ASP A 808 ZN ZN A1001 1555 1555 2.18 LINK ZN ZN A1001 O HOH A1126 1555 1555 1.74 LINK MG MG A1002 O HOH A1114 1555 1555 1.99 LINK MG MG A1002 O HOH A1126 1555 1555 2.00 LINK MG MG A1002 O HOH A1142 1555 1555 2.00 LINK MG MG A1002 O HOH A1150 1555 1555 2.13 LINK MG MG A1002 O HOH A1173 1555 1555 2.01 LINK NE2 HIS B 660 ZN ZN B1001 1555 1555 2.05 LINK NE2 HIS B 696 ZN ZN B1001 1555 1555 2.08 LINK OD2 ASP B 697 ZN ZN B1001 1555 1555 1.98 LINK OD1 ASP B 697 MG MG B1002 1555 1555 2.08 LINK OD1 ASP B 808 ZN ZN B1001 1555 1555 2.19 LINK ZN ZN B1001 O HOH B1135 1555 1555 2.04 LINK ZN ZN B1001 O HOH B1151 1555 1555 2.33 LINK MG MG B1002 O HOH B1112 1555 1555 2.10 LINK MG MG B1002 O HOH B1113 1555 1555 2.10 LINK MG MG B1002 O HOH B1133 1555 1555 1.98 LINK MG MG B1002 O HOH B1135 1555 1555 2.05 LINK MG MG B1002 O HOH B1146 1555 1555 1.81 SITE 1 AC1 6 HIS A 660 HIS A 696 ASP A 697 ASP A 808 SITE 2 AC1 6 MG A1002 HOH A1126 SITE 1 AC2 7 ASP A 697 ZN A1001 HOH A1114 HOH A1126 SITE 2 AC2 7 HOH A1142 HOH A1150 HOH A1173 SITE 1 AC3 10 TYR A 655 LEU A 770 GLN A 812 ILE A 826 SITE 2 AC3 10 TYR A 827 MET A 847 GLN A 859 PHE A 862 SITE 3 AC3 10 HOH A1137 HOH B1107 SITE 1 AC4 6 HIS B 660 HIS B 696 ASP B 697 ASP B 808 SITE 2 AC4 6 HOH B1135 HOH B1151 SITE 1 AC5 7 ASP B 697 GLU B 727 HOH B1112 HOH B1113 SITE 2 AC5 7 HOH B1133 HOH B1135 HOH B1146 SITE 1 AC6 10 LEU B 770 GLN B 812 ILE B 826 TYR B 827 SITE 2 AC6 10 PHE B 830 MET B 847 LEU B 858 GLN B 859 SITE 3 AC6 10 PHE B 862 HOH B1126 CRYST1 171.060 69.520 55.090 90.00 91.16 90.00 C 1 2 1 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 0.005846 0.000000 0.000118 0.00000 SCALE2 0.000000 0.014384 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018156 0.00000