HEADER HYDROLASE/HYDROLASE INHIBITOR 26-JUL-18 6ACB TITLE CRYSTAL STRUCTURE OF PDE5 IN COMPLEX WITH INHIBITOR LW1805 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CGMP-SPECIFIC 3',5'-CYCLIC PHOSPHODIESTERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CGMP-BINDING CGMP-SPECIFIC PHOSPHODIESTERASE,CGB-PDE; 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: PDE5A, PDE5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS PDE5 IN COMPLEX WITH INHIBITOR LW1805, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.WU,Y.D.HUANG,Y.Y.HUANG,H.B.LUO REVDAT 3 22-NOV-23 6ACB 1 COMPND LINK REVDAT 2 10-OCT-18 6ACB 1 COMPND JRNL REVDAT 1 19-SEP-18 6ACB 0 JRNL AUTH D.WU,Y.HUANG,Y.CHEN,Y.Y.HUANG,H.GENG,T.ZHANG,C.ZHANG,Z.LI, JRNL AUTH 2 L.GUO,J.CHEN,H.B.LUO JRNL TITL OPTIMIZATION OF CHROMENO[2,3- C]PYRROL-9(2 H)-ONES AS HIGHLY JRNL TITL 2 POTENT, SELECTIVE, AND ORALLY BIOAVAILABLE PDE5 INHIBITORS: JRNL TITL 3 STRUCTURE-ACTIVITY RELATIONSHIP, X-RAY CRYSTAL STRUCTURE, JRNL TITL 4 AND PHARMACODYNAMIC EFFECT ON PULMONARY ARTERIAL JRNL TITL 5 HYPERTENSION. JRNL REF J. MED. CHEM. V. 61 8468 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 30148362 JRNL DOI 10.1021/ACS.JMEDCHEM.8B01209 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 9913 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 546 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 693 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE SET COUNT : 42 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2499 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.06000 REMARK 3 B12 (A**2) : -0.01000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.397 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.316 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.778 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.867 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2598 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2406 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3514 ; 1.510 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5591 ; 1.001 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 306 ; 7.988 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;42.593 ;24.800 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 474 ;17.535 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;14.837 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 390 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2970 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 515 ; 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): 1230 ; 2.821 ; 4.068 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1229 ; 2.805 ; 4.063 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1534 ; 4.580 ; 6.077 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1535 ; 4.586 ; 6.083 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1366 ; 2.584 ; 4.506 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1367 ; 2.583 ; 4.508 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1979 ; 4.383 ; 6.633 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3067 ; 8.160 ;48.877 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3061 ; 8.150 ;48.958 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 6ACB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1300008517. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 NOVA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5406 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 : 10461 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 24.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 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 1.10 REMARK 200 STARTING MODEL: 4MD6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CACODYLATE SODIUM (PH6.5), 0.2 M REMARK 280 MGSO4, 18% PEG3350, 2.5% ETHANOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.03067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 88.06133 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 88.06133 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 44.03067 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL 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 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 GLY A 790 REMARK 465 ASP A 791 REMARK 465 ARG A 792 REMARK 465 GLU A 793 REMARK 465 ARG A 794 REMARK 465 LYS A 795 REMARK 465 GLU A 796 REMARK 465 LEU A 797 REMARK 465 ASN A 798 REMARK 465 ILE A 799 REMARK 465 GLU A 800 REMARK 465 PRO A 801 REMARK 465 THR A 802 REMARK 465 ASP A 803 REMARK 465 LEU A 804 REMARK 465 MET A 805 REMARK 465 ASN A 806 REMARK 465 ARG A 807 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1014 O HOH A 1014 5554 2.12 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 GLU A 536 -57.37 65.73 REMARK 500 LYS A 555 5.17 84.01 REMARK 500 PHE A 561 138.51 -36.88 REMARK 500 GLN A 589 65.43 33.41 REMARK 500 LYS A 630 -71.20 -82.60 REMARK 500 ASN A 662 57.75 -140.37 REMARK 500 LEU A 672 0.66 93.13 REMARK 500 GLN A 674 -30.98 -132.60 REMARK 500 LEU A 675 -30.53 -36.06 REMARK 500 HIS A 678 -59.48 50.29 REMARK 500 SER A 679 92.00 -41.83 REMARK 500 ILE A 680 -47.61 -155.64 REMARK 500 LYS A 809 -134.04 -67.28 REMARK 500 ILE A 824 -52.13 -129.24 REMARK 500 PHE A 840 -35.50 -39.52 REMARK 500 GLU A 858 26.73 -77.98 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 LEU A 672 ALA A 673 139.75 REMARK 500 HIS A 678 SER A 679 143.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 617 NE2 REMARK 620 2 HIS A 653 NE2 96.3 REMARK 620 3 ASP A 654 OD2 85.3 86.0 REMARK 620 4 ASP A 764 OD1 77.9 83.7 159.2 REMARK 620 5 SO4 A 901 O3 88.6 172.8 99.6 92.3 REMARK 620 6 HOH A1002 O 168.6 91.8 103.3 95.1 82.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 903 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 654 OD1 REMARK 620 2 HOH A1001 O 79.3 REMARK 620 3 HOH A1002 O 97.7 118.1 REMARK 620 4 HOH A1006 O 177.9 99.1 84.3 REMARK 620 5 HOH A1007 O 86.5 95.1 146.8 92.3 REMARK 620 6 HOH A1011 O 99.5 170.2 71.7 81.9 75.1 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 SO4 A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9T9 A 904 DBREF 6ACB A 535 860 UNP O76074 PDE5A_HUMAN 535 860 SEQRES 1 A 326 GLU GLU THR ARG GLU LEU GLN SER LEU ALA ALA ALA VAL SEQRES 2 A 326 VAL PRO SER ALA GLN THR LEU LYS ILE THR ASP PHE SER SEQRES 3 A 326 PHE SER ASP PHE GLU LEU SER ASP LEU GLU THR ALA LEU SEQRES 4 A 326 CYS THR ILE ARG MET PHE THR ASP LEU ASN LEU VAL GLN SEQRES 5 A 326 ASN PHE GLN MET LYS HIS GLU VAL LEU CYS ARG TRP ILE SEQRES 6 A 326 LEU SER VAL LYS LYS ASN TYR ARG LYS ASN VAL ALA TYR SEQRES 7 A 326 HIS ASN TRP ARG HIS ALA PHE ASN THR ALA GLN CYS MET SEQRES 8 A 326 PHE ALA ALA LEU LYS ALA GLY LYS ILE GLN ASN LYS LEU SEQRES 9 A 326 THR ASP LEU GLU ILE LEU ALA LEU LEU ILE ALA ALA LEU SEQRES 10 A 326 SER HIS ASP LEU ASP HIS ARG GLY VAL ASN ASN SER TYR SEQRES 11 A 326 ILE GLN ARG SER GLU HIS PRO LEU ALA GLN LEU TYR CYS SEQRES 12 A 326 HIS SER ILE MET GLU HIS HIS HIS PHE ASP GLN CYS LEU SEQRES 13 A 326 MET ILE LEU ASN SER PRO GLY ASN GLN ILE LEU SER GLY SEQRES 14 A 326 LEU SER ILE GLU GLU TYR LYS THR THR LEU LYS ILE ILE SEQRES 15 A 326 LYS GLN ALA ILE LEU ALA THR ASP LEU ALA LEU TYR ILE SEQRES 16 A 326 LYS ARG ARG GLY GLU PHE PHE GLU LEU ILE ARG LYS ASN SEQRES 17 A 326 GLN PHE ASN LEU GLU ASP PRO HIS GLN LYS GLU LEU PHE SEQRES 18 A 326 LEU ALA MET LEU MET THR ALA CYS ASP LEU SER ALA ILE SEQRES 19 A 326 THR LYS PRO TRP PRO ILE GLN GLN ARG ILE ALA GLU LEU SEQRES 20 A 326 VAL ALA THR GLU PHE PHE ASP GLN GLY ASP ARG GLU ARG SEQRES 21 A 326 LYS GLU LEU ASN ILE GLU PRO THR ASP LEU MET ASN ARG SEQRES 22 A 326 GLU LYS LYS ASN LYS ILE PRO SER MET GLN VAL GLY PHE SEQRES 23 A 326 ILE ASP ALA ILE CYS LEU GLN LEU TYR GLU ALA LEU THR SEQRES 24 A 326 HIS VAL SER GLU ASP CYS PHE PRO LEU LEU ASP GLY CYS SEQRES 25 A 326 ARG LYS ASN ARG GLN LYS TRP GLN ALA LEU ALA GLU GLN SEQRES 26 A 326 GLN HET SO4 A 901 5 HET ZN A 902 1 HET MG A 903 1 HET 9T9 A 904 40 HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM 9T9 3-[(2H-1,3-BENZODIOXOL-5-YL)METHYL]-8-FLUORO-6-{[2-(4- HETNAM 2 9T9 METHYLPIPERAZIN-1-YL)ETHYL]AMINO}-1-(1,3-THIAZOL-2- HETNAM 3 9T9 YL)[1]BENZOPYRANO[2,3-C]PYRROL-9(2H)-ONE FORMUL 2 SO4 O4 S 2- FORMUL 3 ZN ZN 2+ FORMUL 4 MG MG 2+ FORMUL 5 9T9 C29 H28 F N5 O4 S FORMUL 6 HOH *45(H2 O) HELIX 1 AA1 GLU A 536 ALA A 546 1 11 HELIX 2 AA2 SER A 550 LYS A 555 1 6 HELIX 3 AA3 SER A 567 LEU A 582 1 16 HELIX 4 AA4 ASN A 583 PHE A 588 1 6 HELIX 5 AA5 LYS A 591 ASN A 605 1 15 HELIX 6 AA6 ASN A 614 ALA A 631 1 18 HELIX 7 AA7 ILE A 634 LEU A 638 5 5 HELIX 8 AA8 THR A 639 HIS A 653 1 15 HELIX 9 AA9 SER A 663 SER A 668 1 6 HELIX 10 AB1 ILE A 680 SER A 695 1 16 HELIX 11 AB2 SER A 705 THR A 723 1 19 HELIX 12 AB3 ASP A 724 LYS A 741 1 18 HELIX 13 AB4 ASP A 748 SER A 766 1 19 HELIX 14 AB5 ALA A 767 LYS A 770 5 4 HELIX 15 AB6 PRO A 771 ASP A 788 1 18 HELIX 16 AB7 LYS A 812 ILE A 824 1 13 HELIX 17 AB8 ILE A 824 SER A 836 1 13 HELIX 18 AB9 CYS A 839 GLU A 858 1 20 LINK NE2 HIS A 617 ZN ZN A 902 1555 1555 2.30 LINK NE2 HIS A 653 ZN ZN A 902 1555 1555 2.05 LINK OD2 ASP A 654 ZN ZN A 902 1555 1555 2.14 LINK OD1 ASP A 654 MG MG A 903 1555 1555 1.92 LINK OD1 ASP A 764 ZN ZN A 902 1555 1555 2.12 LINK O3 SO4 A 901 ZN ZN A 902 1555 1555 2.16 LINK ZN ZN A 902 O HOH A1002 1555 1555 1.87 LINK MG MG A 903 O HOH A1001 1555 1555 1.88 LINK MG MG A 903 O HOH A1002 1555 1555 2.19 LINK MG MG A 903 O HOH A1006 1555 1555 1.94 LINK MG MG A 903 O HOH A1007 1555 1555 1.76 LINK MG MG A 903 O HOH A1011 1555 1555 2.34 SITE 1 AC1 9 HIS A 613 HIS A 617 ASP A 654 ASP A 764 SITE 2 AC1 9 ZN A 902 9T9 A 904 HOH A1002 HOH A1011 SITE 3 AC1 9 HOH A1023 SITE 1 AC2 7 HIS A 617 HIS A 653 ASP A 654 ASP A 764 SITE 2 AC2 7 SO4 A 901 MG A 903 HOH A1002 SITE 1 AC3 9 HIS A 653 ASP A 654 THR A 723 ZN A 902 SITE 2 AC3 9 HOH A1001 HOH A1002 HOH A1006 HOH A1007 SITE 3 AC3 9 HOH A1011 SITE 1 AC4 13 VAL A 660 PRO A 671 GLN A 674 ILE A 768 SITE 2 AC4 13 ALA A 783 PHE A 786 PHE A 787 ILE A 813 SITE 3 AC4 13 MET A 816 GLN A 817 PHE A 820 SO4 A 901 SITE 4 AC4 13 HOH A1023 CRYST1 74.577 74.577 132.092 90.00 90.00 120.00 P 31 2 1 6 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 0.013409 0.007742 0.000000 0.00000 SCALE2 0.000000 0.015483 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007570 0.00000