HEADER HYDROLASE/INHIBITOR 27-SEP-23 8WKG TITLE RATIONAL DESIGN OF HIGHLY SELECTIVE PDE5 INHIBITORS FOR THE TREATMENT TITLE 2 OF IDIOPATHIC PULMONARY FIBROSIS 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 KEYWDS HYDROLASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.C.ZHANG,Y.Y.HUANG REVDAT 1 02-OCT-24 8WKG 0 JRNL AUTH F.C.ZHANG,Y.Y.HUANG,H.B.LUO,Y.N.WU JRNL TITL RATIONAL DESIGN OF HIGHLY SELECTIVE PDE5 INHIBITORS FOR THE JRNL TITL 2 TREATMENT OF IDIOPATHIC PULMONARY FIBROSIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.16_3549: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16854 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8WKG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300041049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54056 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-3000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16888 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 24.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM SULFATE, 0.1 M SODIUM REMARK 280 CACODYLATE, PH 6.5, 17% PEG3350, 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 43.69467 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 87.38933 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 87.38933 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 43.69467 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1096 LIES ON A SPECIAL POSITION. 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 SER A 527 REMARK 465 TYR A 528 REMARK 465 HIS A 529 REMARK 465 ALA A 530 REMARK 465 SER A 531 REMARK 465 ALA A 532 REMARK 465 ALA A 533 REMARK 465 GLU A 534 REMARK 465 GLU A 535 REMARK 465 GLU A 536 REMARK 465 TYR A 676 REMARK 465 CYS A 677 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 465 GLU A 808 REMARK 465 LYS A 809 REMARK 465 LYS A 810 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 LYS A 630 -72.05 -89.74 REMARK 500 ALA A 673 31.84 -73.56 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 87.9 REMARK 620 3 ASP A 654 OD2 87.9 88.4 REMARK 620 4 ASP A 764 OD1 80.6 83.3 166.0 REMARK 620 5 WDB A 901 O2 77.8 164.0 97.9 87.4 REMARK 620 N 1 2 3 4 DBREF 8WKG A 527 859 UNP O76074 PDE5A_HUMAN 527 859 SEQRES 1 A 333 SER TYR HIS ALA SER ALA ALA GLU GLU GLU THR ARG GLU SEQRES 2 A 333 LEU GLN SER LEU ALA ALA ALA VAL VAL PRO SER ALA GLN SEQRES 3 A 333 THR LEU LYS ILE THR ASP PHE SER PHE SER ASP PHE GLU SEQRES 4 A 333 LEU SER ASP LEU GLU THR ALA LEU CYS THR ILE ARG MET SEQRES 5 A 333 PHE THR ASP LEU ASN LEU VAL GLN ASN PHE GLN MET LYS SEQRES 6 A 333 HIS GLU VAL LEU CYS ARG TRP ILE LEU SER VAL LYS LYS SEQRES 7 A 333 ASN TYR ARG LYS ASN VAL ALA TYR HIS ASN TRP ARG HIS SEQRES 8 A 333 ALA PHE ASN THR ALA GLN CYS MET PHE ALA ALA LEU LYS SEQRES 9 A 333 ALA GLY LYS ILE GLN ASN LYS LEU THR ASP LEU GLU ILE SEQRES 10 A 333 LEU ALA LEU LEU ILE ALA ALA LEU SER HIS ASP LEU ASP SEQRES 11 A 333 HIS ARG GLY VAL ASN ASN SER TYR ILE GLN ARG SER GLU SEQRES 12 A 333 HIS PRO LEU ALA GLN LEU TYR CYS HIS SER ILE MET GLU SEQRES 13 A 333 HIS HIS HIS PHE ASP GLN CYS LEU MET ILE LEU ASN SER SEQRES 14 A 333 PRO GLY ASN GLN ILE LEU SER GLY LEU SER ILE GLU GLU SEQRES 15 A 333 TYR LYS THR THR LEU LYS ILE ILE LYS GLN ALA ILE LEU SEQRES 16 A 333 ALA THR ASP LEU ALA LEU TYR ILE LYS ARG ARG GLY GLU SEQRES 17 A 333 PHE PHE GLU LEU ILE ARG LYS ASN GLN PHE ASN LEU GLU SEQRES 18 A 333 ASP PRO HIS GLN LYS GLU LEU PHE LEU ALA MET LEU MET SEQRES 19 A 333 THR ALA CYS ASP LEU SER ALA ILE THR LYS PRO TRP PRO SEQRES 20 A 333 ILE GLN GLN ARG ILE ALA GLU LEU VAL ALA THR GLU PHE SEQRES 21 A 333 PHE ASP GLN GLY ASP ARG GLU ARG LYS GLU LEU ASN ILE SEQRES 22 A 333 GLU PRO THR ASP LEU MET ASN ARG GLU LYS LYS ASN LYS SEQRES 23 A 333 ILE PRO SER MET GLN VAL GLY PHE ILE ASP ALA ILE CYS SEQRES 24 A 333 LEU GLN LEU TYR GLU ALA LEU THR HIS VAL SER GLU ASP SEQRES 25 A 333 CYS PHE PRO LEU LEU ASP GLY CYS ARG LYS ASN ARG GLN SEQRES 26 A 333 LYS TRP GLN ALA LEU ALA GLU GLN HET WDB A 901 24 HET ZN A 902 1 HET MG A 903 1 HETNAM WDB (~{E})-3-[2-[(3-CHLOROPHENYL)METHYL]-4-OXIDANYLIDENE- HETNAM 2 WDB 3~{H}-QUINAZOLIN-7-YL]PROP-2-ENOIC ACID HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION FORMUL 2 WDB C18 H13 CL N2 O3 FORMUL 3 ZN ZN 2+ FORMUL 4 MG MG 2+ FORMUL 5 HOH *115(H2 O) HELIX 1 AA1 THR A 537 ALA A 546 1 10 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 LYS A 633 LEU A 638 5 6 HELIX 8 AA8 THR A 639 HIS A 653 1 15 HELIX 9 AA9 TYR A 664 GLU A 669 1 6 HELIX 10 AB1 SER A 679 ASN A 694 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 LEU A 765 1 18 HELIX 14 AB5 SER A 766 LYS A 770 5 5 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 2.22 LINK NE2 HIS A 653 ZN ZN A 902 1555 1555 2.13 LINK OD2 ASP A 654 ZN ZN A 902 1555 1555 2.34 LINK OD1 ASP A 654 MG MG A 903 1555 1555 2.16 LINK OD1 ASP A 764 ZN ZN A 902 1555 1555 2.23 LINK O2 WDB A 901 ZN ZN A 902 1555 1555 2.08 CRYST1 74.090 74.090 131.084 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 0.013497 0.007793 0.000000 0.00000 SCALE2 0.000000 0.015585 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007629 0.00000