SMTL ID : 7faq.1

Crystal structure of PDE5A in complex with inhibitor L1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.91, H.127, D.128, D.238 Ligands: MG.2, SO4.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.91, A:H.127, A:D.128, A:D.238, H2O.1

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: H.127, D.128 Ligands: ZN.1, SO4.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.128, H2O.1, H2O.1, H2O.1, H2O.2

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 8 residues within 4Å: Chain A: Y.86, H.87, H.91, D.128, D.238 Ligands: ZN.1, MG.2, 2OI.4 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.87 Salt bridges: A:H.87, A:H.91

1 x 2OI: 2-[(4-chlorophenyl)methyl]-5-methoxy-3,10-diazatricyclo[6.4.1.0^{4,13}]trideca-1,4(13),5,7-tetraen-9-one(Non-covalent)

2OI.4: 13 residues within 4Å: Chain A: Y.86, D.238, A.241, I.242, Q.249, V.256, A.257, F.260, F.261, M.290, Q.291, F.294 Ligands: SO4.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.86, A:A.241, A:V.256, A:V.256, A:F.260, A:F.294 Hydrogen bonds: A:Y.86, A:Q.291, A:Q.291 pi-Stacking: A:F.260, A:F.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, D. et al., Free energy perturbation (FEP)-guided scaffold hopping. Acta Pharm Sin B (2022)

Release Date

2022-05-18

Peptides

cGMP-specific 3',5'-cyclic phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

cGMP-specific 3',5'-cyclic phosphodiesterase

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