SMTL ID : 8w4t.1

Crystal structure of PDE5A in complex with a novel inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.104, H.140, D.141, D.251 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.104, A:H.140, A:D.141, A:D.251, H2O.1, H2O.1

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: H.140, D.141 Ligands: ZN.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.141, A:D.141, H2O.1, H2O.1, H2O.2

1 x VZF: 2-[bis(2-hydroxyethyl)amino]-6-[(4-methoxyphenyl)methylamino]-9-propan-2-yl-7~{H}-purin-8-one(Non-covalent)

VZF.3: 14 residues within 4Å: Chain A: Y.99, L.252, A.254, I.255, Q.262, A.266, V.269, A.270, F.273, F.274, I.300, M.303, Q.304, F.307 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.252, A:M.303, A:F.307 Hydrogen bonds: A:L.252, A:A.254, A:I.255, A:Q.262, A:Q.304, A:Q.304 Water bridges: A:Y.99 pi-Stacking: A:F.273, A:F.273, A:F.307, A:F.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Drug repurposing and structure-based discovery of new PDE4 and PDE5 inhibitors. Eur.J.Med.Chem. (2023)

Release Date

2023-11-22

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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