SMTL ID : 9lsl.1

The crystal structure of PDE5A with L1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x 01: (13~{S},15~{R})-15-(3-chloranyl-4-methoxy-phenyl)-12-ethanoyl-8,12,16-triazatetracyclo[7.7.1.0^{2,7}.0^{13,17}]heptadeca-1(17),2,4,6,8-pentaene-4-carbonitrile

01.1: 13 residues within 4Å: Chain A: Y.78, A.233, I.234, Q.241, A.245, V.248, A.249, F.252, F.253, I.279, M.282, Q.283, F.286 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.248, A:F.252, A:M.282, A:F.286, A:F.286 Hydrogen bonds: A:Q.241, A:Q.283, A:Q.283 pi-Stacking: A:F.252, A:F.286 Halogen bonds: A:A.245

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.83, H.119, D.120, D.230 Ligands: MG.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.83, A:H.119, A:D.120, A:D.230, H2O.1

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.120 Ligands: ZN.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.120, H2O.1, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, D. et al., Plasma metabolites-based drug design: Discovery of novel and highly selective phosphodiesterase 5 inhibitors. Chin.Chem.Lett. (2025)

Release Date

2025-06-18

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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