SMTL ID : 9lsm.1

The crystal structure of PDE5A with L9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

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

01.1: 10 residues within 4Å: Chain A: Y.78, A.245, V.248, A.249, F.252, I.279, M.282, Q.283, F.286 Ligands: SO4.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.248, A:F.286, A:F.286 Hydrogen bonds: A:Q.283 pi-Stacking: 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: SO4.4 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: 4 residues within 4Å: Chain A: D.120, E.148, H.151 Ligands: SO4.4 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

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

SO4.4: 9 residues within 4Å: Chain A: Y.78, H.79, H.83, D.120, D.230, L.231 Ligands: 01.1, ZN.2, MG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.78 Salt bridges: A:H.79, A:H.83

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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