SMTL ID : 7far.1

Crystal structure of PDE5A in complex with inhibitor L12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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, 2VI.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, 2VI.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.128, H2O.1, H2O.1, H2O.2, H2O.2

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

2VI.3: 18 residues within 4Å: Chain A: Y.86, H.87, L.199, D.238, L.239, A.241, I.242, Q.249, I.252, A.253, V.256, F.260, F.261, M.290, Q.291, F.294 Ligands: ZN.1, MG.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.256, A:M.290, A:F.294, A:F.294, A:F.294 Hydrogen bonds: A:Q.291, A:Q.291 pi-Stacking: A:F.260, A:F.294 Halogen bonds: A:Q.249

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

Related Entries With Identical Sequence