SMTL ID : 6l6e.1

Human PDE5 catalytic core in complex with avanafil

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x E6L: 4-[(3-chloranyl-4-methoxy-phenyl)methylamino]-2-[(2S)-2-(hydroxymethyl)pyrrolidin-1-yl]-N-(pyrimidin-2-ylmethyl)pyrimid ine-5-carboxamide(Non-covalent)

E6L.1: 17 residues within 4Å: Chain A: Y.78, L.191, I.195, A.233, I.234, Q.241, A.245, V.248, A.249, F.252, F.253, L.270, I.279, M.282, Q.283, F.286, I.290 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.191, A:I.195, A:A.233, A:I.234, A:L.270, A:M.282 Hydrogen bonds: A:Q.241, A:Q.283 Water bridges: A:F.286, A:F.286 pi-Stacking: A:F.252, A:F.252, A:F.286 Halogen bonds: A:A.245

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.83, H.119, D.120, D.230 Ligands: MG.3, 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.2

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.120 Ligands: ZN.2, SO4.4 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.120, H2O.1, H2O.1, H2O.2, H2O.2, H2O.2

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

SO4.4: 8 residues within 4Å: Chain A: Y.78, H.79, H.83, D.120, D.230, L.231 Ligands: ZN.2, MG.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.78, A:Y.78 Water bridges: A:H.79 Salt bridges: A:H.79, A:H.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsieh, C.M. et al., Structure of Human Phosphodiesterase 5A1 Complexed with Avanafil Reveals Molecular Basis of Isoform Selectivity and Guidelines for Targeting alpha-Helix Backbone Oxygen by Halogen Bonding. J.Med.Chem. (2020)

Release Date

2020-09-02

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

cGMP-specific 3',5'-cyclic phosphodiesterase