SMTL ID : 4md6.1

Crystal structure of PDE5 in complex with inhibitor 5R

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: H.79, H.83, D.120, D.230, L.231 Ligands: 24E.2, ZN.3, MG.4 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.79, A:D.120 Salt bridges: A:H.79, A:H.83

1 x 24E: 3-(4-HYDROXYBENZYL)-1-(THIOPHEN-2-YL)CHROMENO[2,3-C]PYRROL-9(2H)-ONE(Non-covalent)

24E.2: 14 residues within 4Å: Chain A: L.191, A.233, I.234, Q.241, I.244, V.248, A.249, F.252, F.253, I.279, M.282, Q.283, F.286 Ligands: SO4.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.191, A:A.233, A:V.248, A:I.279, A:M.282, A:F.286 Hydrogen bonds: A:Q.283 pi-Stacking: A:F.252, A:F.252, A:F.286, A:F.286

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: H.83, H.119, D.120, D.230 Ligands: SO4.1, MG.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.4: 3 residues within 4Å: Chain A: D.120 Ligands: SO4.1, ZN.3 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.120, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shang, N.N. et al., Discovery of 3-(4-hydroxybenzyl)-1-(thiophen-2-yl)chromeno[2,3-c]pyrrol-9(2H)-one as a phosphodiesterase-5 inhibitor and its complex crystal structure. Biochem Pharmacol (2014)

Release Date

2014-07-09

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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