SMTL ID : 4g2w.1

Crystal structure of PDE5A in complex with its inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

monomer

Ligands

1 x NI0: 5,6-diethyl-2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}pyrimidin-4(3H)-one(Non-covalent)

NI0.1: 11 residues within 4Å: Chain A: Y.99, L.252, I.255, A.266, V.269, A.270, F.273, M.303, Q.304, F.307, I.311 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.99, A:A.266, A:V.269, A:A.270, A:F.273, A:M.303, A:F.307, A:F.307 Hydrogen bonds: A:Q.304, A:Q.304 Water bridges: A:Q.262 pi-Stacking: A:F.307

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.141 Ligands: ZN.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.141, H2O.1, H2O.1, H2O.1, H2O.2

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: H.144, V.147, M.168, E.169, D.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.144 Water bridges: A:D.211

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: H.104, H.140, D.141, D.251 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.104, A:H.140, A:D.141, A:D.251, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, G. et al., Design, synthesis, and pharmacological evaluation of monocyclic pyrimidinones as novel inhibitors of PDE5. J.Med.Chem. (2012)

Release Date

2013-06-26

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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