SMTL ID : 4g2y.1

Crystal structure of PDE5A complexed with its inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: H.144, V.147, E.169, D.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.144

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.104, H.140, D.141, D.251 Ligands: MG.3 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.3

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.141 Ligands: ZN.2 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.1, H2O.1, H2O.3, H2O.3, H2O.3

1 x NI5: 2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}-3,5,6,7-tetrahydro-4H-cyclopenta[d]pyrimidin-4-one(Non-covalent)

NI5.4: 13 residues within 4Å: Chain A: Y.99, L.212, L.252, A.254, I.255, Q.262, A.266, V.269, A.270, F.273, Q.304, F.307, I.311 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.254, A:A.266, A:V.269, A:F.307 Hydrogen bonds: A:Q.304, A:Q.304 pi-Stacking: A:F.307

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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