SMTL ID : 3shy.1

Crystal structure of the PDE5A1 catalytic domain in complex with novel inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

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

5FO.1: 9 residues within 4Å: Chain A: Y.99, A.266, V.269, A.270, F.273, I.300, M.303, Q.304, F.307 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.99, A:V.269, A:I.300, A:M.303, A:F.307, A:F.307 Hydrogen bonds: A:Q.304, A:Q.304 pi-Stacking: A:F.307 Halogen bonds: A:Y.99

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 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.104, A:H.140, A:D.141, A:D.251, H2O.1

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: H.100, D.141 Ligands: ZN.2 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: P.183, G.184 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: S.54, D.55 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Z. et al., Utilization of Halogen Bond in Lead Optimization: A Case Study of Rational Design of Potent Phosphodiesterase Type 5 (PDE5) Inhibitors. J.Med.Chem. (2011)

Release Date

2011-08-24

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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