SMTL ID : 4oex.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

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

5EO.1: 11 residues within 4Å: Chain A: Y.99, H.100, A.266, V.269, A.270, F.273, I.300, M.303, Q.304, F.307, I.311 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.99, A:A.266, A:V.269, A:V.269, A:I.300, A:M.303, A:F.307 Hydrogen bonds: A:Q.304, A:Q.304 Water bridges: A:Q.262 pi-Stacking: A:F.307

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.1

1 x MG: MAGNESIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, J. et al., Thermodynamic and structural characterization of halogen bonding in protein-ligand interactions: a case study of PDE5 and its inhibitors. J.Med.Chem. (2014)

Release Date

2015-04-01

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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