SMTL ID : 4i9z.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

monomer

Ligands

1 x 5BA: 5-bromo-2-{5-[(4-methylpiperazin-1-yl)acetyl]-2-propoxyphenyl}-6-(propan-2-yl)pyrimidin-4(3H)-one(Non-covalent)

5BA.1: 15 residues within 4Å: Chain A: Y.99, L.212, L.252, I.255, A.266, V.269, A.270, F.273, M.303, Q.304, G.306, F.307, A.310, I.311 Ligands: PEG.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.99, A:L.212, A:L.252, A:A.266, A:V.269, A:M.303, A:F.307, A:F.307, A:F.307 Hydrogen bonds: A:Q.304, A:Q.304 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.6

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.141 Ligands: ZN.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.141, H2O.1, H2O.1, H2O.1, H2O.6, H2O.6

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

PEG.4: 4 residues within 4Å: Chain A: G.306, D.309, A.310 Ligands: 5BA.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.310 PEG.5: 6 residues within 4Å: Chain A: S.49, F.51, E.52, P.260, I.261, R.264 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.49, A:S.49, A:R.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gong, X. et al., Exploration of the 5-bromopyrimidin-4(3H)-ones as potent inhibitors of PDE5. Bioorg.Med.Chem.Lett. (2013)

Release Date

2014-01-01

Peptides

cGMP-specific 3',5'-cyclic phosphodiesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

cGMP-specific 3',5'-cyclic phosphodiesterase

Related Entries With Identical Sequence