SMTL ID : 6ezf.1

PDE2 in complex with molecule 5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.123 Ligands: ZN.2, NA.7 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.123, H2O.2, H2O.4, H2O.5, H2O.7, H2O.11

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.86, H.122, D.123, D.234 Ligands: MG.1, NA.7 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.86, A:H.122, A:D.123, A:D.234, H2O.4, H2O.8

1 x C6Z: 6-[(2,4-dichlorophenyl)methyl]pyridazine-3-thiol(Non-covalent)

C6Z.3: 12 residues within 4Å: Chain A: F.133, V.140, A.143, L.144, L.196, Q.238, I.252, Y.253, F.256, M.273, Q.285, F.288 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.144, A:I.252, A:I.252, A:F.256, A:F.256 Hydrogen bonds: A:Q.285 pi-Stacking: A:F.288

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: Y.145, L.200, F.203, H.291, P.295 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.291 GOL.5: 2 residues within 4Å: Chain A: E.290, H.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.290 Water bridges: A:H.291

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 5 residues within 4Å: Chain A: T.32, K.240, G.241, K.243, T.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.241, A:K.243, A:T.244 Water bridges: A:K.243

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 3 residues within 4Å: Chain A: H.82 Ligands: MG.1, ZN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perez-Benito, L. et al., Predicting Binding Free Energies of PDE2 Inhibitors. The Difficulties of Protein Conformation. Sci Rep (2018)

Release Date

2018-04-04

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

cGMP-dependent 3',5'-cyclic phosphodiesterase