SMTL ID : 6b97.1 (1 other biounit)

Crystal structure of PDE2 in complex with complex 9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.114, H.150, D.151, D.262 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.114, A:H.150, A:D.151, A:D.262, H2O.1, H2O.4

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: D.151 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.151, H2O.1, H2O.1, H2O.2, H2O.3, H2O.5

1 x CZY: 6-chloro-1-methyl-N-{(1R)-1-[4-(trifluoromethyl)phenyl]ethyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine(Non-covalent)

CZY.3: 12 residues within 4Å: Chain A: H.110, T.222, D.223, L.224, T.259, D.262, L.263, Q.266, Y.281, F.284, F.316, I.320 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.224, A:L.263, A:F.316 Water bridges: A:Q.266 pi-Stacking: A:F.316, A:F.316 Halogen bonds: A:T.259

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 2 residues within 4Å: Chain A: F.26, Q.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.187, A:Q.187 EDO.5: 4 residues within 4Å: Chain A: I.189, N.193, Y.208, L.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.193, A:Y.208, A:Y.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Forster, A.B. et al., The identification of a novel lead class for phosphodiesterase 2 inhibition by fragment-based drug design. Bioorg. Med. Chem. Lett. (2017)

Release Date

2017-11-22

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

cGMP-dependent 3',5'-cyclic phosphodiesterase

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