SMTL ID : 6b96.2 (1 other biounit)

Crystal Structure of PDE2 in complex with compound 16

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.114, H.150, D.151, D.262 Ligands: MG.2 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.3

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.151 Ligands: ZN.1 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 CZV: 6-chloro-N-{1-[4-(trifluoromethyl)phenyl]cyclopropyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine(Non-covalent)

CZV.3: 15 residues within 4Å: Chain A: H.110, T.222, L.224, T.259, D.262, L.263, Q.266, I.280, Y.281, F.284, Q.313, F.316, I.320, I.324 Ligands: EDO.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.263, A:F.316 Hydrogen bonds: A:Q.266, A:Q.313 Water bridges: A:Y.109 pi-Stacking: A:F.316, A:F.316

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

EDO.4: 4 residues within 4Å: Chain A: T.222, D.223, L.224 Ligands: CZV.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.222, A:L.224

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
B

cGMP-dependent 3',5'-cyclic phosphodiesterase

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