SMTL ID : 5xkm.3 (2 other biounits)

Crystal structure of human phosphodiesterase 2A in complex with 6-methyl-N-(1-(4-(trifluoromethoxy)phenyl)propyl)pyrazolo[1,5-a]pyrimidine-3-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.123 Ligands: ZN.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.123, H2O.1, H2O.1, H2O.2, H2O.2, H2O.3 MG.3: 1 residues within 4Å: Chain A: E.211 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.211, A:E.211, H2O.3, H2O.4 MG.5: 2 residues within 4Å: Chain B: D.123 Ligands: ZN.6 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.123, H2O.6, H2O.6, H2O.6, H2O.8, H2O.8

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.86, H.122, D.123, D.234 Ligands: MG.1 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.1, H2O.3 ZN.6: 5 residues within 4Å: Chain B: H.86, H.122, D.123, D.234 Ligands: MG.5 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.86, B:H.122, B:D.123, B:D.234, H2O.6, H2O.7

2 x 87R: 6-methyl-N-[(1R)-1-[4-(trifluoromethyloxy)phenyl]propyl]pyrazolo[1,5-a]pyrimidine-3-carboxamide(Non-covalent)

87R.4: 17 residues within 4Å: Chain A: H.82, T.194, L.196, H.199, T.231, D.234, L.235, Q.238, I.252, Y.253, F.256, M.273, L.284, Q.285, F.288, I.292, I.296 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.196, A:L.235, A:I.252, A:F.256, A:F.288, A:F.288 Water bridges: A:Y.81, A:L.196, A:Q.238 pi-Stacking: A:F.288, A:F.288 Halogen bonds: A:T.231 87R.7: 18 residues within 4Å: Chain B: Y.81, H.82, T.194, L.196, H.199, T.231, D.234, L.235, Q.238, I.252, Y.253, F.256, M.273, L.284, Q.285, F.288, I.292, I.296 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.235, B:I.252, B:F.256, B:F.288 Hydrogen bonds: B:Y.81 Water bridges: B:Q.238 pi-Stacking: B:F.288, B:F.288 Halogen bonds: B:T.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mikami, S. et al., Discovery of an Orally Bioavailable, Brain-Penetrating, in Vivo Active Phosphodiesterase 2A Inhibitor Lead Series for the Treatment of Cognitive Disorders. J. Med. Chem. (2017)

Release Date

2017-08-16

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
F

cGMP-dependent 3',5'-cyclic phosphodiesterase

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