SMTL ID : 6cyd.1

PDE2 in complex with compound 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

2 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.5 ZN.6: 4 residues within 4Å: Chain B: H.114, H.150, D.151, D.262 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.114, B:H.150, B:D.151, B:D.262, H2O.8, H2O.11

2 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 MG.7: 1 residues within 4Å: Chain B: D.151 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.151, H2O.8, H2O.8, H2O.8, H2O.9, H2O.13

2 x FKG: 3-(hydroxymethyl)-6-methyl-1-{(1S)-1-[4-(trifluoromethyl)phenyl]ethyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one(Non-covalent)

FKG.3: 17 residues within 4Å: Chain A: Y.109, H.110, T.222, D.223, L.224, T.259, D.262, L.263, Q.266, I.276, I.280, Y.281, F.284, M.301, Q.313, F.316 Ligands: EDO.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.263, A:F.284, A:F.316, A:F.316 Hydrogen bonds: A:L.263, A:Q.266, A:Q.313, A:Q.313 Water bridges: A:Y.109 pi-Stacking: A:F.316 FKG.8: 16 residues within 4Å: Chain B: Y.109, H.110, T.222, D.223, L.224, T.259, D.262, L.263, Q.266, I.276, I.280, Y.281, Q.313, F.316, I.324 Ligands: EDO.9 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.263, B:F.316 Hydrogen bonds: B:Y.109, B:L.263, B:Q.266, B:Q.313, B:Q.313 pi-Stacking: B:F.316

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

EDO.4: 3 residues within 4Å: Chain A: L.228, H.319, I.320 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.319 EDO.5: 4 residues within 4Å: Chain A: T.222, D.223, L.224 Ligands: FKG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.222, A:L.224 Water bridges: A:N.159 EDO.9: 4 residues within 4Å: Chain B: T.222, D.223, L.224 Ligands: FKG.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.223, B:L.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stachel, S.J. et al., Structure-Guided Design and Procognitive Assessment of a Potent and Selective Phosphodiesterase 2A Inhibitor. ACS Med Chem Lett (2018)

Release Date

2018-09-19

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

cGMP-dependent 3',5'-cyclic phosphodiesterase

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