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

[1,2,4]Triazolo[1,5-a]pyrimidine Phosphodiesterase 2 Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.85, H.121, D.122, D.233 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.85, A:H.121, A:D.122, A:D.233, H2O.1, H2O.5 ZN.5: 5 residues within 4Å: Chain B: H.85, H.121, D.122, D.233 Ligands: MG.6 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.85, B:H.121, B:D.122, B:D.233, H2O.10, H2O.15

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain A: D.122 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.122, H2O.1, H2O.1, H2O.3, H2O.3, H2O.3 MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: D.122 Ligands: ZN.5 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.122, H2O.10, H2O.11, H2O.11, H2O.15, H2O.16

2 x QOQ: 5-[bis(fluoranyl)methyl]-7-[(3~{S})-1-[(2-chloranyl-6-methyl-pyridin-4-yl)methyl]piperidin-3-yl]-[1,2,4]triazolo[1,5-a]pyrimidine(Non-covalent)

QOQ.3: 15 residues within 4Å: Chain A: Y.80, H.81, L.195, D.233, L.234, D.236, Q.237, I.247, I.251, Y.252, F.255, M.272, Q.284, F.287, I.291 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.234, A:I.251, A:F.255, A:F.287 Hydrogen bonds: A:Q.237, A:Q.284 pi-Stacking: A:F.287 Halogen bonds: A:Y.252 QOQ.7: 14 residues within 4Å: Chain B: Y.80, H.81, L.195, D.233, L.234, D.236, Q.237, I.247, I.251, Y.252, F.255, M.272, Q.284, F.287 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.234, B:I.251, B:F.255, B:F.287 Hydrogen bonds: B:Q.237, B:Q.284 pi-Stacking: B:F.287 Halogen bonds: B:L.234, B:D.236, B:Y.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tresadern, G. et al., [1,2,4]Triazolo[1,5- a ]pyrimidine Phosphodiesterase 2A Inhibitors: Structure and Free-Energy Perturbation-Guided Exploration. J.Med.Chem. (2020)

Release Date

2020-11-04

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

cGMP-dependent 3',5'-cyclic phosphodiesterase

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