SMTL ID : 4jib.1

Crystal structure of of PDE2-inhibitor complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.86, H.122, D.123, D.234 Ligands: MG.2 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.14 ZN.4: 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.15, H2O.29 ZN.7: 5 residues within 4Å: Chain C: H.86, H.122, D.123, D.234 Ligands: MG.8 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.86, C:H.122, C:D.123, C:D.234, H2O.29, H2O.42 ZN.10: 5 residues within 4Å: Chain D: H.86, H.122, D.123, D.234 Ligands: MG.11 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.86, D:H.122, D:D.123, D:D.234, H2O.43, H2O.45

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.123 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.123, H2O.5, H2O.7, H2O.14, H2O.14, H2O.15 MG.5: 2 residues within 4Å: Chain B: D.123 Ligands: ZN.4 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.123, H2O.22, H2O.28, H2O.29, H2O.29, H2O.29 MG.8: 3 residues within 4Å: Chain C: D.123, H.156 Ligands: ZN.7 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.123, H2O.30, H2O.41, H2O.41, H2O.41, H2O.42 MG.11: 2 residues within 4Å: Chain D: D.123 Ligands: ZN.10 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:D.123, H2O.45, H2O.54, H2O.55, H2O.55, H2O.56

4 x 1L6: 1-(2-hydroxyethyl)-3-(2-methylbutan-2-yl)-5-[4-(2-methyl-1H-imidazol-1-yl)phenyl]-6,7-dihydropyrazolo[4,3-e][1,4]diazepin-8(1H)-one(Non-covalent)

1L6.3: 14 residues within 4Å: Chain A: Y.81, L.196, L.235, D.237, Q.238, I.248, I.252, Y.253, F.256, M.273, L.284, Q.285, S.287, F.288 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.196, A:L.235, A:F.256, A:F.288, A:F.288, A:F.288 Hydrogen bonds: A:Y.81, A:L.235, A:D.237, A:Q.238, A:Q.238, A:Y.253, A:Q.285, A:Q.285 Water bridges: A:D.237 1L6.6: 14 residues within 4Å: Chain B: Y.81, H.82, L.235, D.237, Q.238, I.248, I.252, Y.253, F.256, M.273, L.284, Q.285, F.288, I.292 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.235, B:F.256, B:F.288, B:F.288, B:I.292 Hydrogen bonds: B:L.235, B:Q.238, B:Q.285, B:Q.285 Water bridges: B:D.237 1L6.9: 14 residues within 4Å: Chain B: Q.17 Chain C: Y.81, H.82, L.196, D.234, L.235, D.237, Q.238, I.248, I.252, F.256, M.273, S.287, F.288 10 PLIP interactions: 1 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:Q.17, C:L.235, C:Q.238 Hydrophobic interactions: C:L.196, C:L.196, C:L.235, C:F.288 Water bridges: C:D.237, C:Q.285, C:Q.285 1L6.12: 12 residues within 4Å: Chain D: Y.81, H.82, L.196, L.235, D.237, Q.238, I.248, I.252, F.256, M.273, S.287, F.288 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.196, D:L.235, D:F.288, D:F.288 Hydrogen bonds: D:Y.81, D:L.235, D:D.237, D:Q.238 Water bridges: D:D.237, D:Q.285, D:Q.285, D:Q.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Plummer, M.S. et al., Discovery of potent, selective, bioavailable phosphodiesterase 2 (PDE2) inhibitors active in an osteoarthritis pain model, Part I: Transformation of selective pyrazolodiazepinone phosphodiesterase 4 (PDE4) inhibitors into selective PDE2 inhibitors. Bioorg.Med.Chem.Lett. (2013)

Release Date

2013-05-01

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

cGMP-dependent 3',5'-cyclic phosphodiesterase

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