SMTL ID : 4g2j.3 (2 other biounits)

Human pde9 in complex with selective compound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.79, H.115, D.116, D.225 Ligands: MG.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.79, A:H.115, A:D.116, A:D.225, H2O.2 ZN.4: 5 residues within 4Å: Chain B: H.79, H.115, D.116, D.225 Ligands: MG.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.79, B:H.115, B:D.116, B:D.225, H2O.14

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.116, H.148 Ligands: ZN.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.116, H2O.2, H2O.2, H2O.3, H2O.4 MG.5: 3 residues within 4Å: Chain B: D.116, H.148 Ligands: ZN.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.116, H2O.10, H2O.11, H2O.12, H2O.13

2 x 0WF: 1-cyclopentyl-6-[(1R)-1-(3-phenoxyazetidin-1-yl)ethyl]-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one(Non-covalent)

0WF.3: 15 residues within 4Å: Chain A: F.74, H.75, M.188, I.226, N.228, V.240, L.243, L.244, Y.247, F.264, A.275, Q.276, G.278, F.279, V.283 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.226, A:Y.247, A:A.275, A:F.279, A:V.283 Hydrogen bonds: A:Q.276, A:Q.276 pi-Stacking: A:F.279 0WF.6: 11 residues within 4Å: Chain B: F.74, H.75, M.188, I.226, L.243, Y.247, F.264, A.275, Q.276, F.279, V.283 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.247, B:F.264, B:A.275, B:F.279 Hydrogen bonds: B:Y.247, B:Q.276, B:Q.276 pi-Stacking: B:F.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Claffey, M.M. et al., Application of structure-based drug design and parallel chemistry to identify selective, brain penetrant, in vivo active phosphodiesterase 9A inhibitors. J.Med.Chem. (2012)

Release Date

2013-05-29

Peptides

High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A

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