SMTL ID : 3jsw.2 (1 other biounit)

Human PDE9 in complex with selective inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 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.4 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.11

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.116, E.145 Ligands: ZN.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.116, H2O.2, H2O.3, H2O.5 MG.5: 3 residues within 4Å: Chain B: D.116, E.145 Ligands: ZN.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.116, H2O.8, H2O.8, H2O.11

2 x JAR: 6-[(3S,4S)-1-benzyl-4-methylpyrrolidin-3-yl]-1-(1-methylethyl)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one(Non-covalent)

JAR.3: 9 residues within 4Å: Chain A: M.188, I.226, L.243, L.244, Y.247, F.264, Q.276, F.279, V.283 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.243, A:L.244, A:Y.247, A:V.283 Hydrogen bonds: A:Q.276, A:Q.276 pi-Stacking: A:F.279, A:F.279 JAR.6: 8 residues within 4Å: Chain B: M.188, I.226, L.243, Y.247, F.264, A.275, Q.276, F.279 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.226, B:L.243, B:Y.247, B:A.275 Hydrogen bonds: B:Q.276, B:Q.276 pi-Stacking: B:F.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Verhoest, P.R. et al., Identification of a Brain Penetrant PDE9A Inhibitor Utilizing Prospective Design and Chemical Enablement as a Rapid Lead Optimization Strategy. J.Med.Chem. (2009)

Release Date

2009-12-01

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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