SMTL ID : 3k3h.2 (1 other biounit)

Crystal structure of the PDE9A catalytic domain in complex with (S)-BAY73-6691

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.76, H.112, D.113, D.222 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.76, A:H.112, A:D.113, A:D.222, H2O.1, H2O.1 ZN.4: 5 residues within 4Å: Chain B: H.76, H.112, D.113, D.222 Ligands: MG.5 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.76, B:H.112, B:D.113, B:D.222, H2O.1, H2O.1

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.113, E.142, H.145 Ligands: ZN.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.113, H2O.1, H2O.1, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain B: D.113, H.145 Ligands: ZN.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.113, H2O.1, H2O.1, H2O.1, H2O.1

2 x BYE: 1-(2-chlorophenyl)-6-[(2S)-3,3,3-trifluoro-2-methylpropyl]-1,7-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one(Non-covalent)

BYE.3: 11 residues within 4Å: Chain A: H.72, M.185, I.223, N.225, L.240, L.241, Y.244, F.261, A.272, Q.273, F.276 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.240, A:Y.244, A:F.276 Hydrogen bonds: A:Q.273 pi-Stacking: A:F.276 BYE.6: 11 residues within 4Å: Chain B: H.72, M.185, I.223, N.225, L.240, L.241, Y.244, F.261, A.272, Q.273, F.276 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.240 Hydrogen bonds: B:Q.273 pi-Stacking: B:F.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Insight into Binding of Phosphodiesterase-9A Selective Inhibitors by Crystal Structures and Mutagenesis. J.Med.Chem. (2010)

Release Date

2010-02-16

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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