SMTL ID : 4gh6.1

Crystal structure of the PDE9A catalytic domain in complex with inhibitor 28

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

3 x LUO: N-(4-methoxyphenyl)-N~2~-[1-(2-methylphenyl)-4-oxo-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl]-L-alaninamide(Non-covalent)

LUO.1: 8 residues within 4Å: Chain A: H.72, M.185, I.223, L.240, Y.244, A.272, Q.273, F.276 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.240, A:L.240, A:F.276 Hydrogen bonds: A:Q.273, A:Q.273 pi-Stacking: A:F.276 LUO.4: 9 residues within 4Å: Chain B: H.72, M.185, I.223, L.240, Y.244, A.272, Q.273, F.276 Ligands: LUO.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.240, B:L.240, B:A.272, B:F.276 Hydrogen bonds: B:Y.244, B:Q.273, B:Q.273 pi-Stacking: B:F.261, B:F.276 LUO.5: 7 residues within 4Å: Chain B: P.260, F.261, T.271, A.272, I.274, G.275 Ligands: LUO.4 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.260, B:F.261, B:I.274 Hydrogen bonds: B:G.275

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.76, H.112, D.113, D.222 Ligands: MG.3 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.6: 4 residues within 4Å: Chain B: H.76, H.112, D.113, D.222 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.76, B:H.112, B:D.222, H2O.1, H2O.1

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.113, H.145 Ligands: ZN.2 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.7: 4 residues within 4Å: Chain B: D.113, H.116, E.142, H.145 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meng, F. et al., Structure-Based Discovery of Highly Selective Phosphodiesterase-9A Inhibitors and Implications for Inhibitor Design. J.Med.Chem. (2012)

Release Date

2012-10-03

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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