SMTL ID : 4y87.1

Crystal structure of phosphodiesterase 9 in complex with (R)-C33 (6-{[(1R)-1-(4-chlorophenyl)ethyl]amino}-1-cyclopentyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-dimer

Ligands

2 x 49E: 6-{[(1R)-1-(4-chlorophenyl)ethyl]amino}-1-cyclopentyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one(Non-covalent)

49E.1: 7 residues within 4Å: Chain A: H.252, M.365, L.420, Y.424, A.452, Q.453, F.456 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.420, A:Y.424, A:A.452, A:F.456 Hydrogen bonds: A:A.452, A:Q.453, A:Q.453 pi-Stacking: A:F.456 49E.4: 9 residues within 4Å: Chain B: F.251, M.365, I.403, L.420, Y.424, F.441, A.452, Q.453, F.456 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.424, B:F.441, B:F.441, B:A.452, B:F.456 Hydrogen bonds: B:A.452, B:Q.453, B:Q.453 pi-Stacking: B:F.456

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.256, H.292, D.293, D.402 Ligands: MG.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.256, A:H.292, A:D.293, A:D.402, H2O.1 ZN.5: 5 residues within 4Å: Chain B: H.256, H.292, D.293, D.402 Ligands: MG.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.256, B:H.292, B:D.293, B:D.402, H2O.1

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: H.292, D.293, H.325 Ligands: ZN.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.293, H2O.1, H2O.1, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain B: D.293, E.322, H.325 Ligands: ZN.5 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.293, H2O.1, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, M. et al., Structural Asymmetry of Phosphodiesterase-9A and a Unique Pocket for Selective Binding of a Potent Enantiomeric Inhibitor. Mol.Pharmacol. (2015)

Release Date

2015-09-16

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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