SMTL ID : 4y8c.1

Crystal structure of phosphodiesterase 9 in complex with (S)-C33

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

49D.1: 11 residues within 4Å: Chain A: F.251, M.365, L.420, L.421, Y.424, F.425, F.441, M.442, A.452, Q.453, F.456 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.420, A:L.420, A:Y.424, A:A.452 Hydrogen bonds: A:A.452, A:Q.453, A:Q.453 pi-Stacking: A:F.441, A:F.456 49D.4: 11 residues within 4Å: Chain B: M.365, I.403, L.420, L.421, Y.424, F.425, F.441, M.442, A.452, Q.453, F.456 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.403, B:L.420, B:L.420, B:A.452, B:F.456 Hydrogen bonds: B:A.452, B:Q.453, B:Q.453 pi-Stacking: B:Y.424, B:F.441, 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 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.256, A:H.292, A:D.293, A:D.402, H2O.1, H2O.1 ZN.5: 6 residues within 4Å: Chain B: H.252, 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: 3 residues within 4Å: Chain A: D.293, H.325 Ligands: ZN.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.293, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Chain B: D.293, H.325 Ligands: ZN.5 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.1, 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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