SMTL ID : 6lzz.1

Crystal structure of the PDE9 catalytic domain in complex with inhibitor 4a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.72, H.108, D.109, D.218 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.72, A:H.108, A:D.109, A:D.218, H2O.2 ZN.4: 6 residues within 4Å: Chain B: H.68, H.72, H.108, D.109, D.218 Ligands: MG.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.72, B:H.108, B:D.109, B:D.218, H2O.7

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: H.108, D.109, E.138, H.141 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.109, H2O.1, H2O.1, H2O.2, H2O.3 MG.5: 4 residues within 4Å: Chain B: H.108, D.109, E.138 Ligands: ZN.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.109, H2O.4, H2O.4, H2O.5, H2O.7

2 x EZU: 1-cyclopentyl-6-[[(2R)-1-(2-oxa-6-azaspiro[3.3]heptan-6-yl)-1-oxidanylidene-propan-2-yl]amino]-5H-pyrazolo[3,4-d]pyrimidin-4-one(Non-covalent)

EZU.3: 9 residues within 4Å: Chain A: H.68, M.181, I.219, L.236, Y.240, F.257, A.268, Q.269, F.272 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.236, A:L.236, A:F.272 Hydrogen bonds: A:A.268, A:Q.269, A:Q.269 pi-Stacking: A:F.272 EZU.6: 13 residues within 4Å: Chain A: I.312, A.315, M.316, L.319 Chain B: H.68, M.181, I.219, L.236, Y.240, F.257, A.268, Q.269, F.272 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.219, B:L.236, B:F.257, B:A.268 Hydrogen bonds: B:A.268, B:Q.269, B:Q.269 Water bridges: B:F.272 pi-Stacking: B:F.272

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tian, Y.J. et al., Identification of phosphodiesterase-9 as a novel target for pulmonary arterial hypertension by using highly selective and orally bioavailable inhibitors. To Be Published

Release Date

2021-02-24

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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