SMTL ID : 8bpy.1

X-RAY STRUCTURE OF PDE9A IN COMPLEX WITH Inhibitor 13A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.70, H.106, D.107, D.216 Ligands: MG.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.70, A:H.106, A:D.107, A:D.216 ZN.5: 6 residues within 4Å: Chain B: H.66, H.70, H.106, D.107, D.216 Ligands: MG.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.70, B:H.106, B:D.107, B:D.216, B:D.216

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.107, E.136, H.139 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.107, A:D.107 MG.6: 5 residues within 4Å: Chain B: D.107, E.136, T.177, D.216 Ligands: ZN.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.107, B:D.107, B:T.177

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 2 residues within 4Å: Chain A: D.58, Y.60 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.60 NA.7: 4 residues within 4Å: Chain B: H.57, D.58, N.59, Y.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.60, B:Y.60

1 x R4I: (8~{S})-6-[2-(2,3-dihydroindol-1-yl)-2-oxidanylidene-ethyl]-4-(4-methylphenyl)-2-oxidanylidene-8-propyl-1,5,7,8-tetrahydro-1,6-naphthyridine-3-carbonitrile(Non-covalent)

R4I.4: 12 residues within 4Å: Chain A: F.65, M.179, I.217, N.219, L.234, L.235, Y.238, F.255, A.266, Q.267, F.270, V.274 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:M.179, A:I.217, A:L.234, A:L.235, A:Y.238, A:F.255, A:A.266, A:F.270, A:F.270, A:V.274 Hydrogen bonds: A:N.219, A:Q.267, A:Q.267 pi-Stacking: A:F.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meibom, D. et al., BAY-7081: A Potent, Selective, and Orally Bioavailable Cyanopyridone-Based PDE9A Inhibitor. J.Med.Chem. (2022)

Release Date

2022-12-28

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