SMTL ID : 5uoy.1

Crystal structure of human PDE1B catalytic domain in complex with inhibitor 16j (6-(4-Methoxybenzyl)-9-((tetrahydro-2H-pyran-4-yl)methyl)-8,9,10,11-tetrahydropyrido[4',3':4,5]thieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.82, H.118, D.119, D.225 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.82, A:H.118, A:D.119, A:D.225, H2O.1, H2O.3

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.119 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.119, H2O.1, H2O.2, H2O.2, H2O.2, H2O.4

2 x 8HM: 6-[(4-methoxyphenyl)methyl]-9-[(oxan-4-yl)methyl]-8,9,10,11-tetrahydropyrido[4',3':4,5]thieno[3,2-e][1,2,4]triazolo[1,5-c]pyrimidin-5(6H)-one(Non-covalent)

8HM.3: 16 residues within 4Å: Chain A: Y.77, T.126, M.191, I.226, H.228, T.240, L.243, M.244, F.247, S.262, P.263, L.264, T.270, S.275, Q.276, F.279 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.126, A:L.243, A:L.264 Hydrogen bonds: A:Y.77, A:Q.276 pi-Stacking: A:F.247, A:F.247, A:F.279, A:F.279 8HM.4: 6 residues within 4Å: Chain A: Y.5, R.36, T.37, F.40, T.56, M.60 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.36, A:R.36, A:T.56, A:M.60 pi-Stacking: A:F.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dyck, B. et al., Discovery of Selective Phosphodiesterase 1 Inhibitors with Memory Enhancing Properties. J. Med. Chem. (2017)

Release Date

2017-04-26

Peptides

Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B

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