SMTL ID : 5b25.2 (3 other biounits)

Crystal structure of human PDE1B with inhibitor 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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.1, H2O.1, H2O.2, H2O.7

1 x 4QJ: (11R,15S)-4-{[4-(6-fluoropyridin-2-yl)phenyl]methyl}-8-methyl-5-(phenylamino)-1,3,4,8,10-pentaazatetracyclo[7.6.0.02,6.011,15]pentadeca-2,5,9-trien-7-one(Non-covalent)

4QJ.3: 17 residues within 4Å: Chain A: Y.77, H.78, M.191, F.195, I.226, H.228, L.243, F.247, L.264, V.272, S.275, Q.276, G.278, F.279, F.282, I.283 Ligands: GOL.7 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.243, A:F.247, A:L.264, A:Q.276, A:F.279, A:F.282 Hydrogen bonds: A:Q.276, A:Q.276 pi-Stacking: A:F.279, A:F.279

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: K.199, K.202 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.202, A:K.202 Salt bridges: A:K.199, A:K.202 SO4.5: 2 residues within 4Å: Chain A: W.233, R.331 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.233 Salt bridges: A:R.331

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: R.51, K.53, N.169, E.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.51, A:R.51, A:E.174 GOL.7: 6 residues within 4Å: Chain A: T.126, F.247, S.262, P.263, C.265 Ligands: 4QJ.3 No protein-ligand interaction detected (PLIP) GOL.8: 4 residues within 4Å: Chain A: F.129, T.133, S.135, E.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.133, A:E.136 Water bridges: A:C.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, P. et al., Discovery of Potent and Selective Inhibitors of Phosphodiesterase 1 for the Treatment of Cognitive Impairment Associated with Neurodegenerative and Neuropsychiatric Diseases. J.Med.Chem. (2016)

Release Date

2016-02-03

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

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

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