SMTL ID : 5vp1.1 (1 other biounit)

Discovery of Clinical Candidate N-{(1S)-1-[3-Fluoro-4-(trifluoromethoxy)phenyl]-2-methoxyethyl}-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide (TAK-915), A Highly Potent, Selective, and Brain-Penetrating Phosphodiesterase 2A Inhibitor for the Treatment of Cognitive Disorders

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.86, H.122, D.123, D.234 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.86, A:H.122, A:D.123, A:D.234, H2O.1, H2O.1 ZN.5: 4 residues within 4Å: Chain B: H.86, H.122, D.123, D.234 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.86, B:H.122, B:D.123, B:D.234, H2O.5, H2O.6

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: D.123 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.123, H2O.1, H2O.1, H2O.1, H2O.2, H2O.3 MG.3: 1 residues within 4Å: Chain A: E.211 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.211, A:E.211, H2O.2, H2O.4, H2O.4 MG.6: 1 residues within 4Å: Chain B: D.123 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.123, H2O.5, H2O.5, H2O.5, H2O.5, H2O.7

2 x 9GA: N-{(1S)-2-hydroxy-2-methyl-1-[4-(trifluoromethoxy)phenyl]propyl}-6-methyl-5-(3-methyl-1H-1,2,4-triazol-1-yl)pyrazolo[1,5-a]pyrimidine-3-carboxamide(Non-covalent)

9GA.4: 18 residues within 4Å: Chain A: Y.81, H.82, T.194, L.196, H.199, T.231, D.234, L.235, Q.238, I.252, Y.253, F.256, M.273, L.284, Q.285, F.288, I.292, I.296 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.196, A:L.235, A:F.256, A:L.284, A:F.288 Hydrogen bonds: A:Y.81, A:Q.285 Water bridges: A:L.196, A:Q.238, A:F.288 pi-Stacking: A:F.256, A:F.288, A:F.288 Halogen bonds: A:T.231 9GA.7: 18 residues within 4Å: Chain B: Y.81, H.82, T.194, L.196, H.199, T.231, D.234, L.235, Q.238, I.252, Y.253, F.256, M.273, L.284, Q.285, F.288, I.292, I.296 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.196, B:L.235, B:F.288 Hydrogen bonds: B:Q.238, B:Q.285 Water bridges: B:L.196 pi-Stacking: B:F.288, B:F.288 Halogen bonds: B:T.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mikami, S. et al., Discovery of a Novel Series of Pyrazolo[1,5-a]pyrimidine-Based Phosphodiesterase 2A Inhibitors Structurally Different from N-((1S)-1-(3-Fluoro-4-(trifluoromethoxy)phenyl)-2-methoxyethyl)-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide (TAK-915), for the Treatment of Cognitive Disorders. Chem. Pharm. Bull. (2017)

Release Date

2017-12-27

Peptides

cGMP-dependent 3',5'-cyclic phosphodiesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

cGMP-dependent 3',5'-cyclic phosphodiesterase

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