SMTL ID : 5vp0.2 (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 2.20 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.2 ZN.4: 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.3, H2O.4

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.123, E.153 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.123, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1 MG.5: 2 residues within 4Å: Chain B: D.123, E.153 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.123, H2O.3, H2O.3, H2O.3, H2O.3, H2O.3

2 x 9GJ: N-{(1S)-1-[3-fluoro-4-(trifluoromethoxy)phenyl]-2-methoxyethyl}-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide(Non-covalent)

9GJ.3: 19 residues within 4Å: Chain A: Y.81, H.82, T.194, L.196, H.199, T.231, D.234, L.235, Q.238, A.249, I.252, Y.253, F.256, M.273, L.284, Q.285, F.288, I.292, I.296 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.235, A:F.288 Hydrogen bonds: A:Q.238, A:Q.285, A:Q.285 Water bridges: A:Y.81 pi-Stacking: A:F.256, A:F.288 9GJ.6: 19 residues within 4Å: Chain B: Y.81, H.82, T.194, L.196, H.199, T.231, D.234, L.235, Q.238, A.249, I.252, Y.253, F.256, M.273, L.284, Q.285, F.288, I.292, I.296 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.235, B:F.288 Hydrogen bonds: B:Q.238, B:Q.285, B:Q.285 Water bridges: B:Y.81 pi-Stacking: B:F.256, B:F.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mikami, S. et al., 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. J. Med. Chem. (2017)

Release Date

2017-08-23

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

cGMP-dependent 3',5'-cyclic phosphodiesterase

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