SMTL ID : 6t8p.1

HKATII IN COMPLEX WITH LIGAND (2R)-N-benzyl-1-[6-methyl-5-(oxan-4-yl)-7-oxo-6H,7H-[1,3]thiazolo[5,4-d]pyrimidin-2-yl]pyrrolidine-2-carboxamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

4 x MVT: 3,5-bis(fluoranyl)-~{N}-[5-[(2~{R})-2-(3-fluorophenyl)-3-methyl-butyl]-1,3,4-thiadiazol-2-yl]benzenesulfonamide(Non-covalent)

MVT.1: 18 residues within 4Å: Chain A: Q.145, Y.169, N.229, Y.260, K.290, M.381, M.404, L.407, L.409, R.426 Chain B: I.46, M.60, L.63, L.67, P.68, Y.101, L.320 Ligands: MVT.8 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.169, A:L.407, A:L.409, B:I.46, B:L.67, B:Y.101 Hydrogen bonds: A:N.229, A:R.426, A:R.426 Water bridges: B:L.67, B:L.67 MVT.2: 15 residues within 4Å: Chain A: I.46, G.65, G.66, L.67, Y.101, S.102, L.320 Chain B: Q.145, Y.169, S.170, N.229, Y.260, K.290, M.381, R.426 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.101, A:Y.101, A:Y.101, B:Y.169 Hydrogen bonds: A:G.66, B:S.170, B:N.229, B:R.426, B:R.426 Water bridges: A:S.44 MVT.3: 14 residues within 4Å: Chain A: L.117, K.120, L.121, Y.261, F.262, Q.264, K.267, F.268, R.269, E.339, M.343, V.346, D.347, I.350 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.120, A:L.121, A:F.262, A:K.267, A:R.269, A:E.339, A:V.346, A:I.350 Hydrogen bonds: A:R.269, A:R.269 pi-Cation interactions: A:K.120 Halogen bonds: A:L.117, A:E.339 MVT.8: 16 residues within 4Å: Chain B: S.44, I.46, K.58, S.59, M.60, L.63, L.67, Y.101, S.102, P.103, S.104, P.108, Q.316, H.321 Ligands: MVT.1, IOD.9 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:K.58, B:L.67, B:Y.101, B:P.103, B:Q.316 Hydrogen bonds: B:S.104, B:Q.316 Water bridges: B:A.105

7 x IOD: IODIDE ION(Non-functional Binders)

IOD.4: 6 residues within 4Å: Chain A: Q.146, K.150, S.318 Chain B: Q.146, K.150, S.318 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: S.331, Q.332 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: W.113, G.338 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: P.103, S.104 Ligand excluded by PLIP IOD.9: 5 residues within 4Å: Chain B: M.60, R.97, P.103, P.108 Ligands: MVT.8 Ligand excluded by PLIP IOD.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain B: E.83, R.348 Ligands: EDO.13 Ligand excluded by PLIP

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.12: 2 residues within 4Å: Chain B: K.86, E.336 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.336 Water bridges: B:K.86 EDO.13: 6 residues within 4Å: Chain A: N.71, M.72 Chain B: E.83, H.345, R.348 Ligands: IOD.11 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.71, B:R.348, B:R.348 Water bridges: A:K.76 EDO.14: 1 residues within 4Å: Chain B: S.112 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.115, B:Q.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kalliokoski, T. et al., Discovery of sulfonamides and 9-oxo-2,8-diazaspiro[5,5]undecane-2-carboxamides as human kynurenine aminotransferase 2 (KAT2) inhibitors. Bioorg.Med.Chem.Lett. (2020)

Release Date

2020-03-04

Peptides

Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial

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