SMTL ID : 6t8q.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 Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-dimer

Ligands

2 x MVQ: (2~{R})-1-[6-methyl-5-(oxan-4-yl)-7-oxidanylidene-[1,3]thiazolo[5,4-d]pyrimidin-2-yl]-~{N}-(phenylmethyl)pyrrolidine-2-carboxamide(Non-covalent)

MVQ.1: 19 residues within 4Å: Chain A: Q.145, Y.169, S.170, N.229, K.290, F.382, L.409, R.426 Chain B: P.45, I.46, M.49, A.64, G.65, G.66, L.67, Y.101, S.102, P.103, L.320 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:P.45, B:I.46, B:I.46, B:Y.101, A:Y.169, A:L.409 Hydrogen bonds: B:G.66, B:L.67, A:Y.169, A:N.229, A:R.426, A:R.426 Water bridges: B:S.102 pi-Cation interactions: A:R.426 MVQ.12: 19 residues within 4Å: Chain A: P.45, I.46, M.49, A.64, G.65, G.66, L.67, Y.101, S.102, P.103, L.320 Chain B: Q.145, Y.169, S.170, N.229, K.290, F.382, L.409, R.426 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:P.45, A:I.46, A:I.46, A:Y.101, B:Y.169, B:L.409 Hydrogen bonds: A:G.66, A:L.67, B:Y.169, B:Y.169, B:N.229, B:R.426, B:R.426 Water bridges: A:S.102 pi-Cation interactions: B:R.426

16 x CD: CADMIUM ION(Non-covalent)

CD.2: 3 residues within 4Å: Chain A: H.314 Chain B: C.149, E.153 Ligand excluded by PLIP CD.3: 2 residues within 4Å: Chain A: D.196, E.242 Ligand excluded by PLIP CD.4: 3 residues within 4Å: Chain A: E.27, M.28, D.251 Ligand excluded by PLIP CD.5: 2 residues within 4Å: Chain A: D.347, D.351 Ligand excluded by PLIP CD.6: 1 residues within 4Å: Chain A: H.375 Ligand excluded by PLIP CD.7: 3 residues within 4Å: Chain A: L.176, G.180, C.181 Ligand excluded by PLIP CD.8: 1 residues within 4Å: Chain A: D.137 Ligand excluded by PLIP CD.9: 1 residues within 4Å: Chain A: E.309 Ligand excluded by PLIP CD.13: 3 residues within 4Å: Chain A: C.149, E.153 Chain B: H.314 Ligand excluded by PLIP CD.14: 2 residues within 4Å: Chain B: D.196, E.242 Ligand excluded by PLIP CD.15: 3 residues within 4Å: Chain B: E.27, M.28, D.251 Ligand excluded by PLIP CD.16: 2 residues within 4Å: Chain B: D.347, D.351 Ligand excluded by PLIP CD.17: 1 residues within 4Å: Chain B: H.375 Ligand excluded by PLIP CD.18: 3 residues within 4Å: Chain B: L.176, G.180, C.181 Ligand excluded by PLIP CD.19: 1 residues within 4Å: Chain B: D.137 Ligand excluded by PLIP CD.20: 1 residues within 4Å: Chain B: E.309 Ligand excluded by PLIP

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 8 residues within 4Å: Chain A: Q.146, K.150, T.319 Chain B: Q.146, K.150, S.318, T.319 Ligands: CL.21 Ligand excluded by PLIP CL.21: 8 residues within 4Å: Chain A: Q.146, K.150, S.318, T.319 Chain B: Q.146, K.150, T.319 Ligands: CL.10 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 9 residues within 4Å: Chain A: S.62, L.63, A.64, G.65, G.66, L.67 Chain B: S.428, S.430, S.431 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.65, A:L.67, A:L.67 ACT.22: 9 residues within 4Å: Chain A: S.428, S.430, S.431 Chain B: S.62, L.63, A.64, G.65, G.66, L.67 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.65, B:L.67, B:L.67

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
A

Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial

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