SMTL ID : 7s4c.1

Crystal Structure of Inhibitor-bound Galactokinase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.1: 15 residues within 4Å: Chain A: R.37, N.39, E.43, H.44, T.45, D.46, Y.47, M.180, C.182, G.183, M.185, D.186, Y.236, G.345, G.346 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:E.43, A:H.44, A:D.46, A:G.183, A:G.183, A:D.186, A:Y.236, A:G.346 Water bridges: A:R.37, A:T.45, A:S.140, A:S.140, A:D.186, A:Q.187 Salt bridges: A:R.37 GLA.8: 17 residues within 4Å: Chain B: R.37, N.39, G.42, E.43, H.44, T.45, D.46, Y.47, M.180, C.182, G.183, I.184, M.185, D.186, Y.236, G.345, G.346 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:E.43, B:H.44, B:D.46, B:G.183, B:G.183, B:Y.236, B:G.346 Water bridges: B:R.37, B:T.45, B:S.140, B:S.140, B:E.174, B:G.183, B:D.186, B:Q.187 Salt bridges: B:R.37

3 x V3V: 2-({(4R)-4-(2-chlorophenyl)-2-[(6-fluoro-1,3-benzoxazol-2-yl)amino]-6-methyl-1,4-dihydropyrimidine-5-carbonyl}amino)pyridine-4-carboxylic acid(Non-covalent)

V3V.2: 21 residues within 4Å: Chain A: T.61, T.77, S.79, G.81, A.82, D.83, R.105, W.106, N.108, Y.109, V.129, V.130, S.131, L.135, G.136, S.141, S.142, L.145, A.178, S.233 Ligands: PO4.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.106, A:Y.109, A:L.135 Hydrogen bonds: A:Y.109, A:S.141, A:S.141, A:S.141 Water bridges: A:Y.109, A:Y.109 Salt bridges: A:R.105 Halogen bonds: A:D.83 V3V.3: 26 residues within 4Å: Chain A: L.40, M.55, E.58, K.195, G.196, L.213, S.214, D.215, P.216, L.218, A.219, V.220, A.294, L.295, G.298, Y.300, F.303, L.355, L.380, S.381, Q.382, A.383, A.384 Chain B: S.160, G.161, T.162 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:K.195, A:L.213, A:L.218, A:A.219, A:L.355, A:L.355, A:Q.382, A:Q.382 Hydrogen bonds: A:D.215, A:L.218, A:A.383 pi-Stacking: A:F.303 V3V.9: 22 residues within 4Å: Chain B: T.61, T.77, S.79, G.81, A.82, D.83, R.105, W.106, N.108, Y.109, V.129, V.130, S.131, L.135, G.136, S.141, S.142, S.144, L.145, A.178, S.233 Ligands: PO4.11 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.106, B:Y.109, B:L.135, B:L.135 Hydrogen bonds: B:R.105, B:Y.109, B:S.141, B:S.141, B:S.141 Salt bridges: B:R.105 Halogen bonds: B:D.83

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: Q.369, Y.372, G.374, T.375 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.374 NA.10: 5 residues within 4Å: Chain B: Q.369, Y.372, G.373, G.374, T.375 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.369

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 9 residues within 4Å: Chain A: G.136, G.137, G.138, L.139, S.140, S.141, S.142, R.228 Ligands: V3V.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.136, A:G.138, A:L.139, A:S.140, A:S.141, A:S.141, A:S.141, A:S.142, A:S.142, A:R.228 Water bridges: A:R.37, A:S.140, A:S.140, A:S.140, A:S.140, A:S.142 PO4.6: 4 residues within 4Å: Chain A: H.363, H.367, E.370, H.371 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.370 Salt bridges: A:H.363, A:H.367 PO4.7: 2 residues within 4Å: Chain A: Q.172, H.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.172, A:Q.172 Salt bridges: A:H.175 PO4.11: 8 residues within 4Å: Chain B: G.136, G.137, G.138, L.139, S.140, S.141, S.142 Ligands: V3V.9 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.136, B:G.138, B:L.139, B:S.140, B:S.141, B:S.141, B:S.142, B:S.142 Water bridges: B:R.37, B:S.140, B:S.142, B:D.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L. et al., Structure-Based Optimization of Small Molecule Human Galactokinase Inhibitors. J.Med.Chem. (2021)

Release Date

2021-09-29

Peptides

Galactokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Galactokinase

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