SMTL ID : 7s49.1

Crystal Structure of Inhibitor-bound Galactokinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

GLA.1: 14 residues within 4Å: Chain A: R.37, N.39, E.43, H.44, D.46, Y.47, M.180, C.182, G.183, M.185, D.186, Y.236, G.345, G.346 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.43, A:H.44, A:D.46, A:G.183, A:D.186, A:G.346 Water bridges: A:R.37, A:R.37, A:T.45, A:D.186, A:Q.187 Salt bridges: A:R.37 GLA.7: 14 residues within 4Å: Chain B: R.37, N.39, E.43, H.44, D.46, Y.47, M.180, C.182, G.183, M.185, D.186, Y.236, G.345, G.346 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:E.43, B:H.44, B:D.46, B:G.183, B:D.186 Water bridges: B:T.45, B:D.186, B:D.186, B:D.186, B:D.186, B:Q.187, B:G.346 Salt bridges: B:R.37

2 x 4QI: (4R)-2-[(1,3-benzoxazol-2-yl)amino]-4-(4-chloro-1H-pyrazol-5-yl)-4,6,7,8-tetrahydroquinazolin-5(1H)-one(Non-covalent)

4QI.2: 19 residues within 4Å: Chain A: T.61, T.77, S.79, G.81, A.82, D.83, R.105, W.106, Y.109, V.129, S.131, L.135, G.136, S.141, S.142, S.144, L.145, R.228 Ligands: PO4.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.106, A:V.129, A:L.145 Hydrogen bonds: A:R.105, A:S.141 Halogen bonds: A:D.83 4QI.8: 20 residues within 4Å: Chain B: T.61, T.77, S.79, G.81, A.82, D.83, R.105, W.106, Y.109, V.129, S.131, L.135, G.136, S.141, S.142, S.144, L.145, R.228, S.233 Ligands: PO4.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.106, B:V.129, B:L.145 Hydrogen bonds: B:R.105, B:S.141 Halogen bonds: B:D.83

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

PO4.3: 9 residues within 4Å: Chain A: G.136, G.137, G.138, L.139, S.140, S.141, S.142, R.228 Ligands: 4QI.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.136, A:G.136, A:G.138, A:L.139, A:S.140, A:S.141, A:S.142, A:R.228 Water bridges: A:R.37, A:G.137, A:G.138 PO4.4: 4 residues within 4Å: Chain A: H.363, H.367, E.370, H.371 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.363, A:H.367 PO4.5: 2 residues within 4Å: Chain A: Q.172, H.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.172 Salt bridges: A:H.175 PO4.9: 10 residues within 4Å: Chain B: L.135, G.136, G.137, G.138, L.139, S.140, S.141, S.142, R.228 Ligands: 4QI.8 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.136, B:G.138, B:S.140, B:S.141, B:S.141, B:S.142, B:R.228 Water bridges: B:G.137, B:G.137, B:S.142, B:A.143

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

NA.6: 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: 4 residues within 4Å: Chain B: Q.369, Y.372, G.374, T.375 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.369

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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