SMTL ID : 5wbm.1

Structure of human Ketohexokinase complexed with hits from fragment screening

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

3 x A4G: [(3R)-1-(5-methyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl]methanol(Non-covalent)

A4G.1: 14 residues within 4Å: Chain A: A.239, A.241, E.242, G.244, A.245, A.259, P.261, T.268, A.271, F.275, C.297, A.300, G.301, C.304 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.239, A:A.259, A:F.275 Hydrogen bonds: A:E.242 A4G.3: 3 residues within 4Å: Chain B: R.92, V.98, W.103 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.92 Water bridges: B:V.98 pi-Stacking: B:W.103, B:W.103, B:W.103 A4G.4: 13 residues within 4Å: Chain B: A.239, A.241, E.242, G.244, A.259, T.268, A.271, G.272, F.275, C.297, A.300, G.301, C.304 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.239, B:F.275, B:A.300 Hydrogen bonds: B:E.242, B:G.244

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 8 residues within 4Å: Chain A: R.123, E.188, T.268, L.269, G.270, A.271, G.272, D.273 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.188, A:G.270, A:A.271, A:G.272, A:D.273 Water bridges: A:N.60, B:E.44 Salt bridges: A:R.123 SO4.5: 5 residues within 4Å: Chain B: R.51, R.93, R.94, G.308, F.309 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:F.309 Water bridges: B:R.51, B:R.51, B:R.54, B:R.93, B:R.93, B:D.310 Salt bridges: B:R.51, B:R.93, B:R.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huard, K. et al., Discovery of Fragment-Derived Small Molecules for in Vivo Inhibition of Ketohexokinase (KHK). J. Med. Chem. (2017)

Release Date

2017-09-13

Peptides

Ketohexokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ketohexokinase

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