SMTL ID : 5wbr.1

Structure of human Ketohexokinase complexed with hits from fragment screening

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

homo-dimer

Ligands

2 x A3Y: 6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-[(3S)-3-(hydroxymethyl)piperidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile(Non-covalent)

A3Y.1: 20 residues within 4Å: Chain A: N.120, N.122, A.239, W.240, A.241, E.242, G.244, P.261, P.262, V.265, T.268, A.271, G.272, F.275, C.297, A.300, G.301, C.304 Chain B: D.42 Ligands: SO4.2 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.239, A:T.268, A:A.271 Hydrogen bonds: A:N.122 Water bridges: A:C.297 Salt bridges: A:E.242, B:D.42 A3Y.4: 19 residues within 4Å: Chain B: A.239, A.241, E.242, G.244, A.259, F.260, P.261, P.262, V.265, T.268, A.271, G.272, F.275, C.297, A.300, G.301, C.304 Ligands: SO4.6, SO4.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.239, B:T.268, B:F.275 Water bridges: B:F.260

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

SO4.2: 10 residues within 4Å: Chain A: R.123, E.188, T.268, L.269, G.270, A.271, G.272, D.273 Chain B: E.44 Ligands: A3Y.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.270, A:A.271, A:G.272, A:D.273 Salt bridges: A:R.123 SO4.5: 5 residues within 4Å: Chain B: R.93, R.94, G.308, F.309, D.310 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.307, B:F.309, B:D.310 Water bridges: B:R.93 Salt bridges: B:R.93, B:R.94 SO4.6: 4 residues within 4Å: Chain B: K.208, A.241, E.242 Ligands: A3Y.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.242, B:E.242 Water bridges: B:K.208, B:K.208 Salt bridges: B:K.208 SO4.7: 5 residues within 4Å: Chain A: R.46 Chain B: L.26, H.128, R.156, K.189 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.128, B:R.156, B:K.189, A:R.46 SO4.8: 7 residues within 4Å: Chain B: T.268, L.269, G.270, A.271, G.272, D.273 Ligands: A3Y.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.270, B:A.271, B:G.272, B:D.273

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 13 residues within 4Å: Chain A: L.26, V.28, D.30, G.55, G.56, N.57, S.112, I.125, L.127, E.154, E.188, K.189 Chain B: E.44 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.28, A:I.125 Hydrogen bonds: A:G.56, A:N.57, A:N.57, A:S.112, A:S.112 Salt bridges: A:K.189, A:K.189

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: W.52, F.86 Chain B: G.81, H.82, V.83 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.82, B:H.82, B:V.83 Water bridges: B:A.84

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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