SMTL ID : 5wbz.1

Structure of human Ketohexokinase complexed with hits from fragment screening

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x A4J: 6-[(3S,4S)-3,4-dihydroxypyrrolidin-1-yl]-2-[(3S)-3-hydroxy-3-methylpyrrolidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile(Non-covalent)

A4J.1: 19 residues within 4Å: Chain A: N.120, N.122, A.239, W.240, A.241, E.242, A.259, P.261, P.262, V.265, T.268, A.271, G.272, F.275, A.300, G.301, C.304 Chain B: D.42 Ligands: SO4.2 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.239, A:A.271, A:F.275 Hydrogen bonds: A:A.241, A:T.268, B:D.42 Water bridges: A:W.240, A:A.241 A4J.4: 15 residues within 4Å: Chain B: A.239, W.240, A.241, E.242, A.259, P.261, P.262, V.265, T.268, A.271, G.272, F.275, A.300, G.301, C.304 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.239, B:A.271, B:F.275 Hydrogen bonds: B:A.241, B:A.241 Water bridges: B:W.240

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

SO4.2: 9 residues within 4Å: Chain A: R.123, T.268, L.269, G.270, A.271, G.272, D.273 Chain B: E.44 Ligands: A4J.1 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.270, A:A.271, A:G.272, A:D.273 Water bridges: A:N.57, A:N.60, A:N.60, B:E.44 Salt bridges: A:R.123 SO4.5: 4 residues within 4Å: Chain B: R.93, R.94, G.308, F.309 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:F.309, B:D.310 Water bridges: B:R.93, B:R.93, B:R.93, B:R.94 Salt bridges: B:R.93, B:R.94 SO4.6: 5 residues within 4Å: Chain A: R.46 Chain B: L.26, H.128, R.156, K.189 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.46, B:H.128, B:R.156, B:K.189

2 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:L.26, A:V.28 Hydrogen bonds: A:G.56, A:N.57, A:S.112 Water bridges: A:N.57, A:N.60 Salt bridges: A:K.189, A:K.189 CIT.7: 6 residues within 4Å: Chain B: F.281, S.282, Q.285, R.287, E.291, F.295 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.281, B:F.295 Hydrogen bonds: B:S.282, B:Q.285, B:R.287 Water bridges: B:F.295, B:F.295 Salt bridges: B:R.287, B:R.287

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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