SMTL ID : 3nbw.1

X-ray structure of ketohexokinase in complex with a pyrazole compound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: D.30, G.56, N.57, S.112, I.125, E.154 Chain B: E.44 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.30, A:N.57, A:S.112, A:E.154, B:E.44

3 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 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 SO4.4: 6 residues within 4Å: Chain B: R.93, R.94, Q.307, G.308, F.309, D.310 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.309 Water bridges: B:R.93, B:R.93, B:R.94 Salt bridges: B:R.93, B:R.94 SO4.5: 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

2 x TR4: 5-amino-3-(methylsulfanyl)-1-phenyl-1H-pyrazole-4-carbonitrile(Non-covalent)

TR4.3: 12 residues within 4Å: Chain A: A.241, E.242, G.244, A.259, P.261, V.265, A.271, G.272, F.275, C.297, A.300, C.304 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.242, A:A.259, A:P.261, A:V.265 TR4.6: 14 residues within 4Å: Chain B: A.239, A.241, E.242, G.244, A.259, P.261, P.262, V.265, A.271, G.272, F.275, C.297, A.300, C.304 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.259, B:V.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gibbs, A.C. et al., Electron density guided fragment-based lead discovery of ketohexokinase inhibitors. J.Med.Chem. (2010)

Release Date

2010-12-22

Peptides

Ketohexokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ketohexokinase

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