SMTL ID : 3h1v.1

Human glucokinase in complex with a synthetic activator

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

monomer

Ligands

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 15 residues within 4Å: Chain A: S.137, F.138, P.139, T.154, K.155, N.190, D.191, T.192, I.211, G.215, C.216, N.217, E.242, Q.273, E.276 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.154, A:T.154, A:K.155, A:N.190, A:N.190, A:C.216, A:N.217, A:E.242, A:E.242, A:Q.273 Water bridges: A:K.155, A:G.215 Salt bridges: A:K.155

1 x TK1: 1-({5-[4-(methylsulfonyl)phenoxy]-2-pyridin-2-yl-1H-benzimidazol-6-yl}methyl)pyrrolidine-2,5-dione(Non-covalent)

TK1.2: 19 residues within 4Å: Chain A: Y.47, V.48, R.49, S.50, T.51, E.82, G.83, Q.84, I.145, M.196, I.197, Y.200, Y.201, H.204, C.206, M.221, L.437, V.438, V.441 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.145, A:Y.200, A:Y.200, A:V.438, A:V.441, A:V.441 Hydrogen bonds: A:R.49, A:R.49, A:T.51 pi-Stacking: A:Y.200

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

NA.3: 5 residues within 4Å: Chain A: M.224, V.227, V.230, E.231, G.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takahashi, K. et al., The design and optimization of a series of 2-(pyridin-2-yl)-1H-benzimidazole compounds as allosteric glucokinase activators. Bioorg.Med.Chem. (2009)

Release Date

2009-10-06

Peptides

Glucokinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

Glucokinase

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