SMTL ID : 4olh.2 (1 other biounit)

Human GKRP Bound to AMG5106 and Sorbitol-6-Phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x 2TO: 2-(2-{4-[(6-aminopyridin-3-yl)sulfonyl]piperazin-1-yl}-3,3'-bipyridin-5-yl)-1,1,1,3,3,3-hexafluoropropan-2-ol(Non-covalent)

2TO.1: 22 residues within 4Å: Chain A: Y.36, A.39, V.40, P.41, E.44, K.45, S.46, G.193, S.195, N.221, M.225, A.226, R.227, D.229, H.516, K.526, W.529, R.530, A.533, M.534, R.537 Ligands: IOD.11 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.36, A:V.40, A:A.533 Hydrogen bonds: A:N.221, A:M.225, A:R.537 Halogen bonds: A:R.530, A:R.530

1 x S6P: D-SORBITOL-6-PHOSPHATE(Non-covalent)

S6P.2: 16 residues within 4Å: Chain A: G.119, G.120, T.121, S.122, E.162, E.165, S.191, V.192, G.193, A.196, G.268, S.269, S.270, R.271, H.363, K.526 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.121, A:T.121, A:T.121, A:S.122, A:S.122, A:E.162, A:V.192, A:G.193, A:A.196, A:G.268, A:S.270, A:R.271, A:H.363, A:T.364, A:K.526 Water bridges: A:S.122 Salt bridges: A:K.526

14 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 4 residues within 4Å: Chain A: E.479, Y.480, F.484, I.485 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: L.518, V.613 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: R.85, G.262 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: T.310 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: D.57, A.58, L.508 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: R.161, G.163 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: Q.541, S.542, R.593 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: G.15, K.17, A.566 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain A: E.37, K.45, S.46 Ligands: 2TO.1 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: F.19, K.543 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: L.457, S.470 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: C.205, N.208 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: T.25, E.27 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain A: G.139, L.140, Y.480, E.481 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 6 residues within 4Å: Chain A: G.366, D.519, R.521, K.579, E.580, Q.581 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.519, A:K.579, A:Q.581 Water bridges: A:I.522, A:V.582

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

SO4.18: 4 residues within 4Å: Chain A: D.54, K.55, A.56, D.57 No protein-ligand interaction detected (PLIP) SO4.19: 3 residues within 4Å: Chain A: K.30, L.33, S.34 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.30 SO4.20: 3 residues within 4Å: Chain A: Q.348, T.349, L.376 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.348

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hong, F.T. et al., Small molecule disruptors of the glucokinase-glucokinase regulatory protein interaction: 4. Exploration of a novel binding pocket. J.Med.Chem. (2014)

Release Date

2014-07-23

Peptides

Glucokinase Regulatory Protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Glucokinase Regulatory Protein

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