SMTL ID : 4op3.2 (1 other biounit)

Human GKRP bound to AMG-5112 and Sorbitol-6-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.82 Å

Oligo State

monomer

Ligands

1 x 2UY: (2S)-2-{6'-[(6-aminopyridin-3-yl)sulfonyl]-2'-(phenylamino)-2,3'-bipyridin-5-yl}-1,1,1-trifluoropropan-2-ol(Non-covalent)

2UY.1: 20 residues within 4Å: Chain A: I.23, Y.36, A.39, V.40, P.41, E.44, G.193, L.194, N.221, M.225, A.226, R.227, H.516, K.526, W.529, R.530, A.533, M.534, R.537 Ligands: IOD.11 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.23, A:A.39, A:V.40, A:E.44, A:E.44, A:R.530, A:R.530, A:A.533 Hydrogen bonds: A:N.221, A:M.225, A:A.533, A:R.537 Halogen bonds: A:A.533

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

S6P.2: 15 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, S.269, S.270, R.271, H.363, K.526 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:T.121, A:T.121, A:T.121, A:S.122, A:S.122, A:V.192, A:G.193, A:A.196, A:S.269, A:R.271, A:H.363, A:K.526 Water bridges: A:S.122, A:E.162, A:E.165, A:S.270, A:S.270, A:T.364, A:K.526, A:R.530 Salt bridges: A:K.526

13 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: 1 residues within 4Å: Chain A: V.613 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: R.85, G.262 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: I.307, 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: 4 residues within 4Å: Chain A: G.15, T.16, K.17, R.18 Ligand excluded by PLIP IOD.11: 4 residues within 4Å: Chain A: E.37, S.46, R.537 Ligands: 2UY.1 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain A: K.543 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain A: L.457 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, G.540 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 6 residues within 4Å: Chain A: G.366, D.519, R.521, K.579, E.580, Q.581 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.519, A:K.579, A:Q.581 Water bridges: A:R.521 GOL.17: 5 residues within 4Å: Chain A: K.176, A.179, A.180, N.209, F.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.176

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

SO4.18: 5 residues within 4Å: Chain A: D.54, K.55, A.56, D.57, L.508 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.56 SO4.19: 3 residues within 4Å: Chain A: Q.348, T.349, I.352 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.348

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tamayo, N.A. et al., Small Molecule Disruptors of the Glucokinase-Glucokinase Regulatory Protein Interaction: 5. A Novel Aryl Sulfone Series, Optimization Through Conformational Analysis. J.Med.Chem. (2015)

Release Date

2014-07-30

Peptides

Glucokinase Regulatory Protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Glucokinase Regulatory Protein

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