SMTL ID : 4mro.1 (1 other biounit)

Human GKRP bound to AMG-5980 and S6P

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x MG0: 2-(4-{4-[(6-aminopyridin-3-yl)sulfonyl]piperazin-1-yl}phenyl)-1,1,1,3,3,3-hexafluoropropan-2-ol(Non-covalent)

MG0.1: 20 residues within 4Å: Chain A: Y.35, V.39, P.40, E.43, K.44, S.45, G.192, N.220, M.224, A.225, R.226, D.228, H.515, K.525, W.528, R.529, A.532, M.533, R.536 Ligands: IOD.13 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.39, A:V.39, A:E.43, A:A.532 Hydrogen bonds: A:N.220, A:M.224, A:R.536 Water bridges: A:N.227 Salt bridges: A:E.43

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

S6P.2: 15 residues within 4Å: Chain A: G.118, G.119, T.120, S.121, E.161, E.164, S.190, V.191, G.192, A.195, S.268, S.269, R.270, H.362, K.525 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.120, A:T.120, A:S.121, A:S.121, A:V.191, A:G.192, A:A.195, A:S.268, A:S.269, A:R.270, A:H.362, A:K.525 Water bridges: A:E.164, A:S.190 Salt bridges: A:K.525

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

IOD.3: 3 residues within 4Å: Chain A: Y.479, F.483, I.484 Ligand excluded by PLIP IOD.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: R.84, G.261 Ligand excluded by PLIP IOD.6: 3 residues within 4Å: Chain A: A.57, K.329, L.507 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: T.309 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: R.160, G.162 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: G.14, R.17 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: Q.540, S.541, R.592 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: C.204, N.207, W.233 Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: L.456, I.467, S.469 Ligand excluded by PLIP IOD.13: 5 residues within 4Å: Chain A: E.36, K.44, S.45, R.536 Ligands: MG0.1 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 6 residues within 4Å: Chain A: G.14, T.15, F.18, K.542, A.543, I.546 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.542

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

St Jean, D.J. et al., Small molecule disruptors of the glucokinase-glucokinase regulatory protein interaction: 2. Leveraging structure-based drug design to identify analogues with improved pharmacokinetic profiles. J.Med.Chem. (2014)

Release Date

2014-05-07

Peptides

Glucokinase regulatory protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glucokinase regulatory protein

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