SMTL ID : 4ly9.2 (1 other biounit)

Human GKRP complexed to AMG-1694 [(2R)-1,1,1-trifluoro-2-{4-[(2S)-2-{[(3S)-3-methylmorpholin-4-yl]methyl}-4-(thiophen-2-ylsulfonyl)piperazin-1-yl]phenyl}propan-2-ol] and sorbitol-6-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

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

IOD.1: 5 residues within 4Å: Chain A: F.478, E.479, Y.480, F.484, I.485 Ligand excluded by PLIP IOD.2: 2 residues within 4Å: Chain A: C.610, V.613 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain A: R.85, G.262 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: T.310, I.485 Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain A: A.58, L.508 Ligands: SO4.18 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: R.161, G.163 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: Q.541, S.542 Ligand excluded by PLIP IOD.8: 5 residues within 4Å: Chain A: G.15, T.16, K.17, R.18, A.566 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: C.205, N.208 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: L.457, S.470 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: S.34 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain A: K.176 Ligand excluded by PLIP IOD.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: T.16, F.19, K.543 Ligand excluded by PLIP

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

S6P.15: 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 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: 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:S.269, A:S.270, A:R.271, A:K.526 Water bridges: A:S.191, A:S.270, A:T.364, A:K.526, A:K.526 Salt bridges: A:K.526

1 x 1YY: (2R)-1,1,1-trifluoro-2-{4-[(2S)-2-{[(3S)-3-methylmorpholin-4-yl]methyl}-4-(thiophen-2-ylsulfonyl)piperazin-1-yl]phenyl}propan-2-ol(Non-covalent)

1YY.16: 19 residues within 4Å: Chain A: H.21, V.22, I.23, Y.36, V.40, P.41, E.44, K.45, S.46, G.193, M.225, R.227, H.516, K.526, W.529, R.530, A.533, Q.536, R.537 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.40, A:P.41, A:E.44, A:R.227, A:R.227, A:A.533 Hydrogen bonds: A:I.23, A:R.537 Water bridges: A:D.229 Salt bridges: A:E.44

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 7 residues within 4Å: Chain A: F.127, S.130, V.131, N.134, Y.146, T.147, Y.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.127, A:N.134, A:T.147, A:T.147

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

SO4.18: 4 residues within 4Å: Chain A: S.333, T.334, E.337 Ligands: IOD.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.333 SO4.19: 3 residues within 4Å: Chain A: K.55, A.56, D.57 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lloyd, D.J. et al., Antidiabetic effects of glucokinase regulatory protein small-molecule disruptors. Nature (2013)

Release Date

2013-11-20

Peptides

Glucokinase regulatory protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Glucokinase regulatory protein

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