SMTL ID : 4px5.2 (1 other biounit)

Human GKRP bound to AMG-0696 and Sorbitol-6-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x 2WZ: N-[(R)-(2-amino-5-chloro-3-fluoropyridin-4-yl){7-[4-(2-hydroxypropan-2-yl)pyridin-2-yl]-1-benzothiophen-2-yl}methyl]cyclopropanesulfonamide(Non-covalent)

2WZ.1: 19 residues within 4Å: Chain A: H.21, Y.36, A.39, V.40, P.41, E.44, G.193, S.195, N.221, M.225, R.227, N.228, D.229, H.516, K.526, W.529, A.533, R.537 Ligands: IOD.11 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.36, A:V.40, A:V.40, A:R.227, A:W.529, A:A.533, A:R.537 Hydrogen bonds: A:Y.36, A:N.221, A:M.225, A:R.227, A:N.228, A:R.537 Water bridges: A:T.43 Halogen bonds: A:K.526

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 23 PLIP interactions: 23 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:S.270, A:S.270, 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:N.524, A:K.526 Salt bridges: A:K.526

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

IOD.3: 5 residues within 4Å: Chain A: F.478, 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: 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: 2 residues within 4Å: Chain A: Q.541, S.542 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: G.15, K.17, R.18, A.566 Ligand excluded by PLIP IOD.11: 5 residues within 4Å: Chain A: E.37, K.45, S.46, R.537 Ligands: 2WZ.1 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain A: K.543 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: L.457, S.470 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: K.176, C.205, N.208 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: E.24, T.25, S.542 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain A: G.139, L.140, Y.480, E.481 Ligand excluded by PLIP IOD.17: 1 residues within 4Å: Chain A: Q.514 Ligand excluded by PLIP IOD.18: 1 residues within 4Å: Chain A: S.34 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 6 residues within 4Å: Chain A: G.366, D.519, R.521, K.579, E.580, Q.581 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.519, A:K.579, A:Q.581 Water bridges: A:R.521, A:I.522, A:V.582 GOL.20: 3 residues within 4Å: Chain A: K.176, C.205, F.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.176, A:K.176

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

SO4.21: 2 residues within 4Å: Chain A: A.56, D.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.56 SO4.22: 4 residues within 4Å: Chain A: Q.348, T.349, I.352, L.376 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.348, A:T.349 SO4.23: 3 residues within 4Å: Chain A: M.248, K.251, K.253 No protein-ligand interaction detected (PLIP) SO4.24: 4 residues within 4Å: Chain A: K.330, S.333, T.334, E.337 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.334, A:E.337

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pennington, L.D. et al., Discovery and Structure Guided Optimization of Diarylmethanesulfonamide Disruptors of GK-GKRP Binding. To be Published

Release Date

2015-05-13

Peptides

Glucokinase regulatory protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Glucokinase regulatory protein

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