SMTL ID : 4phu.1

Crystal structure of Human GPR40 bound to allosteric agonist TAK-875

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

monomer

Ligands

1 x 2YB: [(3S)-6-({2',6'-dimethyl-4'-[3-(methylsulfonyl)propoxy]biphenyl-3-yl}methoxy)-2,3-dihydro-1-benzofuran-3-yl]acetic acid(Non-covalent)

2YB.1: 15 residues within 4Å: Chain A: P.93, A.96, V.97, F.100, Y.104, L.148, L.151, G.152, F.155, G.156, L.171, W.187, R.196, Y.415, R.433 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.93, A:A.96, A:V.97, A:V.97, A:F.100, A:F.100, A:L.151, A:F.155, A:F.155, A:L.171, A:W.187 Hydrogen bonds: A:Y.415 Salt bridges: A:R.196, A:R.433

5 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)(Non-functional Binders)

OLC.2: 3 residues within 4Å: Chain A: S.198, L.201, F.423 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.201, A:L.201, A:F.423 OLC.3: 2 residues within 4Å: Chain A: F.197 Ligands: OLC.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.197 OLC.4: 12 residues within 4Å: Chain A: P.53, Y.57, G.108, A.112, A.115, A.116, L.119, Y.135, V.139, A.142, L.202, I.210 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.115, A:V.139, A:I.210 OLC.5: 1 residues within 4Å: Ligands: OLC.3 No protein-ligand interaction detected (PLIP) OLC.6: 3 residues within 4Å: Chain A: L.20, L.24, W.442 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.20, A:L.24, A:W.442

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.7: 4 residues within 4Å: Chain A: Q.19, F.22, G.23, L.80 No protein-ligand interaction detected (PLIP)

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.8: 4 residues within 4Å: Chain A: L.409, G.413, P.414, A.417 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Srivastava, A. et al., High-resolution structure of the human GPR40 receptor bound to allosteric agonist TAK-875. Nature (2014)

Release Date

2014-07-16

Peptides

Free fatty acid receptor 1,Lysozyme: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Free fatty acid receptor 1,Lysozyme

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