SMTL ID : 8c7r.1

Crystal structure of rat autotaxin and compound MEY-003

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 9 residues within 4Å: Chain A: L.220, Y.221, S.224, H.433, P.522, N.523, N.524, L.745, H.831 No protein-ligand interaction detected (PLIP)

1 x T8R: 5,7-bis(oxidanyl)-2-(1-pentylindol-3-yl)chromen-4-one(Non-covalent)

T8R.2: 15 residues within 4Å: Chain A: I.167, L.213, Y.214, L.216, A.217, L.243, W.254, L.259, F.273, F.274, W.275, V.277, Y.306, M.512 Ligands: 5JK.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.167, A:L.213, A:L.213, A:L.213, A:Y.214, A:A.217, A:W.254, A:L.259, A:F.274, A:V.277, A:Y.306 Hydrogen bonds: A:W.275, A:W.275 pi-Stacking: A:F.274, A:F.274, A:Y.306, A:Y.306

1 x 5JK: 7alpha-hydroxycholesterol(Non-covalent)

5JK.3: 17 residues within 4Å: Chain A: L.78, S.81, Y.82, F.210, Y.214, K.248, F.249, H.251, W.254, G.256, P.258, W.260, I.261, F.274, W.275, S.276 Ligands: T8R.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.78, A:K.248, A:F.249, A:F.249, A:H.251, A:W.254, A:W.254, A:W.254, A:P.258, A:W.260, A:I.261, A:F.274, A:F.274, A:F.274

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 3 residues within 4Å: Chain A: D.311, H.315, H.474 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.311, A:D.311, A:H.315, A:H.474 ZN.5: 4 residues within 4Å: Chain A: D.171, T.209, D.358, H.359 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.171, A:T.209, A:D.358, A:H.359

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

IOD.6: 4 residues within 4Å: Chain A: N.230, S.231, V.385, R.391 Ligand excluded by PLIP IOD.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: S.636, A.781, D.782 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: P.787, L.788 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 7 residues within 4Å: Chain A: I.506, E.507, N.524, G.525, T.526, R.825, R.827 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.507, A:N.524, A:T.526 CA.11: 6 residues within 4Å: Chain A: D.739, N.741, D.743, L.745, R.746, D.747 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.739, A:D.743, A:L.745, A:D.747

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eymery, M.C. et al., Discovery of potent chromone-based autotaxin inhibitors inspired by cannabinoids. Eur.J.Med.Chem. (2023)

Release Date

2023-11-22

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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