SMTL ID : 8c4w.1

Crystal structure of rat autotaxin and compound MEY-002

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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: 10 residues within 4Å: Chain A: L.220, Y.221, S.224, H.433, P.522, N.523, N.524, D.743, L.745, H.831 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: D.311, H.315, H.474 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.311, A:D.311, A:H.315, A:H.474, H2O.9 ZN.3: 4 residues within 4Å: Chain A: D.171, T.209, D.358, H.359 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.171, A:D.171, A:T.209, A:D.358, A:H.359

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

IOD.4: 5 residues within 4Å: Chain A: K.208, G.229, N.230, S.231, R.391 Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain A: M.232, Y.233, R.393 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: N.250, H.251, R.252 Ligand excluded by PLIP IOD.16: 1 residues within 4Å: Chain A: T.52 Ligand excluded by PLIP IOD.17: 4 residues within 4Å: Chain A: F.562, L.564, C.566, P.654 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: G.387, V.453 Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain A: R.746, E.749 Ligand excluded by PLIP IOD.20: 3 residues within 4Å: Chain A: S.636, A.781, D.782 Ligand excluded by PLIP IOD.21: 2 residues within 4Å: Chain A: F.679, Q.716 Ligand excluded by PLIP

6 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.6: 7 residues within 4Å: Chain A: G.226, R.252, W.253, W.254, G.255, N.437, R.439 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.439, A:R.439 SCN.8: 6 residues within 4Å: Chain A: H.281, S.307, Q.309, E.330, I.331, T.334 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.281 SCN.12: 2 residues within 4Å: Chain A: Y.677, K.709 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.709 SCN.13: 6 residues within 4Å: Chain A: Y.552, P.553, I.611, L.612, Y.613, R.657 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.613, A:R.657 SCN.14: 5 residues within 4Å: Chain A: S.663, Q.664, N.665, S.759, S.760 No protein-ligand interaction detected (PLIP) SCN.15: 6 residues within 4Å: Chain A: L.78, W.260, T.272, F.273, F.274 Ligands: 5JK.9 No protein-ligand interaction detected (PLIP)

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

5JK.9: 20 residues within 4Å: Chain A: L.78, S.81, Y.82, F.210, Y.214, K.248, F.249, H.251, W.254, G.255, G.256, P.258, W.260, I.261, F.274, W.275, S.276, V.277 Ligands: TIJ.10, SCN.15 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.78, A:F.210, A:F.249, A:F.249, A:H.251, A:W.254, A:W.254, A:I.261, A:F.274, A:V.277 Hydrogen bonds: A:W.260

1 x TIJ: 5,7-bis(oxidanyl)-2-[1-(phenylmethyl)indol-3-yl]chromen-4-one(Non-covalent)

TIJ.10: 15 residues within 4Å: Chain A: I.167, S.169, F.210, L.213, L.216, A.217, F.273, F.274, W.275, V.277, A.304, Y.306, D.358, M.512 Ligands: 5JK.9 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.167, A:I.167, A:F.210, A:L.213, A:L.216, A:L.216, A:A.217, A:F.274, A:Y.306, A:Y.306, A:D.358 Hydrogen bonds: A:W.275 pi-Stacking: A:F.273, A:Y.306, A:Y.306

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.11: 2 residues within 4Å: Chain A: S.278 Ligands: GOL.22 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.22: 4 residues within 4Å: Chain A: V.277, E.308 Ligands: P6G.11, GOL.23 No protein-ligand interaction detected (PLIP) GOL.23: 2 residues within 4Å: Chain A: F.312 Ligands: GOL.22 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.24: 5 residues within 4Å: Chain A: D.739, N.741, D.743, L.745, D.747 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.739, A:D.743, A:L.745, A:D.747, H2O.8

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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