SMTL ID : 8c3o.1 (1 other biounit)

Crystal structure of autotaxin gamma and compound MEY-003

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 8 residues within 4Å: Chain A: L.221, H.434, P.523, N.524, N.525, L.771, H.857 Ligands: GOL.5 No protein-ligand interaction detected (PLIP)

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

5JK.2: 15 residues within 4Å: Chain A: L.79, S.82, Y.83, Y.215, K.249, F.250, H.252, W.255, P.259, W.261, I.262, F.275, W.276, S.277 Ligands: T8R.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.79, A:F.250, A:H.252, A:W.255, A:W.255, A:W.255, A:W.255, A:P.259, A:I.262, A:F.275, A:F.275 Hydrogen bonds: A:G.257

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

T8R.3: 14 residues within 4Å: Chain A: I.168, F.211, L.214, Y.215, L.217, A.218, W.255, F.274, F.275, W.276, V.278, Y.307, M.513 Ligands: 5JK.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.168, A:F.211, A:L.214, A:Y.215, A:L.217, A:A.218, A:W.255, A:F.274, A:F.275, A:V.278, A:Y.307, A:Y.307 Hydrogen bonds: A:W.276, A:W.276 pi-Stacking: A:F.275

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: P.542, Y.871, P.872 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.542, A:Y.871 GOL.5: 2 residues within 4Å: Ligands: NAG-NAG-BMA.1, NAG-NAG-BMA.1 No protein-ligand interaction detected (PLIP) GOL.6: 5 residues within 4Å: Chain A: P.423, Y.424, L.425, H.428, R.824 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.425, A:H.428, A:R.824 GOL.7: 3 residues within 4Å: Chain A: N.437, N.438, R.439 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.439

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: D.172, D.312, H.316, H.475 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.312, A:D.312, A:H.316, A:H.475 ZN.9: 4 residues within 4Å: Chain A: D.172, T.210, D.359, H.360 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.172, A:D.172, A:T.210, A:D.359, A:H.360

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

IOD.10: 3 residues within 4Å: Chain A: T.84, S.85, C.86 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: G.625, R.626, K.866 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain A: F.803 Ligand excluded by PLIP IOD.13: 4 residues within 4Å: Chain A: Y.631, F.651, H.772, T.774 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain A: P.72 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: S.277, V.279 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain A: E.449, R.450 Ligand excluded by PLIP IOD.17: 4 residues within 4Å: Chain A: F.563, L.565, C.567, P.680 Ligand excluded by PLIP IOD.18: 1 residues within 4Å: Chain A: R.743 Ligand excluded by PLIP IOD.19: 4 residues within 4Å: Chain A: S.668, S.712, S.714, P.715 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain A: K.500, P.502 Ligand excluded by PLIP IOD.21: 1 residues within 4Å: Chain A: G.388 Ligand excluded by PLIP IOD.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.23: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.24: 3 residues within 4Å: Chain A: N.251, H.252, R.253 Ligand excluded by PLIP IOD.25: 2 residues within 4Å: Chain A: P.732, K.735 Ligand excluded by PLIP IOD.26: 3 residues within 4Å: Chain A: K.696, M.701, S.702 Ligand excluded by PLIP IOD.27: 2 residues within 4Å: Chain A: N.231, R.392 Ligand excluded by PLIP IOD.28: 2 residues within 4Å: Chain A: L.814, E.873 Ligand excluded by PLIP IOD.29: 4 residues within 4Å: Chain A: T.660, P.806, A.807, D.808 Ligand excluded by PLIP IOD.30: 3 residues within 4Å: Chain A: S.232, T.241, R.394 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.31: 5 residues within 4Å: Chain A: D.765, D.767, D.769, L.771, D.773 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.765, A:D.767, A:D.769, A:L.771, A:D.773

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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