SMTL ID : 5lia.1

Crystal structure of murine autotaxin in complex with a small molecule inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.1: 14 residues within 4Å: Chain A: L.185, E.188, S.189, H.190, G.220, N.401, N.402, P.487, N.488, N.489, N.704, L.706, H.792 Ligands: EDO.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.188, A:E.188 Water bridges: A:N.401

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

NAG.2: 3 residues within 4Å: Chain A: L.341, T.342, N.375 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.342, A:T.342, A:N.375

1 x 6XN: ~{N}-[(1~{S})-1-(4-chlorophenyl)ethyl]-3-[3-[[4-(trifluoromethyloxy)phenyl]methyl]imidazo[4,5-b]pyridin-2-yl]propanamide(Non-covalent)

6XN.3: 16 residues within 4Å: Chain A: I.132, S.134, F.175, L.178, Y.179, L.181, A.182, K.213, F.214, W.219, F.238, F.239, W.240, V.242, Y.271 Ligands: EDO.12 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.175, A:L.178, A:L.178, A:K.213, A:F.214, A:F.214, A:W.219, A:V.242, A:Y.271, A:Y.271 Hydrogen bonds: A:W.240 pi-Stacking: A:F.175, A:F.238, A:F.239 pi-Cation interactions: A:K.213 Halogen bonds: A:K.213

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain A: D.136, T.174, D.276, D.323, H.324 Ligands: SO4.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.136, A:D.136, A:T.174, A:D.323, A:H.324 ZN.5: 4 residues within 4Å: Chain A: D.276, H.280, H.439 Ligands: SO4.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.276, A:D.276, A:H.280, A:H.439

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

SO4.6: 11 residues within 4Å: Chain A: D.136, K.173, T.174, N.195, L.208, D.276, H.280, H.324, H.439 Ligands: ZN.4, ZN.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.174, A:T.174, A:N.195 Salt bridges: A:H.324, A:H.439

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 5 residues within 4Å: Chain A: D.700, N.702, N.704, L.706, D.708 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.700, A:L.706, A:D.708, H2O.5

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 4 residues within 4Å: Chain A: N.762, D.763, S.765, S.768 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.768 Water bridges: A:S.769

1 x K: POTASSIUM ION(Non-covalent)

K.9: 3 residues within 4Å: Chain A: Y.630, D.633, M.636 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.630, A:D.633, A:M.636, H2O.12

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 8 residues within 4Å: Chain A: A.668, F.669, V.672, P.757, R.759, D.761, N.762, L.779 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.759, A:R.759 EDO.11: 6 residues within 4Å: Chain A: G.191, N.402, R.403, R.404 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.402, A:R.403 Water bridges: A:H.190, A:R.404 EDO.12: 6 residues within 4Å: Chain A: F.214, H.216, W.219, W.225, F.239 Ligands: 6XN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shah, P. et al., Discovery of potent inhibitors of the lysophospholipase autotaxin. Bioorg. Med. Chem. Lett. (2016)

Release Date

2016-11-09

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2