SMTL ID : 6leh.1

Crystal structure of Autotaxin in complex with an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

NAG-NAG-MAN-MAN-MAN-MAN.1: 14 residues within 4Å: Chain A: L.185, E.188, S.189, H.190, G.220, H.398, N.401, N.402, P.487, N.488, N.489, L.710, H.796 Ligands: EDO.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.188 Water bridges: A:S.189, A:N.401

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

NAG-NAG-MAN.2: 4 residues within 4Å: Chain A: Y.340, L.341, T.342, N.375 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: D.136, T.174, D.276, D.323, H.324 Ligands: SO4.8 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.4: 4 residues within 4Å: Chain A: D.276, H.280, H.439 Ligands: SO4.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.276, A:D.276, A:H.280, A:H.439

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.704, N.706, N.708, L.710, D.712 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.704, A:L.710, A:D.712, H2O.5

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

NA.6: 4 residues within 4Å: Chain A: N.766, D.767, S.769, S.772 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.769 Water bridges: A:S.773

1 x K: POTASSIUM ION(Non-covalent)

K.7: 3 residues within 4Å: Chain A: Y.634, D.637, M.640 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.634, A:D.637, A:M.640, H2O.9

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

SO4.8: 8 residues within 4Å: Chain A: T.174, N.195, L.208, D.276, H.280, H.439 Ligands: ZN.3, ZN.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.174, A:N.195 Salt bridges: A:H.280, A:H.439

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 5 residues within 4Å: Chain A: S.196, M.197, Y.198, V.350, R.358 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: G.194, N.195, R.356 Ligand excluded by PLIP

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

EDO.11: 7 residues within 4Å: Chain A: F.673, P.761, H.762, R.763, D.765, N.766, L.783 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: P.509, R.792, E.795, D.801, Y.810, L.814, K.817 Ligand excluded by PLIP EDO.13: 9 residues within 4Å: Chain A: E.115, I.116, C.159, G.160, Y.455, G.456, F.459, K.460, Y.461 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: G.643, F.644, P.648, Y.649, W.677, Q.681 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: K.386, E.768, S.769, E.782, L.783, M.786 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: R.157, H.162, K.464 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: Y.670, Y.705, Q.719, V.728, P.729, T.730, H.762 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: Q.383, F.385, K.386, L.411, E.413 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: I.357, R.358, Y.367, E.406, D.407, L.408 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: I.589, E.714, Y.720, S.725, P.727 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: G.191, N.402, R.403, R.404 Ligands: NAG-NAG-MAN-MAN-MAN-MAN.1, NAG-NAG-MAN-MAN-MAN-MAN.1 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: L.740, S.754, V.755, L.816, Y.819 Ligands: EDO.25 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain A: L.569, R.711, G.799 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain A: N.339, K.379, K.380 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain A: R.692, S.754, V.755, Y.819, H.821 Ligands: EDO.22, EDO.26 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain A: Y.688, R.692, I.736, S.756, H.821, Y.823 Ligands: EDO.25 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: C.749, D.750, G.751, L.753, T.806, S.807 Ligand excluded by PLIP

1 x EAR: ethyl 2-[2-(4-chlorophenyl)-7-methyl-5-oxidanylidene-imidazo[1,2-a]pyrimidin-8-yl]ethanoate(Non-covalent)

EAR.28: 11 residues within 4Å: Chain A: F.175, L.178, Y.179, L.181, A.182, W.219, F.238, F.239, W.240, A.269, Y.271 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.178, A:W.219, A:F.238, A:F.238, A:A.269, A:Y.271 Hydrogen bonds: A:W.240 pi-Stacking: A:Y.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawaguchi, M. et al., Identification of PotentIn VivoAutotaxin Inhibitors that Bind to Both Hydrophobic Pockets and Channels in the Catalytic Domain. J.Med.Chem. (2020)

Release Date

2020-03-18

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2