SMTL ID : 7z3l.1

Autotaxin in complex with hybrid compound ziritaxestat (GLPG1690)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose

BMA-MAN-MAN-MAN-MAN-MAN-MAN.1: 17 residues within 4Å: Chain A: L.165, E.168, S.169, H.170, G.171, G.200, G.201, Q.202, K.210, N.381, N.382, R.383, R.384, A.466, P.467 Ligands: NAG.3, GOL.27 No protein-ligand interaction detected (PLIP)

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

NAG.2: 13 residues within 4Å: Chain A: L.165, Y.166, S.169, H.378, P.467, N.468, N.469, D.688, G.689, L.690, H.776 Ligands: NAG.3, GOL.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.467, A:N.469 NAG.3: 11 residues within 4Å: Chain A: L.165, S.169, G.201, L.690 Ligands: BMA-MAN-MAN-MAN-MAN-MAN-MAN.1, BMA-MAN-MAN-MAN-MAN-MAN-MAN.1, BMA-MAN-MAN-MAN-MAN-MAN-MAN.1, BMA-MAN-MAN-MAN-MAN-MAN-MAN.1, BMA-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG.2, GOL.27 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.165

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.256, H.260, H.304, H.419 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.256, A:D.256, A:H.260, A:H.419, H2O.3 ZN.5: 6 residues within 4Å: Chain A: D.116, G.117, T.154, D.303, H.304, H.419 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.116, A:T.154, A:D.303, A:H.304

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.684, N.686, D.688, L.690, D.692 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.684, A:D.688, A:L.690, A:D.692, H2O.1

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

IOD.7: 7 residues within 4Å: Chain A: K.153, G.174, N.175, S.176, V.330, L.334, R.336 Ligand excluded by PLIP IOD.8: 6 residues within 4Å: Chain A: S.176, M.177, Y.178, H.187, V.330, R.338 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: P.99, P.108 Ligand excluded by PLIP IOD.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: K.360 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain A: F.507, L.509, C.511, P.599 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: S.587, P.634, K.637 Ligand excluded by PLIP IOD.14: 6 residues within 4Å: Chain A: P.732, L.733, R.788, E.792, I.793, L.796 Ligand excluded by PLIP IOD.15: 7 residues within 4Å: Chain A: R.539, T.579, S.581, G.674, P.725, A.726, D.727 Ligand excluded by PLIP IOD.16: 6 residues within 4Å: Chain A: R.485, P.486, S.789, Y.790, S.791 Ligands: GOL.26 Ligand excluded by PLIP

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

SCN.17: 5 residues within 4Å: Chain A: I.589, Y.622, G.623, F.624, K.654 No protein-ligand interaction detected (PLIP) SCN.18: 5 residues within 4Å: Chain A: L.23, T.217, F.218, F.219 Ligands: 7NB.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.218 SCN.19: 4 residues within 4Å: Chain A: K.25, S.26, V.222, S.223 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.222 SCN.20: 7 residues within 4Å: Chain A: H.226, F.250, S.252, Q.254, E.275, I.276, T.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.226, A:S.252 Water bridges: A:T.279 SCN.21: 4 residues within 4Å: Chain A: K.440, Y.441, T.443, R.480 No protein-ligand interaction detected (PLIP) SCN.22: 3 residues within 4Å: Chain A: T.552, S.553, I.569 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.553 SCN.23: 5 residues within 4Å: Chain A: P.144, K.444, V.445, P.446, P.447 No protein-ligand interaction detected (PLIP) SCN.24: 5 residues within 4Å: Chain A: Y.550, F.570, R.691, T.693, E.694 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.694 SCN.32: 3 residues within 4Å: Chain A: D.393, R.394, V.425 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.394

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

NA.25: 3 residues within 4Å: Chain A: N.746, D.747, S.752 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.747, A:S.749 Water bridges: A:N.746

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.26: 5 residues within 4Å: Chain A: P.486, T.487, M.488, Y.790 Ligands: IOD.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.488 GOL.27: 7 residues within 4Å: Chain A: P.467 Ligands: BMA-MAN-MAN-MAN-MAN-MAN-MAN.1, BMA-MAN-MAN-MAN-MAN-MAN-MAN.1, BMA-MAN-MAN-MAN-MAN-MAN-MAN.1, BMA-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG.2, NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.467 GOL.28: 14 residues within 4Å: Chain A: C.68, L.69, G.72, D.73, C.74, C.75, T.76, L.231, L.234, Q.235, S.238, G.286, Q.289, L.290 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.68, A:C.74, A:Q.289 GOL.29: 3 residues within 4Å: Chain A: P.144, Y.145, P.447 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.145, A:Y.145 GOL.30: 7 residues within 4Å: Chain A: K.582, S.670, E.671, R.672, N.673, F.722, T.723 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.582, A:N.673 GOL.31: 10 residues within 4Å: Chain A: C.311, T.314, P.331, G.332, H.397, V.398, A.399, V.405, F.415, D.418 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.314

1 x 7NB: 2-[[2-ethyl-8-methyl-6-[4-[2-(3-oxidanylazetidin-1-yl)-2-oxidanylidene-ethyl]piperazin-1-yl]imidazo[1,2-a]pyridin-3-yl]-methyl-amino]-4-(4-fluorophenyl)-1,3-thiazole-5-carbonitrile(Non-covalent)

7NB.33: 23 residues within 4Å: Chain A: L.23, I.112, S.114, T.154, F.155, L.158, Y.159, L.161, A.162, L.188, K.193, F.194, H.196, W.199, P.203, W.205, I.206, F.218, F.219, A.249, Y.251, M.457 Ligands: SCN.18 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.112, A:F.155, A:A.162, A:K.193, A:F.194, A:F.219, A:A.249, A:Y.251 Hydrogen bonds: A:W.205 pi-Stacking: A:F.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salgado-Polo, F. et al., Autotaxin facilitates selective LPA receptor signaling. Cell Chem Biol (2023)

Release Date

2023-01-25

Peptides

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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