SMTL ID : 6y5m.1

Crystal structure of mouse Autotaxin in complex with compound 1a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 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: 13 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.706, H.792 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.188 Water bridges: A:N.401

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

NAG.2: 2 residues within 4Å: Chain A: N.18, S.20 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain A: Y.340, L.341, T.342, N.375 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.342, A:T.342, A:N.375 Water bridges: A:N.343

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: PO4.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: 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: PO4.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.276, A:D.276, A:H.280, A:H.439

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.174, A:T.174, A:T.174, A:N.195 Salt bridges: A:H.280, A:H.439

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

CL.7: 4 residues within 4Å: Chain A: N.762, D.763, S.765, S.768 Ligand excluded by PLIP CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x O9W: (~{E})-3-[4-chloranyl-2-[(5-methyl-1,2,3,4-tetrazol-2-yl)methyl]phenyl]-1-[(2~{R})-4-[(4-fluorophenyl)methyl]-2-methyl-piperazin-1-yl]prop-2-en-1-one(Non-covalent)

O9W.8: 14 residues within 4Å: Chain A: S.134, F.175, L.178, Y.179, L.181, A.182, K.213, F.214, W.219, W.225, F.238, F.239, W.240, Y.271 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.175, A:F.175, A:L.178, A:K.213, A:F.214, A:W.219, A:W.219, A:F.239, A:F.239, A:Y.271, A:Y.271, A:Y.271 Hydrogen bonds: A:W.240 pi-Stacking: A:F.238

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

NA.10: 5 residues within 4Å: Chain A: D.700, N.702, N.704, L.706, D.708 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.702, A:N.704, A:L.706, A:D.708 NA.11: 4 residues within 4Å: Chain A: E.553, L.557, Y.574, E.579 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.579 NA.12: 3 residues within 4Å: Chain A: R.127, P.129, S.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.127 Water bridges: A:V.126 NA.13: 4 residues within 4Å: Chain A: Y.170, P.187, L.397, H.398 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.170, A:Y.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomson, C.G. et al., Development of autotaxin inhibitors: A series of tetrazole cinnamides. Bioorg.Med.Chem.Lett. (2021)

Release Date

2020-11-18

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2