SMTL ID : 5l0b.1 (1 other biounit)

Crystal Structure of Autotaxin and Compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

monomer

Ligands

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

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1: 17 residues within 4Å: Chain A: L.220, E.223, S.224, H.225, G.255, G.256, Q.257, K.265, H.433, N.436, N.437, P.522, N.523, N.524, D.743, L.745, H.831 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.220

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

NAG.2: 5 residues within 4Å: Chain A: L.376, T.377, N.378, T.406, N.410 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.406 Hydrogen bonds: A:T.377, A:T.377, A:N.410

1 x 6ZM: 1-{2-[(2,3-dihydro-1H-inden-2-yl)amino]-7,8-dihydropyrido[4,3-d]pyrimidin-6(5H)-yl}ethan-1-one(Non-covalent)

6ZM.3: 11 residues within 4Å: Chain A: S.169, F.210, L.213, L.216, F.273, F.274, W.275, V.277, A.304, Y.306, E.308 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.213, A:L.216, A:F.274, A:V.277, A:A.304, A:Y.306 Hydrogen bonds: A:F.273, A:W.275 pi-Stacking: A:F.273, A:Y.306

3 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.171, T.209, D.358, H.359 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.171, A:D.171, A:T.209, A:D.358, A:H.359 ZN.5: 3 residues within 4Å: Chain A: D.311, H.315, H.474 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.311, A:D.311, A:H.315, A:H.474, H2O.9 ZN.6: 5 residues within 4Å: Chain A: D.739, N.741, D.743, L.745, D.747 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.739, A:D.743, A:L.745, A:D.747, H2O.7

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

CL.7: 5 residues within 4Å: Chain A: G.229, N.230, S.231, V.385, R.391 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, S.B. et al., Novel Autotaxin Inhibitors for the Treatment of Osteoarthritis Pain: Lead Optimization via Structure-Based Drug Design. Acs Med.Chem.Lett. (2016)

Release Date

2016-08-10

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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