SMTL ID : 5l0k.1 (1 other biounit)

Crystal Structure of Autotaxin and Compound PF-8380

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 9 residues within 4Å: Chain A: L.170, S.174, H.383, P.472, N.473, N.474, D.693, L.695, H.781 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.261, H.265, H.424 Ligands: 6ZO.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.261, A:D.261, A:H.265, A:H.424 ZN.3: 5 residues within 4Å: Chain A: D.121, T.159, D.308, H.309 Ligands: 6ZO.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.121, A:D.121, A:T.159, A:D.308, A:H.309

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.689, N.691, D.693, L.695, D.697 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.689, A:D.693, A:L.695, A:D.697

1 x 6ZO: (3,5-dichlorophenyl)methyl 4-[3-oxo-3-(2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)propyl]piperazine-1-carboxylate(Non-covalent)

6ZO.5: 21 residues within 4Å: Chain A: I.117, S.119, D.121, T.159, F.160, L.163, Y.164, A.167, N.180, W.210, F.223, F.224, W.225, V.227, Y.256, D.261, F.262, H.265, H.424 Ligands: ZN.2, ZN.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.159, A:L.163, A:F.223, A:F.262 Hydrogen bonds: A:N.180, A:W.225 pi-Stacking: A:F.224

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 9 residues within 4Å: Chain A: W.93, D.96, D.97, C.98, E.99, K.140, H.298, R.299, Y.440 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.97, A:D.97, A:E.99, A:Y.440 Salt bridges: A:E.99, A:K.140, A:R.299

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

CL.7: 5 residues within 4Å: Chain A: K.158, G.179, N.180, S.181, R.341 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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