SMTL ID : 5olb.1

crystal structure of autotaxin in complex with PF-8380

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- FUC- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC-FUC.1: 4 residues within 4Å: Chain A: W.20, N.22, S.24, G.25 No protein-ligand interaction detected (PLIP)

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.2: 4 residues within 4Å: Chain A: L.345, T.346, A.375, N.379 No protein-ligand interaction detected (PLIP)

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.3: 13 residues within 4Å: Chain A: L.189, E.192, S.193, H.194, G.224, N.405, N.406, P.491, N.492, N.493, G.709, L.710, H.796 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.405, A:N.406

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.280, H.284, H.443 Ligands: 6ZO.14 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.280, A:D.280, A:H.284, A:H.443 ZN.5: 4 residues within 4Å: Chain A: D.140, T.178, D.327, H.328 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.140, A:D.140, A:T.178, A:D.327, A:H.328

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 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.1 CA.9: 1 residues within 4Å: Chain A: Q.440 No protein-ligand interaction detected (PLIP)

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

NA.7: 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.772 NA.11: 6 residues within 4Å: Chain A: N.46, L.47, C.48, K.49, S.50, S.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.46, A:K.49, A:S.50 Water bridges: A:S.245

1 x K: POTASSIUM ION(Non-covalent)

K.8: 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.26

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

CL.10: 4 residues within 4Å: Chain A: G.198, N.199, S.200, R.360 Ligand excluded by PLIP

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.12: 6 residues within 4Å: Chain A: F.179, W.229, G.240, F.242, F.243 Ligands: 6ZO.14 No protein-ligand interaction detected (PLIP)

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

SO4.13: 6 residues within 4Å: Chain A: F.531, D.532, L.533, G.534, C.535, P.619 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.533, A:G.534, A:C.535, A:C.535

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.14: 18 residues within 4Å: Chain A: I.136, S.138, D.140, T.178, F.179, L.182, A.186, L.212, W.229, F.242, F.243, W.244, Y.275, D.280, H.284, H.443 Ligands: ZN.4, PGE.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.178, A:L.212 Hydrogen bonds: A:W.244 Water bridges: A:N.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuttruff, C.A. et al., Discovery of BI-2545: A Novel Autotaxin Inhibitor That Significantly Reduces LPA Levels in Vivo. ACS Med Chem Lett (2017)

Release Date

2018-01-03

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2