SMTL ID : 5ohi.1

Crystal structure of autotaxin in complex with BI-2545

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

2 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: 3 residues within 4Å: Chain A: W.16, N.18, S.20 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: Y.340, L.341, T.342, N.375 Ligands: P3G.9 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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.3: 15 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, N.704, G.705, L.706, H.792 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.276, H.280, H.439 Ligands: 9V8.12 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.276, A:D.276, A:H.280, A:H.439, H2O.1 ZN.5: 4 residues within 4Å: Chain A: D.136, T.174, D.323, H.324 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.136, A:D.136, A:T.174, A:D.323, H2O.1

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.700, N.702, N.704, L.706, D.708 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.700, A:L.706, A:D.708, H2O.6 CA.11: 2 residues within 4Å: Chain A: N.339 Ligands: P3G.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:N.339

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

NA.7: 4 residues within 4Å: Chain A: N.762, D.763, S.765, S.768 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.765

1 x K: POTASSIUM ION(Non-covalent)

K.8: 3 residues within 4Å: Chain A: Y.630, D.633, M.636 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.630, A:D.633, A:M.636, H2O.18, H2O.19

1 x P3G: 3,6,9,12,15-PENTAOXAHEPTADECANE(Non-covalent)

P3G.9: 7 residues within 4Å: Chain A: S.338, N.339, Y.340, K.379, K.380 Ligands: NAG-NAG.2, CA.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.375

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

CL.10: 3 residues within 4Å: Chain A: G.194, N.195, R.356 Ligand excluded by PLIP

1 x 9V8: [3,5-bis(trifluoromethyl)phenyl]methyl (1~{S},5~{R})-6-[(1~{H}-benzotriazol-5-ylcarbonylamino)methyl]-3-azabicyclo[3.1.0]hexane-3-carboxylate(Non-covalent)

9V8.12: 20 residues within 4Å: Chain A: I.132, S.134, D.136, T.174, F.175, L.178, Y.179, L.181, A.182, N.195, L.208, W.225, F.238, F.239, W.240, Y.271, D.276, H.280, H.439 Ligands: ZN.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.174, A:F.175, A:L.178, A:L.208, A:F.239, A:Y.271 Hydrogen bonds: A:N.195, A:W.240, A:Y.271

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