SMTL ID : 5mhp.1

Novel Imidazo[1,2-a]pyridine Derivatives with Potent Autotaxin/ENPP2 Inhibitor Activity

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

monomer

Ligands

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-(1-6)-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-MAN.1: 17 residues within 4Å: Chain A: L.221, E.224, S.225, H.226, G.256, G.257, Q.258, N.437, N.438, A.522, P.523, N.524, N.525, D.740, G.741, L.742, H.828 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.257

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

NAG.2: 4 residues within 4Å: Chain A: L.377, T.378, A.407, N.411 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.407 Hydrogen bonds: A:T.378, A:T.378, A:T.378

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: D.172, T.210, D.359, H.360 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.172, A:D.172, A:T.210, A:D.359, A:H.360 ZN.4: 4 residues within 4Å: Chain A: D.312, H.316, H.475 Ligands: PO4.13 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.312, A:D.312, A:H.316, A:H.475

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.736, D.738, D.740, L.742, D.744 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.738, A:D.740, A:L.742, A:D.744, H2O.5

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: Y.666, D.669, M.672 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:Y.666, A:D.669, A:M.672, H2O.5, H2O.6, H2O.6

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.7: 4 residues within 4Å: Chain A: G.230, N.231, S.232, R.392 Ligand excluded by PLIP

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

CL.8: 3 residues within 4Å: Chain A: P.784, L.785, R.840 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: S.633, A.778, D.779 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: C.157, F.161, R.163, P.164 Ligand excluded by PLIP

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.11: 3 residues within 4Å: Chain A: K.500, V.501, P.502 No protein-ligand interaction detected (PLIP)

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

PO4.12: 6 residues within 4Å: Chain A: F.563, D.564, L.565, G.566, C.567, P.651 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.565, A:C.567, A:C.567 PO4.13: 7 residues within 4Å: Chain A: T.210, N.231, L.244, D.312, H.316, H.475 Ligands: ZN.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.210, A:N.231 Salt bridges: A:H.316, A:H.475

1 x 7NB: 2-[[2-ethyl-8-methyl-6-[4-[2-(3-oxidanylazetidin-1-yl)-2-oxidanylidene-ethyl]piperazin-1-yl]imidazo[1,2-a]pyridin-3-yl]-methyl-amino]-4-(4-fluorophenyl)-1,3-thiazole-5-carbonitrile(Non-covalent)

7NB.14: 18 residues within 4Å: Chain A: I.168, S.170, T.210, F.211, L.214, Y.215, K.249, F.250, H.252, W.255, P.259, W.261, F.274, F.275, W.276, A.305, F.306, Y.307 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.210, A:F.211, A:L.214, A:F.250, A:F.275, A:F.275 Hydrogen bonds: A:W.255 pi-Stacking: A:F.274 pi-Cation interactions: A:W.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Desroy, N. et al., Discovery of 2-[[2-Ethyl-6-[4-[2-(3-hydroxyazetidin-1-yl)-2-oxoethyl]piperazin-1-yl]-8-methylimidazo[1,2-a]pyridin-3-yl]methylamino]-4-(4-fluorophenyl)thiazole-5-carbonitrile (GLPG1690), a First-in-Class Autotaxin Inhibitor Undergoing Clinical Evaluation for the Treatment of Idiopathic Pulmonary Fibrosis. J. Med. Chem. (2017)

Release Date

2017-08-30

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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