SMTL ID : 5m7m.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

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.1: 14 residues within 4Å: Chain A: L.221, E.224, S.225, H.226, G.256, H.434, N.437, N.438, P.523, N.524, N.525, L.742, H.828 Ligands: CL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.224, A:N.437

1 x 7HR: ~{N}-[6-[1-[3-(dimethylamino)propylsulfonyl]piperidin-4-yl]-2-ethyl-imidazo[1,2-a]pyridin-3-yl]-4-(4-fluorophenyl)-~{N}-methyl-1,3-thiazol-2-amine(Non-covalent)

7HR.2: 16 residues within 4Å: Chain A: I.168, F.211, L.214, Y.215, L.217, K.249, F.250, H.252, W.255, G.256, G.257, P.259, W.261, F.274, F.275, A.305 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.211, A:L.214, A:L.214, A:F.250, A:W.255, A:W.255, A:F.275, A:A.305 pi-Stacking: A:F.274

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

IOD.3: 4 residues within 4Å: Chain A: G.230, N.231, S.232, R.392 Ligand excluded by PLIP

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

CL.4: 2 residues within 4Å: Chain A: R.439 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: Y.497, R.536 Ligand excluded by PLIP

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

SCN.5: 4 residues within 4Å: Chain A: P.200, K.500, P.502, P.503 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.500

7 x NI: NICKEL (II) ION(Non-covalent)

NI.6: 1 residues within 4Å: Chain A: P.200 No protein-ligand interaction detected (PLIP) NI.14: 1 residues within 4Å: Chain A: Y.711 No protein-ligand interaction detected (PLIP) NI.15: 2 residues within 4Å: Chain A: A.778, D.779 No protein-ligand interaction detected (PLIP) NI.16: 2 residues within 4Å: Chain A: L.785, R.840 No protein-ligand interaction detected (PLIP) NI.17: 4 residues within 4Å: Chain A: D.382, N.400, K.402, Y.403 No protein-ligand interaction detected (PLIP) NI.18: 2 residues within 4Å: Chain A: F.563, L.565 No protein-ligand interaction detected (PLIP) NI.19: 2 residues within 4Å: Chain A: S.673, K.706 No protein-ligand interaction detected (PLIP)

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

PO4.7: 7 residues within 4Å: Chain A: L.623, S.660, Q.661, N.662, S.756, S.757, I.758 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.660, A:N.662, A:S.757, A:S.757

1 x K: POTASSIUM ION(Non-covalent)

K.9: 1 residues within 4Å: Chain A: N.662 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.10: 3 residues within 4Å: Chain A: D.312, H.316, H.475 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.312, A:H.316, A:H.475, H2O.1, H2O.2 ZN.11: 4 residues within 4Å: Chain A: D.172, T.210, D.359, H.360 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.172, A:D.172, A:D.359, A:H.360, H2O.1 ZN.12: 2 residues within 4Å: Chain A: M.233, T.241 No protein-ligand interaction detected (PLIP) ZN.13: 5 residues within 4Å: Chain A: D.736, D.738, D.740, L.742, D.744 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.736, A:D.738, A:D.740, A:L.742, A:D.744

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joncour, A. et al., Discovery, Structure-Activity Relationship, and Binding Mode of an Imidazo[1,2-a]pyridine Series of Autotaxin Inhibitors. 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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