SMTL ID : 5lqq.1

Structure of Autotaxin (ENPP2) with LM350

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.1: 15 residues within 4Å: Chain A: L.185, E.188, S.189, H.190, G.220, G.221, Q.222, H.398, N.401, N.402, P.487, N.488, N.489, L.710, H.796 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.185

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: D.276, H.280, H.439 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.3 ZN.3: 5 residues within 4Å: Chain A: D.136, T.174, D.276, D.323, H.324 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.136, A:T.174, A:D.323, A:H.324

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.704, N.706, D.708, L.710, D.712 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.704, A:D.708, A:L.710, A:D.712, H2O.2

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

IOD.5: 3 residues within 4Å: Chain A: G.194, N.195, R.356 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: M.197 Ligand excluded by PLIP IOD.7: 4 residues within 4Å: Chain A: H.246, S.272, I.296, T.299 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: L.529, C.531 Ligand excluded by PLIP IOD.9: 4 residues within 4Å: Chain A: S.601, P.745, A.746, D.747 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: L.753, E.812 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: R.711, T.713, E.714 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: P.506, S.811 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain A: P.128 Ligand excluded by PLIP IOD.14: 2 residues within 4Å: Chain A: K.464, P.466 Ligand excluded by PLIP

1 x 72P: 3-(6-chloranyl-2-methyl-1-phenyl-indol-3-yl)sulfanylbenzoic acid(Non-covalent)

72P.15: 12 residues within 4Å: Chain A: S.46, F.175, Y.179, K.213, F.214, H.216, W.219, W.225, F.239, W.240, S.241, V.242 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.175, A:F.214, A:F.214, A:W.219, A:W.225, A:W.225, A:F.239, A:F.239 Hydrogen bonds: A:S.46, A:W.240, A:V.242 Salt bridges: A:K.213 pi-Stacking: A:W.219, A:W.219, A:W.219

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

NA.16: 4 residues within 4Å: Chain A: Y.634, D.637, K.638, M.640 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.637

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, L.M. et al., Structure-Activity Relationships of Small Molecule Autotaxin Inhibitors with a Discrete Binding Mode. J. Med. Chem. (2017)

Release Date

2016-12-28

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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