SMTL ID : 4zg6.2 (1 other biounit)

Structural basis for inhibition of human autotaxin by four novel compounds

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 7 residues within 4Å: Chain A: L.205, P.507, N.508, N.509, D.728, L.730, H.816 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.156, T.194, D.343, H.344 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.156, A:D.156, A:T.194, A:D.343, A:H.344 ZN.3: 4 residues within 4Å: Chain A: D.296, H.300, H.459 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.296, A:D.296, A:H.300, A:H.459

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

NA.4: 4 residues within 4Å: Chain A: N.786, E.787, S.789, S.792 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.792, A:S.792 NA.6: 3 residues within 4Å: Chain A: Y.654, D.657, M.660 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.657, A:M.660

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.724, D.726, D.728, L.730, D.732 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.724, A:D.726, A:D.728, A:L.730, A:D.732, H2O.10

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: K.193, T.194, N.215, L.228, D.296, H.300, H.459 Ligands: ZN.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.194, A:N.215

1 x 4NY: 4-{(Z)-2-[6-chloro-1-(4-fluorobenzyl)-1H-indol-3-yl]-1-cyanoethenyl}benzoic acid(Non-covalent)

4NY.8: 15 residues within 4Å: Chain A: I.152, S.154, T.194, L.198, L.201, A.202, L.228, K.233, F.258, F.259, W.260, V.262, A.289, Y.291, D.343 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.152, A:T.194, A:L.198, A:L.201, A:F.259, A:A.289, A:Y.291, A:Y.291, A:Y.291, A:D.343 Hydrogen bonds: A:W.260 Water bridges: A:K.233 Salt bridges: A:K.233 pi-Stacking: A:F.258, A:Y.291

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

SCN.9: 5 residues within 4Å: Chain A: H.266, F.290, S.292, I.316, I.319 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.294 SCN.10: 3 residues within 4Å: Chain A: L.773, R.828, L.836 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.773 SCN.11: 6 residues within 4Å: Chain A: H.210, G.211, R.237, W.238, G.240, R.424 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.424 Water bridges: A:W.239 SCN.12: 7 residues within 4Å: Chain A: P.191, K.193, G.214, N.215, S.216, V.370, R.376 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.215 SCN.13: 3 residues within 4Å: Chain A: C.141, R.147, P.148 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stein, A.J. et al., Structural Basis for Inhibition of Human Autotaxin by Four Potent Compounds with Distinct Modes of Binding. Mol.Pharmacol. (2015)

Release Date

2015-10-14

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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