SMTL ID : 4zg9.2 (1 other biounit)

Structural basis for inhibition of human autotaxin by four novel compounds

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 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: 6 residues within 4Å: Chain A: L.221, P.523, N.524, N.525, L.746, H.832 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.312, H.316, H.475 Ligands: EDO.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.312, A:D.312, A:H.316, A:H.475 ZN.3: 5 residues within 4Å: Chain A: D.172, G.173, T.210, D.359, H.360 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.172, A:T.210, A:D.359, A:D.359, A:H.360

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.740, D.742, D.744, L.746, D.748 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.740, A:D.742, A:L.746, A:D.748, H2O.1

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

NA.5: 3 residues within 4Å: Chain A: Y.670, D.673, M.676 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.670 NA.6: 3 residues within 4Å: Chain A: N.802, S.805, S.808 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.802, A:S.808

2 x 4O2: 3-[(11aS)-6-(4-fluorobenzyl)-1,3-dioxo-5,6,11,11a-tetrahydro-1H-imidazo[1',5':1,6]pyrido[3,4-b]indol-2(3H)-yl]propanoic acid(Non-covalent)

4O2.7: 13 residues within 4Å: Chain A: I.168, S.170, F.211, L.214, Y.215, R.247, F.274, F.275, W.276, V.278, R.285, Y.307, E.309 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.211, A:F.211, A:L.214, A:Y.215, A:F.275 Hydrogen bonds: A:W.276 Salt bridges: A:R.247, A:R.285 pi-Stacking: A:F.275, A:Y.307 4O2.8: 6 residues within 4Å: Chain A: M.233, F.242, K.249, W.254, W.255, R.440 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.242, A:W.254, A:W.254, A:W.254, A:W.255 Hydrogen bonds: A:K.249 pi-Stacking: A:F.242, A:W.254 pi-Cation interactions: A:R.440 Halogen bonds: A:M.233

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 6 residues within 4Å: Chain A: K.209, T.210, N.231, H.316, H.475 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.210, A:T.210, A:N.231, A:N.231

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

Related Entries With Identical Sequence