SMTL ID : 4zga.1

Structural basis for inhibition of human autotaxin by four novel compounds

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain A: L.221, H.434, P.523, N.524, N.525, D.744, L.746, H.832 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: D.312, H.316, H.360, H.475 Ligands: EDO.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.312, A:D.312, A:H.316, A:H.475

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.740, D.742, D.744, L.746, H.747, D.748 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.740, A:D.742, A:D.744, A:L.746, A:D.748 CA.7: 3 residues within 4Å: Chain A: Y.670, D.673, M.676 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.670, A:D.673, A:M.676

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

EDO.4: 7 residues within 4Å: Chain A: D.172, T.210, N.231, D.312, H.316, H.475 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.210, A:N.231 Water bridges: A:D.172, A:T.210

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

SCN.5: 6 residues within 4Å: Chain A: H.282, F.306, S.308, E.331, I.332, I.335 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.308 SCN.6: 5 residues within 4Å: Chain A: P.788, L.789, R.844, E.848, L.852 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.844

1 x ACD: ARACHIDONIC ACID(Non-covalent)

ACD.8: 6 residues within 4Å: Chain A: S.82, K.249, F.250, W.255, W.261, F.275 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.250, A:F.250, A:W.255, A:F.275, A:F.275 Salt bridges: A:K.249

1 x 4O3: (11aS)-6-(4-fluorobenzyl)-5,6,11,11a-tetrahydro-1H-imidazo[1',5':1,6]pyrido[3,4-b]indole-1,3(2H)-dione(Non-covalent)

4O3.9: 10 residues within 4Å: Chain A: I.168, S.170, F.211, L.214, Y.215, W.255, F.274, F.275, W.276, Y.307 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.211, A:L.214, A:L.214, A:Y.215, A:W.255, A:W.255, A:F.275 Hydrogen bonds: A:W.276, A:W.276 pi-Stacking: A:F.211, A:F.274

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
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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