SMTL ID : 6ty5.2 (1 other biounit)

Crystal structure of human TLR8 in complex with Compound 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

monomer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: 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.1: 14 residues within 4Å: Chain A: K.200, F.202, S.204, L.224, D.226, S.228, Y.265, N.267, D.436, H.438, S.439, N.440, F.441, Y.442 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.224, A:Y.265 Hydrogen bonds: A:H.438 NAG-NAG-BMA-MAN-MAN.3: 9 residues within 4Å: Chain A: Q.452, Y.508, V.532, D.534, S.536, V.562, N.564, E.586, V.588 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.452, A:Q.452 Hydrophobic interactions: A:V.532

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.2: 10 residues within 4Å: Chain A: S.400, I.449, K.450, D.461, S.463, L.464, N.485, S.487, Y.508, D.510 No protein-ligand interaction detected (PLIP)

2 x O0W: 5-methyl-7-(7-methyl-2-piperidin-4-yl-indazol-5-yl)furo[3,2-c]pyridin-4-one(Non-covalent)

O0W.4: 11 residues within 4Å: Chain A: F.235, F.320, Y.322, I.323, K.324, G.325, S.326, V.352, I.377, F.379, E.401 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.235, A:F.320, A:Y.322, A:F.379 Hydrogen bonds: A:G.325 pi-Stacking: A:Y.322, A:F.379 O0W.11: 8 residues within 4Å: Chain A: F.468, F.469, S.490, A.492, Q.493, V.494, R.515, Y.541 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.492, A:Y.541 Water bridges: A:Y.541 pi-Stacking: A:F.468, A:F.469

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

NAG.5: 2 residues within 4Å: Chain A: S.496, N.520 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.520 NAG.6: 4 residues within 4Å: Chain A: N.630, L.634, N.654, L.657 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.630 NAG.7: 5 residues within 4Å: Chain A: L.341, S.342, R.344, P.368, N.369 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.368 Hydrogen bonds: A:R.344, A:R.344 NAG.8: 2 residues within 4Å: Chain A: E.358, N.390 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.390 NAG.9: 5 residues within 4Å: Chain A: K.561, K.582, S.583, V.585, N.614 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain A: K.37, G.59, Q.61, N.62 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.61 Hydrogen bonds: A:N.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knoepfel, T. et al., Target-Based Identification and Optimization of 5-Indazol-5-yl Pyridones as Toll-like Receptor 7 and 8 Antagonists Using a Biochemical TLR8 Antagonist Competition Assay. J.Med.Chem. (2020)

Release Date

2020-08-12

Peptides

Toll-like receptor 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Toll-like receptor 8

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