SMTL ID : 5awb.1

Crystal structure of human TLR8 in complex with N1-3-aminomethylbenzyl (meta-amine)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN: 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.1: 14 residues within 4Å: Chain A: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, D.440, H.442, S.443, N.444, F.445, Y.446 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.440, A:K.204 Hydrophobic interactions: A:K.204 NAG-NAG-BMA-MAN.8: 14 residues within 4Å: Chain B: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, D.440, H.442, S.443, N.444, F.445, Y.446 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.440, B:K.204 Hydrophobic interactions: B:K.204

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

NAG-NAG.2: 12 residues within 4Å: Chain A: S.404, R.450, I.453, K.454, C.457, S.467, L.468, N.489, S.491, Y.512, D.514 Chain B: R.547 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.450 NAG-NAG.9: 12 residues within 4Å: Chain A: R.547 Chain B: S.404, R.450, I.453, K.454, C.457, S.467, L.468, N.489, S.491, Y.512, D.514 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.450

2 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.3: 8 residues within 4Å: Chain A: Q.456, Y.512, D.538, S.540, V.566, N.568, E.590, V.592 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.456, A:Q.456 NAG-NAG-BMA.10: 8 residues within 4Å: Chain B: Q.456, Y.512, D.538, S.540, V.566, N.568, E.590, V.592 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.456, B:Q.456, B:Y.512

2 x M0A: 1-[[3-(aminomethyl)phenyl]methyl]-2-butyl-imidazo[4,5-c]quinolin-4-amine(Non-covalent)

M0A.4: 14 residues within 4Å: Chain A: F.324, Y.326, G.329, S.330, Y.331, G.354, V.356, F.383, R.407 Chain B: D.521, D.523, G.550, V.551, T.552 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.324, A:Y.326, A:V.356, A:F.383 pi-Stacking: A:Y.331, A:F.383, A:F.383 Hydrogen bonds: B:D.521, B:D.523, B:D.523, B:T.552, B:T.552 M0A.11: 14 residues within 4Å: Chain A: D.521, D.523, G.550, V.551, T.552 Chain B: F.324, Y.326, G.329, S.330, Y.331, G.354, V.356, F.383, R.407 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.324, B:Y.326, B:V.356, B:F.383 pi-Stacking: B:Y.331, B:F.383, B:F.383 Hydrogen bonds: A:D.521, A:D.523, A:T.552, A:T.552 Water bridges: A:D.521

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

NAG.5: 4 residues within 4Å: Chain A: L.345, S.346, R.348, N.373 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.348, A:R.348 Water bridges: A:N.373 NAG.6: 5 residues within 4Å: Chain A: K.565, K.586, S.587, V.589, N.618 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.618, A:N.618 NAG.7: 5 residues within 4Å: Chain A: N.634, F.656, N.658, T.660, L.661 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.656 Hydrogen bonds: A:N.634 NAG.12: 4 residues within 4Å: Chain B: L.345, S.346, R.348, N.373 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.348, B:R.348, B:N.373, B:N.373 NAG.13: 5 residues within 4Å: Chain B: K.565, K.586, S.587, V.589, N.618 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.618, B:N.618 NAG.14: 5 residues within 4Å: Chain B: N.634, F.656, N.658, T.660, L.661 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.656 Hydrogen bonds: B:N.634

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beesu, M. et al., Structure-Based Design of Human TLR8-Specific Agonists with Augmented Potency and Adjuvanticity. J.Med.Chem. (2015)

Release Date

2015-09-23

Peptides

Toll-like receptor 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Toll-like receptor 8

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