SMTL ID : 5awd.1

Crystal structure of human TLR8 in complex with N1-4-aminomethylbenzyl (IMDQ)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

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.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 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.228, A:Y.269 Hydrogen bonds: A:K.204 NAG-NAG-BMA-MAN-MAN.12: 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 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.228, B:Y.269 Hydrogen bonds: 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: 10 residues within 4Å: Chain A: S.404, I.453, K.454, C.457, S.467, L.468, N.489, S.491, Y.512, D.514 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 10 residues within 4Å: Chain B: S.404, I.453, K.454, C.457, S.467, L.468, N.489, S.491, Y.512, D.514 No protein-ligand interaction detected (PLIP)

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: 9 residues within 4Å: Chain A: K.454, Q.456, Y.512, D.538, S.540, V.566, N.568, E.590, V.592 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.456, A:K.454, A:Q.456 NAG-NAG-BMA.14: 9 residues within 4Å: Chain B: K.454, Q.456, Y.512, D.538, S.540, V.566, N.568, E.590, V.592 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.456, B:K.454, B:Q.456, B:Y.512

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

IDQ.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 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.324, A:Y.326, A:V.356, A:F.383, B:T.552 Hydrogen bonds: A:G.329, B:D.521, B:D.523, B:T.552, B:T.552 pi-Stacking: A:Y.331, A:F.383, A:F.383 IDQ.15: 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: 4 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:T.552, B:F.324, B:Y.326, B:V.356, B:F.383 Hydrogen bonds: A:D.521, A:T.552, B:G.329 Water bridges: A:D.521 pi-Stacking: B:Y.331, B:F.383, B:F.383

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

NAG.5: 2 residues within 4Å: Chain A: H.55, N.93 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.93 NAG.6: 5 residues within 4Å: Chain A: S.307, A.309, T.312, S.338, N.340 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.312, A:T.312, A:N.340 NAG.7: 5 residues within 4Å: Chain A: L.345, S.346, R.348, P.372, N.373 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.372 Hydrogen bonds: A:R.348, A:R.348, A:N.373 NAG.8: 2 residues within 4Å: Chain A: S.500, N.524 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.500 Water bridges: A:A.525 NAG.9: 2 residues within 4Å: Chain A: T.529, N.560 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain A: 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.11: 4 residues within 4Å: Chain A: N.634, F.656, N.658, L.661 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.656 Hydrogen bonds: A:N.634 NAG.16: 2 residues within 4Å: Chain B: H.55, N.93 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.93 NAG.17: 5 residues within 4Å: Chain B: S.307, A.309, T.312, S.338, N.340 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.312, B:N.340 NAG.18: 5 residues within 4Å: Chain B: L.345, S.346, R.348, P.372, N.373 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.372 Hydrogen bonds: B:R.348, B:R.348, B:N.373 NAG.19: 2 residues within 4Å: Chain B: S.500, N.524 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.500 Water bridges: B:A.525 NAG.20: 2 residues within 4Å: Chain B: T.529, N.560 No protein-ligand interaction detected (PLIP) NAG.21: 4 residues within 4Å: Chain B: 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.22: 4 residues within 4Å: Chain B: N.634, F.656, N.658, 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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