SMTL ID : 4qbz.1

Crystal structure of human TLR8 in complex with DS-802

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- BMA: alpha-D-mannopyranose-(2-3)-[beta-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(Post Translational Modification)

NAG-NAG-BMA-MAN-BMA.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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.440, A:K.204, A:H.442 Hydrophobic interactions: A:L.228, A:Y.269

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: 9 residues within 4Å: Chain A: S.404, R.450, K.454, C.457, S.467, L.468, N.489, Y.512, D.514 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.468 NAG-NAG.5: 11 residues within 4Å: Chain A: R.547 Chain B: S.404, R.450, 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(Post Translational Modification)

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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.456, A:K.454, A:Q.456 Hydrophobic interactions: A:Q.456, A:Y.512 NAG-NAG-BMA.6: 9 residues within 4Å: Chain B: 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 B Hydrogen bonds: B:Q.456, B:K.454, B:Q.456

1 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(Post Translational Modification)

NAG-NAG-BMA-MAN.4: 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 Hydrogen bonds: B:D.440, B:K.204 Hydrophobic interactions: B:L.228, B:Y.269

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

NAG.7: 4 residues within 4Å: Chain A: N.58, E.59, Q.62, N.101 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.59, A:Q.62 Hydrogen bonds: A:N.101 NAG.8: 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.9: 2 residues within 4Å: Chain A: S.500, N.524 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.500 NAG.10: 4 residues within 4Å: Chain A: S.526, T.529, Q.559, N.560 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.559, A:N.560 NAG.11: 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.12: 5 residues within 4Å: Chain A: N.634, F.656, N.658, T.660, L.661 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.656 Hydrogen bonds: A:N.634, A:N.658, A:T.660 NAG.15: 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.16: 2 residues within 4Å: Chain B: S.500, N.524 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.500 NAG.17: 3 residues within 4Å: Chain B: T.529, Q.559, N.560 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.559, B:N.560 NAG.18: 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 Water bridges: B:K.565 NAG.19: 4 residues within 4Å: Chain B: N.634, N.658, T.660, L.661 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.634

2 x D80: 2-butyl[1,3]oxazolo[4,5-c]quinolin-4-amine(Non-covalent)

D80.13: 13 residues within 4Å: Chain A: D.521, D.523, G.550, V.551, T.552 Chain B: F.324, Y.326, Y.331, G.354, V.356, I.381, F.383, R.407 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.324, B:Y.326, B:V.356, B:V.356, B:F.383, A:V.551 pi-Stacking: B:Y.331, B:F.383, B:F.383 Hydrogen bonds: A:D.521, A:T.552, A:T.552 Water bridges: A:D.521 D80.14: 13 residues within 4Å: Chain A: F.324, Y.326, Y.331, G.354, V.356, I.381, F.383, R.407 Chain B: D.521, D.523, G.550, V.551, T.552 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.324, A:Y.326, A:V.356, A:V.356, A:F.383 pi-Stacking: A:Y.331, A:F.383, A:F.383 Hydrogen bonds: B:D.521, B:T.552 Water bridges: B:D.521, B:T.552

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoo, E. et al., Determinants of Activity at Human Toll-like Receptors 7 and 8: Quantitative Structure-Activity Relationship (QSAR) of Diverse Heterocyclic Scaffolds. J.Med.Chem. (2014)

Release Date

2014-10-22

Peptides

Toll-like receptor 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Toll-like receptor 8

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