SMTL ID : 4qc0.1

Crystal structure of human TLR8 in complex with XG-1-236

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

3 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.1: 13 residues within 4Å: Chain A: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, H.442, S.443, N.444, F.445, Y.446 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.228, A:Y.269 Hydrogen bonds: A:K.204, A:H.442 NAG-NAG-BMA.2: 9 residues within 4Å: Chain A: 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 A Hydrogen bonds: A:Q.456, A:K.454, A:Q.456, A:Y.512 NAG-NAG-BMA.4: 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

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.3: 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 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.228, B:Y.269 Hydrogen bonds: B:K.204, B:S.443

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

NAG.5: 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.6: 10 residues within 4Å: Chain A: S.404, I.453, K.454, C.457, D.465, S.467, L.468, N.489, Y.512, D.514 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.454, A:Y.512 Hydrogen bonds: A:S.404, A:S.404, A:K.454, A:S.467, A:N.489, A:D.514, A:D.514 NAG.7: 4 residues within 4Å: Chain A: K.586, S.587, V.589, N.618 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.618 NAG.10: 9 residues within 4Å: Chain B: S.404, K.454, C.457, D.465, S.467, L.468, N.489, Y.512, D.514 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:K.454, B:Y.512 Hydrogen bonds: B:S.404, B:S.404, B:K.454, B:S.467, B:N.489, B:D.514 NAG.11: 4 residues within 4Å: Chain B: K.586, S.587, V.589, N.618 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.618

2 x XG1: 2-butyl-2H-pyrazolo[3,4-c]quinolin-4-amine(Non-covalent)

XG1.8: 12 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, F.383, R.407 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.324, B:Y.326, B:V.356, B:V.356 pi-Stacking: B:Y.331, B:F.383, B:F.383 Hydrogen bonds: A:D.521, A:T.552 XG1.9: 11 residues within 4Å: Chain A: Y.326, Y.331, G.354, V.356, F.383, R.407 Chain B: D.521, D.523, G.550, V.551, T.552 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.326, A:V.356, A:V.356 pi-Stacking: A:Y.331, A:F.383, A:F.383 Hydrogen bonds: B:D.521, B:T.552, 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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