SMTL ID : 6kya.1

Crystal structure of human TLR8 in complex TH1027

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.89 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.440, A:H.442 Hydrophobic interactions: A:K.204, A:F.206, A:L.228 NAG-NAG-BMA-MAN.4: 13 residues within 4Å: Chain B: 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 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.204, B:F.206, B:L.228

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: R.450, I.453, K.454, C.457, D.465, S.467, N.489, S.491, Y.512, D.514 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 10 residues within 4Å: Chain A: R.547 Chain B: R.450, I.453, K.454, C.457, S.467, N.489, S.491, Y.512, D.514 No protein-ligand interaction detected (PLIP)

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.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:Q.456, A:Y.512 NAG-NAG-BMA-MAN-MAN.6: 10 residues within 4Å: Chain B: K.454, Q.456, Y.512, V.536, D.538, S.540, V.566, N.568, E.590, V.592 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.456, B:K.454, B:Q.456 Hydrophobic interactions: B:Y.512, B:V.536

2 x DY3: 3-[5-methylsulfanyl-4-(3,4,5-trimethylphenyl)-1,2,4-triazol-3-yl]propan-1-ol(Non-covalent)

DY3.7: 16 residues within 4Å: Chain A: F.239, N.240, F.324, Y.326, K.328, G.329, S.330, V.356, I.381, F.383 Chain B: F.472, F.473, S.494, A.496, V.498, Y.545 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.472, B:F.472, B:A.496, B:Y.545, A:F.324, A:Y.326, A:I.381, A:F.383 Hydrogen bonds: A:Y.326, A:G.329 pi-Stacking: A:Y.326 DY3.12: 17 residues within 4Å: Chain A: F.472, F.473, S.494, A.496, Q.497, V.498, Y.545 Chain B: F.239, F.324, Y.326, I.327, K.328, G.329, S.330, V.356, I.381, F.383 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.324, B:Y.326, B:I.381, B:F.383, A:F.472, A:F.472, A:F.473, A:A.496, A:Y.545 Hydrogen bonds: B:Y.326, B:Y.326, B:G.329 pi-Stacking: B:Y.326, A:F.473

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

NAG.8: 2 residues within 4Å: Chain A: R.203, N.225 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.203, A:R.203 NAG.9: 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, A:N.373 NAG.10: 3 residues within 4Å: Chain A: K.586, V.589, N.618 No protein-ligand interaction detected (PLIP) NAG.11: 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:T.660 NAG.13: 5 residues within 4Å: Chain B: T.179, S.200, S.201, R.203, N.225 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.203 NAG.14: 4 residues within 4Å: Chain B: L.345, S.346, R.348, N.373 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.348, B:R.348, B:N.373 NAG.15: 3 residues within 4Å: Chain B: K.586, V.589, N.618 No protein-ligand interaction detected (PLIP) NAG.16: 6 residues within 4Å: Chain B: N.634, L.638, F.656, N.658, T.660, L.661 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.660

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, S. et al., Rationally Designed Small-Molecule Inhibitors Targeting an Unconventional Pocket on the TLR8 Protein-Protein Interface. J.Med.Chem. (2020)

Release Date

2020-05-27

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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