SMTL ID : 7rc9.1

Crystal structure of human TLR8 ectodomain bound to small molecule antagonist 21

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

homo-dimer

Ligands

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.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: 8 residues within 4Å: Chain A: I.453, K.454, C.457, S.467, N.489, S.491, Y.512, D.514 No protein-ligand interaction detected (PLIP)

3 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: 10 residues within 4Å: Chain A: Q.456, Y.512, V.536, D.538, S.540, V.566, N.568, E.590, V.592, R.621 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.456, A:Q.456, A:Y.512 Hydrophobic interactions: A:V.536 NAG-NAG-BMA-MAN-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 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.228, B:Y.269 Hydrogen bonds: B:K.204, B:H.442 NAG-NAG-BMA-MAN-MAN.6: 9 residues within 4Å: Chain B: Q.456, Y.512, V.536, 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:Q.456, B:Y.512 Hydrophobic interactions: B:V.536

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

NAG-NAG-BMA-MAN.5: 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)

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

NAG.7: 2 residues within 4Å: Chain A: H.55, N.93 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain A: K.221, Q.262, N.263 No protein-ligand interaction detected (PLIP) NAG.9: 3 residues within 4Å: Chain A: L.345, S.346, N.373 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain A: Q.366, M.369, N.394 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.369 Hydrogen bonds: A:N.394 NAG.11: 3 residues within 4Å: Chain A: S.500, N.524, S.526 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.526 Water bridges: A:N.524 NAG.12: 4 residues within 4Å: Chain A: K.586, S.587, V.589, N.618 No protein-ligand interaction detected (PLIP) NAG.13: 4 residues within 4Å: Chain A: N.634, L.638, N.658, L.661 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain B: H.55, N.93 No protein-ligand interaction detected (PLIP) NAG.16: 2 residues within 4Å: Chain B: Q.262, N.263 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.262 NAG.17: 3 residues within 4Å: Chain B: L.345, S.346, N.373 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain B: Q.366, M.369, N.394 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:M.369 Hydrogen bonds: B:Q.366, B:Q.366, B:N.394 NAG.19: 3 residues within 4Å: Chain B: S.500, N.524, S.526 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.526 NAG.20: 5 residues within 4Å: Chain B: K.586, S.587, V.589, N.618, T.620 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.620 NAG.21: 4 residues within 4Å: Chain B: N.634, L.638, N.658, L.661 No protein-ligand interaction detected (PLIP)

2 x RQY: 2-(2,6-dimethylpyridin-4-yl)-5-(piperidin-4-yl)-3-(propan-2-yl)-1H-indole(Non-covalent)

RQY.14: 16 residues within 4Å: Chain A: F.239, Y.326, I.327, K.328, G.329, S.330, V.356, I.381, F.383, E.405 Chain B: F.472, F.473, S.494, A.496, R.519, Y.545 17 PLIP interactions: 4 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:F.472, B:F.472, B:F.472, A:F.239, A:Y.326, A:Y.326, A:Y.326, A:K.328, A:V.356, A:V.356, A:I.381, A:F.383 Hydrogen bonds: B:F.472, A:G.329, A:E.405 pi-Stacking: A:F.383, A:F.383 RQY.22: 16 residues within 4Å: Chain A: F.472, F.473, S.494, A.496, R.519, Y.545 Chain B: F.239, Y.326, I.327, K.328, G.329, S.330, V.356, I.381, F.383, E.405 18 PLIP interactions: 12 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.239, B:Y.326, B:Y.326, B:Y.326, B:K.328, B:V.356, B:V.356, B:F.383, A:F.472, A:F.472, A:F.472, A:F.473 Hydrogen bonds: B:G.329, B:E.405, A:F.472 pi-Stacking: B:F.383, B:F.383, A:Y.545

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sreekantha, R.K. et al., Identification of 2-Pyridinylindole-Based Dual Antagonists of Toll-like Receptors 7 and 8 (TLR7/8). Acs Med.Chem.Lett. (2022)

Release Date

2022-05-04

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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