SMTL ID : 6v9u.1

Crystal structure of human TLR8 ectodomain bound to small molecule antagonist 14c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

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.1: 14 residues within 4Å: Chain A: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, D.295, 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-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: 15 residues within 4Å: Chain B: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, D.295, D.440, 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

1 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, I.453, K.454, C.457, S.467, L.468, N.489, S.491, D.514 No protein-ligand interaction detected (PLIP)

1 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.5: 9 residues within 4Å: Chain B: S.404, I.453, K.454, C.457, S.467, L.468, N.489, S.491, D.514 No protein-ligand interaction detected (PLIP)

1 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.6: 11 residues within 4Å: Chain B: Q.456, Y.512, T.516, V.536, D.538, S.540, V.566, N.568, E.590, V.592, R.621 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.456, B:Q.456, B:Y.512 Hydrophobic interactions: B:V.536

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

NAG.7: 2 residues within 4Å: Chain A: H.55, N.93 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: Q.262, N.263, N.287 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: S.346, N.373 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: E.362, Q.393, N.394 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: S.500, N.524, S.526 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: K.586, S.587, N.618 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.634, L.638, N.658, L.661 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: S.200, S.201, N.225 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: S.307, A.309, S.338, N.340 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.93 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: I.224, N.263 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: S.346, N.373 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: E.362, Q.393, N.394 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: S.500, N.524, S.526 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: K.586, S.587, N.618 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: N.634, L.638, N.658, L.661 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: S.526, T.529, N.560 Ligand excluded by PLIP

2 x QSM: 2-(3,4-dimethoxyphenyl)-5-(piperidin-4-yl)-3-(propan-2-yl)-1H-indole(Non-covalent)

QSM.16: 19 residues within 4Å: Chain A: F.239, F.324, Y.326, I.327, K.328, G.329, S.330, G.354, V.356, I.381, F.383, E.405 Chain B: F.472, F.473, S.494, A.496, Q.497, V.498, R.519 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.239, A:Y.326, A:Y.326, A:V.356, A:F.383, B:F.472, B:F.473, B:F.473, B:A.496 Hydrogen bonds: A:G.329, A:E.405, B:F.472 pi-Stacking: A:F.383, B:F.472 QSM.25: 19 residues within 4Å: Chain A: F.472, F.473, S.494, A.496, Q.497, V.498, R.519 Chain B: F.239, F.324, Y.326, I.327, K.328, G.329, S.330, G.354, V.356, I.381, F.383, E.405 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.239, B:Y.326, B:Y.326, B:V.356, B:F.383, A:F.472, A:F.473, A:A.496 Hydrogen bonds: B:G.329, B:E.405, A:F.472 pi-Stacking: B:F.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mussari, C.P. et al., Discovery of Potent and Orally Bioavailable Small Molecule Antagonists of Toll-like Receptors 7/8/9 (TLR7/8/9). Acs Med.Chem.Lett. (2020)

Release Date

2020-08-12

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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