SMTL ID : 7ytx.1

Crystal structure of TLR8 in complex with its antagonist

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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-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 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.269 Hydrogen bonds: A:K.204, A:H.442

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: 8 residues within 4Å: Chain A: R.450, I.453, K.454, C.457, S.467, N.489, S.491, D.514 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain B: R.450, I.453, K.454, S.467, N.489, S.491, Y.512, D.514 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.454, B:K.454

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-MAN-MAN.3: 11 residues within 4Å: Chain A: K.454, Q.456, Y.512, V.536, D.538, S.540, V.566, N.568, S.570, E.590, V.592 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.456, A:Q.456 Hydrophobic interactions: A:V.536 NAG-NAG-BMA-MAN-MAN-MAN-MAN.6: 11 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, R.621 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.456, B:Y.512 Hydrophobic interactions: B:V.536, B:V.566

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.4: 14 residues within 4Å: Chain B: 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 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.269 Hydrogen bonds: B:K.204

2 x JRI: (2R,6R)-4-(8-cyanoquinolin-5-yl)-N-[(3S,4R)-4-fluoranylpyrrolidin-3-yl]-6-methyl-morpholine-2-carboxamide(Non-covalent)

JRI.7: 16 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.473, A.496, Q.497, Y.545 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.324, A:Y.326, A:Y.326, A:V.356, A:V.356, A:I.381, B:F.473, B:A.496 Hydrogen bonds: A:G.329, B:Q.497, B:V.498 pi-Stacking: B:F.473 JRI.17: 17 residues within 4Å: Chain A: F.472, F.473, A.496, Q.497, Y.545 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: 5 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.472, A:F.473, A:A.496, B:F.324, B:Y.326, B:Y.326, B:Y.326, B:V.356, B:V.356 Hydrogen bonds: A:Q.497, B:G.329 pi-Stacking: A:F.473

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

NAG.8: 3 residues within 4Å: Chain A: S.200, R.203, N.225 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: I.224, Q.262, N.263, N.287 Ligand excluded by PLIP NAG.10: 5 residues within 4Å: Chain A: A.306, S.307, G.308, S.338, N.340 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: S.500, N.524 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: T.529, Q.559, N.560 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: K.586, V.589, N.618, T.620 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: E.362, Q.366, M.369, N.394 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: L.345, S.346, R.348, N.373 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain A: N.634, F.656, N.658, T.660, L.661 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: S.200, S.201, N.225 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: K.221, I.224, N.263, T.265 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain B: A.306, S.307, G.308, S.338, R.339, N.340 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: S.500, N.524 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain B: A.525, T.529, E.556, Q.559, N.560 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: K.586, N.618 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: K.41, Q.65, N.66 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: R.348, N.373 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: N.634, N.658, T.660, L.661 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishizaka, S.T. et al., A novel Toll-like receptor 7/8-specific antagonist E6742 ameliorates clinically relevant disease parameters in murine models of lupus. Eur.J.Pharmacol. (2023)

Release Date

2023-09-27

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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