SMTL ID : 8pfi.1

Crystal structure of human TLR8 in complex with compound 34

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

homo-dimer

Ligands

4 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: 16 residues within 4Å: Chain A: K.200, F.202, S.204, L.224, D.226, S.228, Y.265, N.267, V.289, D.291, D.436, H.438, S.439, N.440, F.441, Y.442 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.224, A:Y.265 Hydrogen bonds: A:H.438 NAG-NAG-BMA-MAN-MAN.3: 10 residues within 4Å: Chain A: K.450, Q.452, Y.508, V.532, D.534, S.536, V.562, N.564, E.586, V.588 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.452, A:K.450, A:Q.452 Hydrophobic interactions: A:V.532, A:V.562 NAG-NAG-BMA-MAN-MAN.4: 14 residues within 4Å: Chain B: K.200, F.202, S.204, L.224, D.226, S.228, Y.265, N.267, D.436, H.438, S.439, N.440, F.441, Y.442 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.224, B:Y.265 Hydrogen bonds: B:H.438 NAG-NAG-BMA-MAN-MAN.6: 10 residues within 4Å: Chain B: K.450, Q.452, Y.508, V.532, D.534, S.536, V.562, N.564, E.586, V.588 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.452, B:K.450, B:Q.452 Hydrophobic interactions: B:V.532, B:V.562

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.2: 11 residues within 4Å: Chain A: S.400, R.446, I.449, K.450, C.453, D.461, S.463, N.485, S.487, Y.508, D.510 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.446, A:N.513 Water bridges: A:S.487 NAG-NAG-BMA.5: 11 residues within 4Å: Chain B: R.446, I.449, K.450, C.453, S.463, L.464, N.485, S.487, Y.508, D.510, N.513 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.446, B:N.513

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

NAG.7: 3 residues within 4Å: Chain A: S.496, N.520, S.522 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.522 NAG.8: 3 residues within 4Å: Chain A: N.630, N.654, L.657 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.630 NAG.9: 5 residues within 4Å: Chain A: L.341, S.342, R.344, P.368, N.369 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.368 Hydrogen bonds: A:R.344, A:R.344 NAG.10: 4 residues within 4Å: Chain A: E.358, Q.362, M.365, N.390 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.362, A:Q.366 Water bridges: A:E.358, A:N.390 NAG.11: 5 residues within 4Å: Chain A: K.561, K.582, S.583, V.585, N.614 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.614 Water bridges: A:N.614, A:N.614 NAG.12: 4 residues within 4Å: Chain A: K.37, G.59, Q.61, N.62 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.61 Hydrogen bonds: A:N.62 NAG.15: 3 residues within 4Å: Chain B: S.496, N.520, S.522 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.522 NAG.16: 3 residues within 4Å: Chain B: N.630, N.654, L.657 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.630 NAG.17: 5 residues within 4Å: Chain B: L.341, S.342, R.344, P.368, N.369 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.368 Hydrogen bonds: B:R.344, B:R.344 NAG.18: 4 residues within 4Å: Chain B: E.358, Q.362, M.365, N.390 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.366 Water bridges: B:Q.362 NAG.19: 5 residues within 4Å: Chain B: K.561, K.582, S.583, V.585, N.614 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.614 Water bridges: B:N.614, B:N.614 NAG.20: 4 residues within 4Å: Chain B: K.37, G.59, Q.61, N.62 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.61 Hydrogen bonds: B:N.62

2 x YHG: (3~{S})-~{N}-[4-[[5-(1,6-dimethylpyrazolo[3,4-b]pyridin-4-yl)-3-methyl-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-1-yl]methyl]-1-bicyclo[2.2.2]octanyl]morpholine-3-carboxamide(Non-covalent)

YHG.13: 19 residues within 4Å: Chain A: F.235, F.320, Y.322, I.323, K.324, G.325, S.326, G.350, V.352, I.377, F.379, E.401, L.464 Chain B: F.468, F.469, S.490, A.492, Q.493, R.515 18 PLIP interactions: 11 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.320, A:Y.322, A:Y.322, A:Y.322, A:V.352, A:V.352, A:I.377, B:F.468, B:F.469, B:F.469, B:A.492 Hydrogen bonds: A:G.325, A:E.401, B:S.490, B:S.490, B:V.494 pi-Stacking: A:F.235, A:F.379 YHG.14: 19 residues within 4Å: Chain A: F.468, F.469, S.490, A.492, Q.493, R.515 Chain B: F.235, F.320, Y.322, I.323, K.324, G.325, S.326, G.350, V.352, I.377, F.379, E.401, L.464 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:F.320, B:Y.322, B:V.352, B:V.352, B:F.379, A:F.468, A:F.469, A:F.469, A:A.492 Hydrogen bonds: B:G.325, A:S.490, A:S.490, A:V.494 Water bridges: B:R.403, B:R.403, A:R.515 pi-Stacking: B:F.235, B:F.379

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alper, P. et al., Discovery of the TLR7/8 Antagonist MHV370 for Treatment of Systemic Autoimmune Diseases. Acs Med.Chem.Lett. (2023)

Release Date

2023-08-16

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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