SMTL ID : 9mhy.1

Human TLR8 ectodomain with small molecule agonist 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(2-6)]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: 19 residues within 4Å: Chain A: S.183, F.184, K.200, F.202, S.204, N.205, L.224, D.226, S.228, Y.265, N.267, V.289, D.436, P.437, 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:K.200 NAG-NAG-BMA-MAN-MAN.4: 19 residues within 4Å: Chain B: S.183, F.184, K.200, F.202, S.204, N.205, L.224, D.226, S.228, Y.265, N.267, V.289, D.436, P.437, 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:K.200

4 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: 12 residues within 4Å: Chain A: S.400, R.446, I.449, K.450, C.453, S.463, L.464, N.485, S.487, Y.508, D.510 Chain B: R.543 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.446 Water bridges: A:R.446, A:K.450 NAG-NAG-BMA.3: 13 residues within 4Å: Chain A: K.450, Q.452, Y.508, T.512, V.532, D.534, S.536, Y.537, V.562, N.564, E.586, V.588, R.617 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.452, A:Q.452, A:Y.508 Hydrophobic interactions: A:V.532 NAG-NAG-BMA.5: 13 residues within 4Å: Chain B: S.400, R.446, I.449, K.450, C.453, S.463, L.464, C.483, N.485, S.487, Y.508, D.510 Ligands: SO4.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.446 Water bridges: B:R.446 NAG-NAG-BMA.6: 13 residues within 4Å: Chain B: K.450, Q.452, Y.508, T.512, V.532, D.534, S.536, Y.537, V.562, N.564, E.586, V.588, R.617 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.452, B:Q.452, B:Y.508 Hydrophobic interactions: B:V.532 Water bridges: B:K.450

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

NAG.7: 5 residues within 4Å: Chain A: K.37, Y.38, G.59, Q.61, N.62 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: H.51, T.53, N.89, T.91 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: S.196, S.197, R.199, N.221 Ligand excluded by PLIP NAG.10: 5 residues within 4Å: Chain A: L.341, S.342, R.344, P.368, N.369 Ligand excluded by PLIP NAG.11: 5 residues within 4Å: Chain A: E.358, Q.362, M.365, Q.366, N.390 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain A: S.496, T.498, N.520, A.521 Ligands: 01.18 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: S.522, T.525, Q.555, N.556 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: K.561, K.582, S.583, V.585, N.614 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: N.630, L.634, N.654, T.656, L.657 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain B: K.37, Y.38, G.59, Q.61, N.62 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: H.51, T.53, N.89, T.91 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: S.196, S.197, R.199, N.221 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain B: L.341, S.342, R.344, P.368, N.369 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain B: E.358, Q.362, M.365, Q.366, N.390 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain B: S.496, T.498, N.520, A.521 Ligands: 01.29 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: S.522, T.525, Q.555, N.556 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain B: K.561, K.582, S.583, V.585, N.614 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain B: N.630, L.634, N.654, T.656, L.657 Ligand excluded by PLIP

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.16: 3 residues within 4Å: Chain A: R.593, R.624 Ligands: NAG-NAG-BMA.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.593 Water bridges: A:R.624 SO4.17: 6 residues within 4Å: Chain A: P.238, F.239, F.294, F.435, F.441, Y.442 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.441 SO4.28: 6 residues within 4Å: Chain B: P.238, F.239, F.294, F.435, F.441, Y.442 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.442

2 x 01: (3S,4R)-4-[({3-[(5-amino-7-{[(3S)-1-hydroxyhexan-3-yl]amino}-1H-pyrazolo[4,3-d]pyrimidin-1-yl)methyl]-4-methoxyphenyl}methyl)amino]oxolan-3-ol

01.18: 21 residues within 4Å: Chain A: V.494, D.517, D.519, N.520, Y.541, G.546, V.547, T.548 Chain B: F.235, F.320, Y.322, I.323, K.324, G.325, S.326, Y.327, G.350, V.352, I.377, F.379 Ligands: NAG.12 17 PLIP interactions: 9 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:T.548, B:Y.322, B:Y.322, B:Y.327, B:Y.327, B:V.352 Hydrogen bonds: A:D.519, A:N.520, A:T.548, A:T.548, B:G.325 Water bridges: A:D.519, A:D.519 Salt bridges: A:D.517, A:D.519 pi-Stacking: B:F.379, B:F.379 01.29: 21 residues within 4Å: Chain A: F.235, F.320, Y.322, I.323, K.324, G.325, S.326, Y.327, G.350, V.352, I.377, F.379 Chain B: V.494, D.517, D.519, N.520, Y.541, G.546, V.547, T.548 Ligands: NAG.24 16 PLIP interactions: 8 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:Y.322, A:Y.322, A:Y.327, A:Y.327, A:V.352, B:T.548 Hydrogen bonds: A:G.325, B:D.519, B:N.520, B:T.548, B:T.548 pi-Stacking: A:F.379, A:F.379 Water bridges: B:D.517 Salt bridges: B:D.517, B:D.519

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Poudel, Y.B. et al., Structure-Based Design of Novel TLR7/8 Agonist Payloads Enabling an Immunomodulatory Conjugate Approach. Acs Med.Chem.Lett. (2025)

Release Date

2025-03-05

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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