SMTL ID : 9mhx.1

Human TLR8 ectodomain with small molecule agonist 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 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: 18 residues within 4Å: Chain A: 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: 18 residues within 4Å: Chain B: 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

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.2: 16 residues within 4Å: Chain A: S.400, I.449, K.450, C.453, D.461, S.463, L.464, C.483, N.485, S.487, Y.508, D.510 Chain B: R.543, R.593, I.596, R.624 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.593, B:R.593 Water bridges: A:N.513, A:N.513

2 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: 12 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.452, A:K.450, A:Q.452, A:Y.508 Hydrophobic interactions: A:Y.508, A:V.532 NAG-NAG-BMA-MAN-MAN.5: 14 residues within 4Å: Chain A: R.543, R.624 Chain B: S.400, I.449, K.450, C.453, D.461, S.463, L.464, C.483, N.485, S.487, Y.508, D.510 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.624 Water bridges: B:N.513

1 x NAG- NAG- BMA- MAN: 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.6: 12 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 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.452, B:K.450, B:Q.452, B:Y.508 Hydrophobic interactions: B:Y.508, B:V.532

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

NAG.7: 3 residues within 4Å: Chain A: N.54, E.55, N.97 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: H.51, N.89, T.91, P.112 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: S.196, S.197, R.199, I.220, N.221 Ligand excluded by PLIP NAG.10: 6 residues within 4Å: Chain A: S.496, T.498, N.520, A.521, S.522 Ligands: 01.19 Ligand excluded by PLIP NAG.11: 6 residues within 4Å: Chain A: K.561, K.582, S.583, V.585, N.614, T.616 Ligand excluded by PLIP NAG.12: 6 residues within 4Å: Chain A: N.630, L.634, F.652, N.654, T.656, L.657 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: A.521, S.522, T.525, N.556 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: G.218, I.220, Q.258, N.259, N.283 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: Y.38, Q.61, N.62, N.100 Ligand excluded by PLIP NAG.16: 7 residues within 4Å: Chain A: Q.113, Y.133, N.134, E.162, K.163, T.164, N.165 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: G.299, A.302, S.303, N.332 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: L.341, S.342, R.344, P.368, N.369 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.54, E.55, N.97 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: H.51, N.89, T.91, P.112 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: N.134, T.136, N.165, E.167 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain B: S.196, S.197, R.199, I.220, N.221 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain B: S.496, T.498, N.520, A.521, S.522 Ligands: 01.30 Ligand excluded by PLIP NAG.25: 6 residues within 4Å: Chain B: K.561, K.582, S.583, V.585, N.614, T.616 Ligand excluded by PLIP NAG.26: 6 residues within 4Å: Chain B: N.630, L.634, F.652, N.654, T.656, L.657 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain B: A.521, S.522, T.525, S.528, N.556 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain B: G.218, I.220, Q.258, N.259, N.283 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain B: L.341, S.342, R.344, P.368, N.369 Ligand excluded by PLIP

2 x 01: (3S,4R)-4-[({3-[(2-amino-4-{[(3S)-1-hydroxyhexan-3-yl]amino}-5H-pyrimido[5,4-b]indol-5-yl)methyl]-4-methoxyphenyl}methyl)amino]oxolan-3-ol

01.19: 24 residues within 4Å: Chain A: V.494, S.496, 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, K.381, R.403 Ligands: NAG.10 19 PLIP interactions: 12 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.320, B:Y.322, B:Y.322, B:Y.327, B:Y.327, B:V.352, B:F.379, B:F.379, B:F.379 Hydrogen bonds: B:G.325, A:N.520, A:T.548, A:T.548, A:T.548 pi-Stacking: B:F.379, B:F.379 Water bridges: A:D.517 Salt bridges: A:D.517, A:D.519 01.30: 24 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, K.381, R.403 Chain B: V.494, S.496, D.517, D.519, N.520, Y.541, G.546, V.547, T.548 Ligands: NAG.24 22 PLIP interactions: 10 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:V.494, A:F.320, A:Y.322, A:Y.322, A:Y.327, A:Y.327, A:V.352, A:F.379, A:F.379 Hydrogen bonds: B:N.520, B:T.548, B:T.548, B:T.548, A:G.325 Water bridges: B:D.519, B:D.519, B:D.519 Salt bridges: B:D.517, B:D.519 pi-Stacking: A:F.379, A:F.379, A:F.379

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

Related Entries With Identical Sequence