SMTL ID : 9mhw.1

Human TLR8 ectodomain with small molecule agonist 9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.1: 19 residues within 4Å: Chain A: Y.150, 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, 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-MAN.15: 19 residues within 4Å: Chain B: Y.150, 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, 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, I.449, K.450, C.453, D.461, S.463, L.464, N.485, S.487, Y.508, D.510 Chain B: R.543 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.513 NAG-NAG-BMA.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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.452, A:K.450, A:Q.452, A:Y.508 Hydrophobic interactions: A:V.532 NAG-NAG-BMA.16: 12 residues within 4Å: Chain A: R.543 Chain B: S.400, I.449, K.450, C.453, D.461, S.463, L.464, N.485, S.487, Y.508, D.510 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.513 NAG-NAG-BMA.17: 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.452, B:K.450, B:Q.452, B:Y.508 Hydrophobic interactions: B:V.532

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

NAG.4: 4 residues within 4Å: Chain A: N.54, E.55, Q.58, N.97 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: H.51, N.89, T.91 Ligand excluded by PLIP NAG.6: 5 residues within 4Å: Chain A: S.196, S.197, R.199, I.220, N.221 Ligand excluded by PLIP NAG.7: 6 residues within 4Å: Chain A: S.496, T.498, N.520, A.521, S.522 Ligands: 01.28 Ligand excluded by PLIP NAG.8: 5 residues within 4Å: Chain A: K.561, K.582, S.583, V.585, N.614 Ligand excluded by PLIP NAG.9: 6 residues within 4Å: Chain A: N.630, L.634, F.652, N.654, T.656, L.657 Ligand excluded by PLIP NAG.10: 5 residues within 4Å: Chain A: K.217, G.218, I.220, Q.258, N.259 Ligand excluded by PLIP NAG.11: 5 residues within 4Å: Chain A: K.37, Y.38, G.59, Q.61, N.62 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain A: E.358, Q.362, M.365, Q.366, N.390 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: N.54, E.55, Q.58, N.97 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: H.51, N.89, T.91 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain B: S.196, S.197, R.199, I.220, N.221 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain B: S.496, T.498, N.520, A.521, S.522 Ligands: 01.14 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain B: K.561, K.582, S.583, V.585, N.614 Ligand excluded by PLIP NAG.23: 6 residues within 4Å: Chain B: N.630, L.634, F.652, N.654, T.656, L.657 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain B: K.217, G.218, I.220, Q.258, N.259 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain B: K.37, Y.38, G.59, Q.61, N.62 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain B: E.358, Q.362, M.365, Q.366, N.390 Ligand excluded by PLIP

2 x NI: NICKEL (II) ION(Non-covalent)

NI.13: 3 residues within 4Å: Chain A: E.731, T.732, H.764 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.731, A:H.764, H2O.5, H2O.11, H2O.18 NI.27: 3 residues within 4Å: Chain B: E.731, T.732, H.764 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.731, B:H.764, H2O.38, H2O.44, H2O.52

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

01.14: 22 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, D.517, D.519, N.520, G.546, V.547, T.548 Ligands: NAG.21 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Y.322, A:Y.322, A:Y.327, A:V.352, A:F.379, A:F.379, A:F.379 Hydrogen bonds: A:G.325, B:N.520, B:T.548, B:T.548 pi-Stacking: A:F.379, A:F.379 Water bridges: B:D.519, B:D.519 Salt bridges: B:D.517, B:D.519 01.28: 22 residues within 4Å: Chain A: V.494, D.517, D.519, N.520, 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.7 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.322, B:Y.322, 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 pi-Stacking: B:F.379, B:F.379 Water bridges: A:D.517 Salt bridges: A:D.517, A: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
A

Toll-like receptor 8

Related Entries With Identical Sequence