SMTL ID : 6wml.1 (1 other biounit)

Human TLR8 bound to the potent agonist, GS-9688 (Selgantolimod)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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.1: 14 residues within 4Å: Chain A: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, H.442, S.443, N.444, F.445, Y.446 Ligands: MAN.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.228, A:Y.269 Hydrogen bonds: A:K.204, A:H.442 Water bridges: A:N.444

1 x NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-BMA.2: 1 residues within 4Å: Ligands: NAG.8 No protein-ligand interaction detected (PLIP)

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.3: 10 residues within 4Å: Chain A: Q.456, Y.512, V.536, D.538, S.540, V.566, N.568, E.590, V.592 Ligands: MAN.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.456, A:Q.456, A:Y.512 Hydrophobic interactions: A:Y.512, A:V.536 NAG-NAG-BMA.4: 15 residues within 4Å: Chain B: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, H.442, S.443, N.444, F.445, Y.446 Ligands: MAN.15, MAN.16 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.228, B:Y.269 Hydrogen bonds: B:K.204, B:H.442 NAG-NAG-BMA.5: 9 residues within 4Å: Chain A: R.547 Chain B: I.453, K.454, C.457, S.467, L.468, N.489, Y.512, D.514 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.454 NAG-NAG-BMA.6: 11 residues within 4Å: Chain B: Q.456, Y.512, V.536, D.538, S.540, V.566, N.568, E.590, V.592 Ligands: MAN.18, MAN.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.456, B:Q.456, B:Y.512 Hydrophobic interactions: B:V.536

6 x MAN: alpha-D-mannopyranose(Non-covalent)(Non-functional Binders)

MAN.7: 3 residues within 4Å: Chain A: D.440, H.442 Ligands: NAG-NAG-BMA-MAN.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.440 MAN.10: 1 residues within 4Å: Ligands: NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP) MAN.15: 4 residues within 4Å: Chain B: D.440, H.442, S.443 Ligands: NAG-NAG-BMA.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.440 MAN.16: 1 residues within 4Å: Ligands: NAG-NAG-BMA.4 No protein-ligand interaction detected (PLIP) MAN.18: 1 residues within 4Å: Ligands: NAG-NAG-BMA.6 No protein-ligand interaction detected (PLIP) MAN.19: 1 residues within 4Å: Ligands: NAG-NAG-BMA.6 No protein-ligand interaction detected (PLIP)

9 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.8: 9 residues within 4Å: Chain A: I.453, K.454, C.457, S.467, L.468, N.489, Y.512, D.514 Ligands: NAG-BMA.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:K.454, A:Y.512 Hydrogen bonds: A:S.404, A:S.404, A:K.454, A:S.467, A:N.489, A:D.514, A:D.514 Water bridges: A:S.491 NAG.9: 3 residues within 4Å: Chain A: S.500, D.523, N.524 No protein-ligand interaction detected (PLIP) NAG.11: 4 residues within 4Å: Chain A: N.634, F.656, N.658, L.661 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.656 Hydrogen bonds: A:N.634, A:N.658 NAG.12: 2 residues within 4Å: Chain A: P.372, N.373 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.373 NAG.13: 4 residues within 4Å: Chain A: K.586, S.587, V.589, N.618 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.618, A:N.618 NAG.17: 4 residues within 4Å: Chain B: S.500, D.523, N.524, A.525 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.525 NAG.20: 4 residues within 4Å: Chain B: N.634, L.638, N.658, L.661 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.634 NAG.21: 3 residues within 4Å: Chain B: R.348, P.372, N.373 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.348, B:N.373 NAG.22: 4 residues within 4Å: Chain B: K.586, S.587, V.589, N.618 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.618

2 x U57: (2R)-2-[(2-amino-7-fluoropyrido[3,2-d]pyrimidin-4-yl)amino]-2-methylhexan-1-ol(Non-covalent)

U57.14: 12 residues within 4Å: Chain A: D.521, D.523, G.550, V.551, T.552 Chain B: Y.326, I.327, K.328, G.329, Y.331, V.356, F.383 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.326, B:Y.326, B:Y.326 Hydrogen bonds: B:G.329, A:D.523, A:T.552, A:T.552 pi-Stacking: B:Y.331, B:F.383 Salt bridges: A:D.521, A:D.523 U57.23: 13 residues within 4Å: Chain A: F.324, Y.326, I.327, G.329, Y.331, V.356, F.383 Chain B: V.498, D.521, D.523, G.550, V.551, T.552 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:V.498, B:V.551, A:F.324, A:Y.326, A:Y.326, A:Y.326 Hydrogen bonds: B:D.523, B:T.552, B:T.552, B:T.552, A:G.329 Salt bridges: B:D.521, B:D.523 pi-Stacking: A:Y.331, A:F.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mackman, R.L. et al., Discovery of GS-9688 (Selgantolimod) as a Potent and Selective Oral Toll-Like Receptor 8 Agonist for the Treatment of Chronic Hepatitis B. J.Med.Chem. (2020)

Release Date

2021-02-03

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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