SMTL ID : 7r52.1

Crystal structure of human TLR8 in complex with Compound 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.94 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: 15 residues within 4Å: Chain A: K.200, F.202, S.204, L.224, D.226, S.228, Y.265, N.267, D.291, D.436, H.438, S.439, N.440, F.441, Y.442 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.224, A:Y.265 Hydrogen bonds: A:K.200, 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: 15 residues within 4Å: Chain B: K.200, F.202, S.204, L.224, D.226, S.228, Y.265, N.267, D.291, D.436, H.438, S.439, N.440, F.441, Y.442 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.224, B:Y.265 Hydrogen bonds: B:K.200, B:H.438 NAG-NAG-BMA-MAN-MAN.6: 9 residues within 4Å: Chain B: Q.452, Y.508, V.532, D.534, S.536, V.562, N.564, E.586, V.588 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.452, 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: 10 residues within 4Å: Chain A: S.400, I.449, K.450, C.453, D.461, S.463, N.485, S.487, Y.508, D.510 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 10 residues within 4Å: Chain B: S.400, I.449, K.450, C.453, D.461, S.463, N.485, S.487, Y.508, D.510 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.487

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

NAG.7: 2 residues within 4Å: Chain A: S.496, N.520 No protein-ligand interaction detected (PLIP) 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: 2 residues within 4Å: Chain A: R.344, N.369 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.369 Water bridges: A:R.344, A:N.369 NAG.10: 3 residues within 4Å: Chain A: Q.362, M.365, N.390 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.390 Water bridges: A:E.358 NAG.11: 4 residues within 4Å: Chain A: K.561, K.582, V.585, N.614 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain A: K.37, Y.38, G.59, N.62 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.37 Hydrogen bonds: A:N.62 Water bridges: A:N.62 NAG.14: 2 residues within 4Å: Chain B: S.496, N.520 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.520 NAG.15: 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.16: 2 residues within 4Å: Chain B: R.344, N.369 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.369 NAG.17: 2 residues within 4Å: Chain B: M.365, N.390 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.390 NAG.18: 4 residues within 4Å: Chain B: K.561, K.582, V.585, N.614 No protein-ligand interaction detected (PLIP) NAG.19: 4 residues within 4Å: Chain B: K.37, Y.38, G.59, N.62 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.37 Hydrogen bonds: B:N.62

2 x I6A: 5-methoxy-6-pyridin-4-yl-1~{H}-indole(Non-covalent)

I6A.13: 11 residues within 4Å: Chain A: F.468, F.469, S.490, A.492, R.515 Chain B: F.320, Y.322, K.324, G.325, V.352, F.379 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.468, A:F.468, A:A.492, B:Y.322, B:V.352 Hydrogen bonds: A:S.490, B:G.325 pi-Stacking: B:F.379, B:F.379 I6A.20: 14 residues within 4Å: Chain A: F.320, Y.322, I.323, K.324, G.325, S.326, G.350, V.352, F.379 Chain B: F.468, F.469, S.490, A.492, R.515 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.322, A:Y.322, A:V.352, A:F.379, B:F.468, B:F.468, B:A.492 Hydrogen bonds: A:G.325, B:F.468, B:A.492 pi-Stacking: A:F.379

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Betschart, C. et al., Structure-Based Optimization of a Fragment-like TLR8 Binding Screening Hit to an In Vivo Efficacious TLR7/8 Antagonist. Acs Med.Chem.Lett. (2022)

Release Date

2022-03-23

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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