SMTL ID : 7r54.1

Crystal structure of human TLR8 in complex with Compound 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.84 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: 14 residues within 4Å: Chain A: K.200, F.202, S.204, L.224, D.226, S.228, Y.265, N.267, 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: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: 14 residues within 4Å: Chain B: K.200, F.202, S.204, L.224, D.226, S.228, Y.265, N.267, 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:H.438 NAG-NAG-BMA-MAN-MAN.6: 9 residues within 4Å: Chain B: K.450, Q.452, Y.508, D.534, S.536, V.562, N.564, E.586, V.588 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.562 Hydrogen bonds: B:K.450, B:Q.452

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: 9 residues within 4Å: Chain A: S.400, I.449, K.450, C.453, S.463, N.485, S.487, Y.508, D.510 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 9 residues within 4Å: Chain B: S.400, I.449, K.450, C.453, S.463, N.485, S.487, Y.508, D.510 No protein-ligand interaction detected (PLIP)

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

NAG.7: 4 residues within 4Å: Chain A: S.496, T.498, N.520, S.522 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.520 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: 4 residues within 4Å: Chain A: L.341, S.342, R.344, N.369 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.344, A:R.344 NAG.10: 2 residues within 4Å: Chain A: E.358, N.390 No protein-ligand interaction detected (PLIP) NAG.11: 5 residues within 4Å: Chain A: K.561, K.582, S.583, V.585, N.614 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain A: K.37, G.59, N.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.62 NAG.15: 2 residues within 4Å: Chain B: S.496, N.520 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.496, B:N.520 NAG.16: 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.17: 4 residues within 4Å: Chain B: L.341, S.342, R.344, N.369 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.344, B:R.344 NAG.18: 4 residues within 4Å: Chain B: E.358, Q.362, M.365, N.390 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.362, B:Q.362 NAG.19: 5 residues within 4Å: Chain B: K.561, K.582, S.583, V.585, N.614 No protein-ligand interaction detected (PLIP) NAG.20: 4 residues within 4Å: Chain B: K.37, G.59, Q.61, N.62 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.61, B:N.62

2 x I5B: (5-methoxy-6-pyridin-4-yl-1~{H}-indazol-3-yl)-(4-methylpiperazin-1-yl)methanone(Non-covalent)

I5B.13: 14 residues within 4Å: Chain A: F.468, F.469, S.490, A.492, Y.541 Chain B: F.320, Y.322, K.324, G.325, G.350, V.352, I.377, F.379, E.401 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.468, A:F.468, A:F.469, A:A.492, B:Y.322, B:V.352 Hydrogen bonds: A:S.490, A:Y.541, B:G.325 pi-Stacking: A:Y.541, B:F.379, B:F.379 Salt bridges: B:E.401 I5B.14: 14 residues within 4Å: Chain A: F.320, Y.322, K.324, G.325, G.350, V.352, I.377, F.379, E.401 Chain B: F.468, F.469, S.490, A.492, Y.541 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.468, B:F.468, B:A.492, A:Y.322, A:Y.322, A:V.352 Hydrogen bonds: B:S.490, B:Y.541, A:G.325 Salt bridges: A:E.401 pi-Stacking: A:F.379, 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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