SMTL ID : 7r53.1

Crystal structure of human TLR8 in complex with Compound 15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.12 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: 13 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, 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: 13 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, 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: 10 residues within 4Å: Chain B: K.450, Q.452, Y.508, V.532, D.534, S.536, V.562, N.564, E.586, V.588 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.452, B:Q.452 Hydrophobic interactions: B:V.532

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: 11 residues within 4Å: Chain A: I.449, K.450, C.453, D.461, S.463, L.464, N.485, S.487, Y.508, D.510, N.513 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.513 NAG-NAG-BMA.5: 10 residues within 4Å: Chain B: S.400, I.449, K.450, C.453, S.463, L.464, N.485, S.487, Y.508, D.510 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.513

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

NAG.7: 3 residues within 4Å: Chain A: S.496, N.520, S.522 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.520 NAG.8: 4 residues within 4Å: Chain A: N.630, L.634, N.654, L.657 No protein-ligand interaction detected (PLIP) NAG.9: 5 residues within 4Å: Chain A: L.341, S.342, R.344, P.368, N.369 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.368 Hydrogen bonds: A:R.344, A:R.344 NAG.10: 4 residues within 4Å: Chain A: E.358, K.386, Q.389, N.390 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.389 Hydrogen bonds: A:N.390 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, Y.38, N.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.62 NAG.15: 3 residues within 4Å: Chain B: S.496, N.520, S.522 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.520 NAG.16: 4 residues within 4Å: Chain B: N.630, L.634, N.654, L.657 No protein-ligand interaction detected (PLIP) NAG.17: 4 residues within 4Å: Chain B: S.342, R.344, P.368, N.369 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.368 Hydrogen bonds: B:R.344, B:R.344 NAG.18: 4 residues within 4Å: Chain B: E.358, K.386, Q.389, N.390 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.389 Hydrogen bonds: B:N.390 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: 3 residues within 4Å: Chain B: K.37, Y.38, N.62 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.62

2 x I5N: 5-cyclopropyl-6-(2,6-dimethylpyridin-4-yl)-~{N}-[(3~{R},4~{R})-3-fluoranylpiperidin-4-yl]-1~{H}-indazol-3-amine(Non-covalent)

I5N.13: 16 residues within 4Å: Chain A: F.468, F.469, S.490, A.492, Y.541 Chain B: F.235, F.320, Y.322, I.323, K.324, G.325, S.326, G.350, V.352, F.379, E.401 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.235, B:F.320, B:Y.322, B:Y.322, B:Y.322, B:Y.322, B:V.352, A:F.468, A:F.468, A:Y.541 Hydrogen bonds: B:G.325, A:S.490, A:Y.541 pi-Stacking: B:F.379, B:F.379 I5N.14: 17 residues within 4Å: Chain A: F.235, F.320, Y.322, I.323, K.324, G.325, S.326, G.350, V.352, I.377, F.379, E.401 Chain B: F.468, S.490, A.492, R.515, Y.541 17 PLIP interactions: 7 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:F.468, B:F.468, B:A.492, B:Y.541, A:F.235, A:F.320, A:Y.322, A:Y.322, A:Y.322, A:K.324, A:V.352 Hydrogen bonds: B:S.490, B:Y.541, A:G.325 pi-Stacking: B:Y.541, 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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