SMTL ID : 7crf.1

Crystal structure of human TLR8 in complex with CU-CPD107

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.1: 14 residues within 4Å: Chain A: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, D.440, H.442, S.443, N.444, F.445, Y.446 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.228, A:Y.269 Hydrogen bonds: A:H.442

1 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: S.404, R.450, I.453, K.454, C.457, D.465, S.467, N.489, S.491, Y.512, D.514 No protein-ligand interaction detected (PLIP)

1 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.3: 11 residues within 4Å: Chain A: K.454, Q.456, Y.512, T.516, V.536, D.538, S.540, V.566, N.568, E.590, V.592 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.456, A:K.454, A:Q.456 Hydrophobic interactions: A:V.536

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-MAN-MAN.4: 15 residues within 4Å: Chain B: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, D.440, H.442, S.443, N.444, F.445, Y.446 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.6 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.228, B:Y.269 Hydrogen bonds: B:K.204, B:H.442

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.5: 8 residues within 4Å: Chain B: R.450, I.453, K.454, D.465, S.467, N.489, Y.512, D.514 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.450

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN.6: 11 residues within 4Å: Chain B: K.454, Q.456, Y.512, V.536, D.538, S.540, V.566, N.568, E.590, V.592 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.456, B:Q.456, B:Y.512 Hydrophobic interactions: B:Y.512, B:V.536

2 x GD0: 1-[2-(ethoxymethyl)-4-iodanyl-5-phenyl-imidazol-1-yl]-2-methyl-propan-2-ol(Non-covalent)

GD0.7: 15 residues within 4Å: Chain A: F.472, F.473, A.496, Q.497, V.498, D.521, Y.545 Chain B: F.239, Y.326, I.327, K.328, G.329, S.330, V.356, F.383 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.239, B:F.239, B:Y.326, B:V.356, B:F.383, A:F.472, A:F.473 Hydrogen bonds: A:V.498 pi-Stacking: A:F.473 GD0.19: 14 residues within 4Å: Chain A: F.239, Y.326, I.327, K.328, G.329, S.330, V.356 Chain B: F.472, F.473, A.496, Q.497, V.498, D.521, Y.545 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.472, A:F.239, A:Y.326, A:V.356, A:V.356 Hydrogen bonds: B:A.496, B:V.498, A:Y.326 pi-Stacking: B:F.473

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

NAG.8: 4 residues within 4Å: Chain A: N.138, T.140, N.169, E.171 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: E.362, M.369, N.394 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: S.200, R.203, N.225 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.263 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: N.634, N.658, T.660, L.661 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: K.565, S.587, V.589, N.618 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: T.529, Q.559, N.560 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: L.345, S.346, R.348, P.372, N.373 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: K.41, Y.42, N.66 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: S.500, N.524, S.526 Chain B: K.328 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: H.55, N.93 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: E.362, N.394 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: S.200, R.203, I.224, N.225 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: I.224, Q.262, N.263 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain B: N.634, L.638, N.658, T.660, L.661 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: K.586, S.587, N.618 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: T.529, Q.559, N.560 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: L.345, S.346, R.348, N.373 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: K.41, Y.42, Q.65, N.66 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: K.328 Chain B: S.500, D.523, N.524 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: H.55, N.93 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., Tetrasubstituted imidazoles as incognito Toll-like receptor 8 a(nta)gonists. Nat Commun (2021)

Release Date

2021-06-23

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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