SMTL ID : 5wyx.1

Crystal structure of human TLR8 in complex with CU-CPT8m

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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.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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.440, A:K.204, A:H.442 Hydrophobic interactions: A:K.204, A:F.206, A:L.228

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 10 residues within 4Å: Chain A: R.450, I.453, K.454, C.457, D.465, S.467, N.489, S.491, Y.512, D.514 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.450 NAG-NAG.5: 10 residues within 4Å: Chain A: R.547 Chain B: I.453, K.454, C.457, D.465, S.467, N.489, S.491, Y.512, D.514 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.547

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

2 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.4: 14 residues within 4Å: Chain B: K.204, F.206, S.208, L.228, D.230, S.232, Y.269, N.271, P.441, H.442, S.443, N.444, F.445, Y.446 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.204, B:F.206, B:L.228 Hydrogen bonds: B:K.204, B:P.441 NAG-NAG-BMA-MAN.6: 9 residues within 4Å: Chain B: K.454, Q.456, Y.512, D.538, S.540, V.566, N.568, E.590, V.592 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.456, B:K.454, B:Q.456, B:Y.512

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

NAG.7: 4 residues within 4Å: Chain A: S.200, S.201, R.203, N.225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.203 NAG.8: 4 residues within 4Å: Chain A: L.345, S.346, R.348, N.373 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.348, A:R.348, A:N.373 NAG.9: 3 residues within 4Å: Chain A: K.586, V.589, N.618 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.618, A:N.618 NAG.10: 5 residues within 4Å: Chain A: N.634, F.656, N.658, T.660, L.661 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.656 Hydrogen bonds: A:T.660 NAG.13: 2 residues within 4Å: Chain B: H.55, N.93 No protein-ligand interaction detected (PLIP) NAG.14: 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 CU8: 7-(3-methylphenyl)pyrazolo[1,5-a]pyrimidine-3-carboxamide(Non-covalent)

CU8.11: 17 residues within 4Å: Chain A: F.472, F.473, A.496, Q.497, V.498 Chain B: F.239, N.240, F.324, Y.326, I.327, K.328, G.329, S.330, G.354, V.356, I.381, F.383 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:F.472, A:F.473, A:A.496, B:F.239, B:F.324, B:Y.326, B:Y.326, B:Y.326, B:I.381, B:F.383 Hydrogen bonds: A:Q.497, A:V.498, B:N.240, B:G.329 pi-Stacking: A:F.473, A:Y.545 CU8.12: 17 residues within 4Å: Chain A: F.239, N.240, F.324, Y.326, I.327, K.328, G.329, S.330, G.354, V.356, F.383 Chain B: F.472, F.473, A.496, Q.497, V.498, Y.545 16 PLIP interactions: 7 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:F.472, B:F.473, B:A.496, B:Y.545, A:F.239, A:F.324, A:Y.326, A:Y.326, A:Y.326, A:V.356, A:F.383 Hydrogen bonds: B:Q.497, B:V.498, A:N.240, A:G.329 pi-Stacking: B:F.473

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S. et al., Small-molecule inhibition of TLR8 through stabilization of its resting state. Nat. Chem. Biol. (2018)

Release Date

2017-12-13

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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