SMTL ID : 6zjz.1

Discovery of M5049: a novel selective TLR7/8 inhibitor for treatment of autoimmunity

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

homo-dimer

Ligands

2 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: 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.224, A:Y.265 Hydrogen bonds: A:K.200, A:H.438 Water bridges: A:N.440 NAG-NAG-BMA-MAN-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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.452, A:Q.452, A:Y.508 Hydrophobic interactions: A: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: S.400, I.449, K.450, C.453, D.461, S.463, L.464, N.485, S.487, Y.508, D.510 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 11 residues within 4Å: Chain B: S.400, I.449, K.450, C.453, D.461, S.463, L.464, N.485, S.487, Y.508, D.510 No protein-ligand interaction detected (PLIP)

2 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.4: 14 residues within 4Å: Chain B: K.200, F.202, S.204, L.224, D.226, S.228, Y.265, N.267, D.291, H.438, S.439, N.440, F.441, Y.442 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.224, B:Y.265 Hydrogen bonds: B:K.200, B:H.438 Water bridges: B:N.440 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.452, B:K.450, B:Q.452 Hydrophobic interactions: B:V.532

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

NAG.7: 2 residues within 4Å: Chain A: S.496, N.520 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.496, A:N.520 NAG.8: 4 residues within 4Å: Chain A: L.341, S.342, R.344, N.369 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.344, A:R.344, A:N.369 Water bridges: A:S.342 NAG.9: 5 residues within 4Å: Chain A: N.630, L.634, F.652, N.654, L.657 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.652 NAG.10: 3 residues within 4Å: Chain A: H.51, N.89, T.91 No protein-ligand interaction detected (PLIP) NAG.11: 5 residues within 4Å: Chain A: K.561, S.583, V.585, N.614, T.616 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.583, A:N.614 NAG.13: 2 residues within 4Å: Chain B: S.496, N.520 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.496, B:N.520 Water bridges: B:S.522 NAG.14: 4 residues within 4Å: Chain B: L.341, S.342, R.344, N.369 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.344, B:R.344, B:N.369 NAG.15: 5 residues within 4Å: Chain B: N.630, L.634, F.652, N.654, L.657 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.652 NAG.16: 4 residues within 4Å: Chain B: K.582, S.583, V.585, N.614 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.614, B:N.614

2 x QLH: 5-[(3~{R},5~{S})-3-azanyl-5-(trifluoromethyl)piperidin-1-yl]quinoline-8-carbonitrile(Non-covalent)

QLH.12: 16 residues within 4Å: Chain A: F.320, Y.322, I.323, K.324, G.325, S.326, G.350, V.352, I.377, F.379 Chain B: F.468, F.469, S.490, A.492, Y.541, F.542 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.468, B:F.469, B:Y.541, A:V.352, A:V.352, A:F.379 Hydrogen bonds: B:S.490, A:G.325 Water bridges: B:Q.493 pi-Stacking: B:F.469, A:Y.322 Halogen bonds: A:G.350, A:I.377 QLH.17: 16 residues within 4Å: Chain A: F.468, F.469, S.490, A.492, Y.541, F.542 Chain B: F.320, Y.322, I.323, K.324, G.325, S.326, G.350, V.352, I.377, F.379 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.468, A:F.469, A:Y.541, B:V.352, B:V.352, B:F.379 Hydrogen bonds: A:S.490, B:G.325 pi-Stacking: A:F.469, B:Y.322 Halogen bonds: B:G.350, B:I.377

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.18: 5 residues within 4Å: Chain B: R.349, F.441, Y.442, H.443, F.444 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.349 Water bridges: B:F.444

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vlach, J. et al., Discovery of M5049: A Novel Selective Toll-Like Receptor 7/8 Inhibitor for Treatment of Autoimmunity. J.Pharmacol.Exp.Ther. (2021)

Release Date

2020-12-30

Peptides

Toll-like receptor 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Toll-like receptor 8