SMTL ID : 8tty.1

Crystal structure of monkey TLR7 ectodomain with compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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.1: 10 residues within 4Å: Chain A: C.161, Y.162, Y.163, P.166, C.167, Y.168, V.169, S.170, N.193, M.214 No protein-ligand interaction detected (PLIP)

3 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: 8 residues within 4Å: Chain A: H.24, I.26, N.47, V.70, E.71, K.108, S.109, Q.129 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 10 residues within 4Å: Chain B: C.161, Y.162, Y.163, P.166, C.167, Y.168, V.169, S.170, N.193, M.214 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain B: H.24, I.26, N.47, V.70, E.71, K.108, S.109, Q.129 No protein-ligand interaction detected (PLIP)

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

NAG.5: 10 residues within 4Å: Chain A: S.407, S.468, C.469, S.479, K.480, C.499, N.501, S.503, Y.524, D.526 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.524 Hydrogen bonds: A:C.469, A:S.479, A:N.501, A:D.526 Water bridges: A:K.480 NAG.6: 8 residues within 4Å: Chain A: S.537, M.566, N.568, F.569, K.571, N.572, T.590, S.591 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.571 Hydrogen bonds: A:S.537, A:N.568 NAG.7: 4 residues within 4Å: Chain A: R.674, R.695, N.698, R.701 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.674 Hydrogen bonds: A:R.695, A:N.698, A:R.701, A:R.701 Water bridges: A:R.674 NAG.8: 4 residues within 4Å: Chain A: N.391, S.393, K.396, H.493 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.391, A:K.396 NAG.9: 3 residues within 4Å: Chain A: F.485, N.512, S.514 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.512, A:N.512 NAG.10: 4 residues within 4Å: Chain A: K.306, G.309, D.310, N.339 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.309, A:N.339 Water bridges: A:R.335, A:N.339 NAG.11: 7 residues within 4Å: Chain A: E.632, L.633, D.634, N.657, S.659, T.681, N.705 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.633, A:N.657 NAG.13: 10 residues within 4Å: Chain B: S.407, S.468, C.469, S.479, K.480, C.499, N.501, S.503, Y.524, D.526 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.524 Hydrogen bonds: B:C.469, B:S.479, B:N.501, B:D.526, B:D.526 NAG.14: 9 residues within 4Å: Chain B: S.537, M.566, N.568, F.569, K.571, N.572, T.590, S.591 Ligands: SO4.23 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.571 Hydrogen bonds: B:S.537, B:N.568, B:K.571 NAG.15: 4 residues within 4Å: Chain B: F.485, N.512, S.514, T.538 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.512, B:N.512 Water bridges: B:E.515 NAG.16: 5 residues within 4Å: Chain B: N.391, S.393, M.394, K.396, H.493 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.391, B:K.396 NAG.17: 4 residues within 4Å: Chain B: K.306, G.309, D.310, N.339 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.309, B:N.339 Water bridges: B:R.335, B:N.339 NAG.18: 5 residues within 4Å: Chain B: E.631, E.632, N.657, T.681, N.705 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.631, B:E.631, B:T.681 Water bridges: B:N.657, B:N.657 NAG.19: 3 residues within 4Å: Chain B: E.671, R.674, N.698 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.671, B:E.671, B:R.674, B:N.698

2 x QEC: N~7~-butyl-2-({4-[(cyclobutylamino)methyl]-2-methoxyphenyl}methyl)-2H-pyrazolo[4,3-d]pyrimidine-5,7-diamine(Non-covalent)

QEC.12: 20 residues within 4Å: Chain A: T.510, D.533, L.535, H.536, Y.557, G.562, I.563, T.564 Chain B: Y.242, N.243, F.327, F.329, Q.332, V.333, Y.334, G.357, V.359, T.384, F.386, K.410 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.327, B:F.329, B:Y.334, B:Y.334, B:V.359, B:F.386, A:L.535 Hydrogen bonds: B:Q.332, A:T.564, A:T.564, A:T.564 Water bridges: B:Y.242, B:Y.242, A:D.533 pi-Stacking: B:F.386, B:F.386 Salt bridges: A:D.533 QEC.20: 19 residues within 4Å: Chain A: Y.242, N.243, F.327, F.329, Q.332, V.333, Y.334, G.357, V.359, K.361, T.384, F.386 Chain B: T.510, D.533, L.535, H.536, G.562, I.563, T.564 15 PLIP interactions: 6 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:L.535, A:F.327, A:F.329, A:Y.334, A:Y.334, A:V.359, A:F.386 Hydrogen bonds: B:T.564, B:T.564, B:T.564, A:Q.332 Water bridges: B:D.533 Salt bridges: B:D.533 pi-Stacking: A:F.386, A:F.386

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.21: 7 residues within 4Å: Chain A: N.243, A.244 Chain B: S.589, T.590, R.592, R.619, Y.620 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.592, B:Y.620, A:N.243, A:A.244 Water bridges: B:S.589, B:T.590, B:R.619 Salt bridges: B:R.619 SO4.22: 4 residues within 4Å: Chain B: N.568, S.591, R.592, T.593 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.592, B:T.593, B:T.593 Water bridges: B:N.568, B:N.568 SO4.23: 5 residues within 4Å: Chain B: H.536, S.537, T.538, M.566 Ligands: NAG.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.537, B:S.537 Water bridges: B:H.536, B:T.538

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Poudel, Y.B. et al., Discovery of Novel TLR7 Agonists as Systemic Agent for Combination With aPD1 for Use in Immuno-oncology. Acs Med.Chem.Lett. (2024)

Release Date

2024-02-07

Peptides

Toll-like receptor 7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Toll-like receptor 7

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