SMTL ID : 8ttz.1

Crystal structure of monkey TLR7 ectodomain with compound 20

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.14 Å

Oligo State

homo-dimer

Ligands

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.1: 8 residues within 4Å: Chain A: C.161, Y.162, P.166, C.167, Y.168, V.169, S.170, N.193 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 8 residues within 4Å: Chain B: C.161, Y.162, P.166, C.167, Y.168, V.169, S.170, N.193 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain B: N.47, V.70, E.71, S.109 No protein-ligand interaction detected (PLIP)

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

NAG.2: 8 residues within 4Å: Chain A: S.468, C.469, S.479, K.480, N.501, S.503, Y.524, D.526 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.524 Hydrogen bonds: A:S.479, A:D.526 NAG.3: 4 residues within 4Å: Chain A: N.47, V.70, E.71, S.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.47, A:S.109, A:S.109 NAG.4: 6 residues within 4Å: Chain A: S.537, M.566, N.568, K.571, N.572 Ligands: SO4.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.537, A:S.537, A:K.571 NAG.5: 4 residues within 4Å: Chain A: R.674, R.695, N.698, R.701 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.674 Hydrogen bonds: A:R.695, A:N.698 NAG.6: 5 residues within 4Å: Chain A: N.391, S.393, K.396, Q.492 Ligands: SO4.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.396, A:K.396 NAG.7: 2 residues within 4Å: Chain A: N.512, S.514 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.512, A:S.514 NAG.8: 4 residues within 4Å: Chain A: K.306, G.309, D.310, N.339 No protein-ligand interaction detected (PLIP) NAG.32: 7 residues within 4Å: Chain B: S.468, C.469, S.479, K.480, N.501, Y.524, D.526 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.524 Hydrogen bonds: B:S.479, B:D.526 NAG.33: 7 residues within 4Å: Chain B: S.537, M.566, N.568, K.571, N.572, S.591 Ligands: SO4.39 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.537, B:S.537, B:N.568 NAG.34: 2 residues within 4Å: Chain B: N.512, S.514 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.512, B:S.514 NAG.35: 5 residues within 4Å: Chain B: N.391, S.393, K.396, Q.492, H.493 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.391, B:K.396, B:K.396 NAG.36: 4 residues within 4Å: Chain B: K.306, G.309, D.310, N.339 No protein-ligand interaction detected (PLIP)

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

SO4.9: 1 residues within 4Å: Chain A: R.286 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: F.485, Q.509, T.510 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain A: L.363, K.364, S.365, N.391, M.394 Ligands: NAG.6 Ligand excluded by PLIP SO4.12: 6 residues within 4Å: Chain A: L.535, H.536, S.537, T.538, M.566 Ligands: NAG.4 Ligand excluded by PLIP SO4.13: 6 residues within 4Å: Chain A: I.41, P.42, T.43, R.65 Chain B: H.798, T.810 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: R.714, R.762 Ligands: SO4.21 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain A: K.396, Q.397, F.398, K.399, R.400 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain A: G.39, G.40, R.65 Ligand excluded by PLIP SO4.17: 9 residues within 4Å: Chain A: C.161, Y.162, D.191, N.192, N.193, N.212, N.213, M.214, Y.446 Ligand excluded by PLIP SO4.18: 7 residues within 4Å: Chain A: R.354, V.379, V.403, D.405, V.437, L.438, Y.470 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain A: N.705, Y.729 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain A: K.471, Y.472, R.523 Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Chain A: R.714, K.736, R.762 Ligands: SO4.14, SO4.26 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain A: S.85, K.86, S.87 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain A: Q.474, K.498, E.521 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain A: R.728, K.754 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain A: K.185, V.186, T.206, E.207, Q.230 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain A: Q.712, K.736 Ligands: SO4.21 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain A: K.388, K.410 Ligand excluded by PLIP SO4.37: 2 residues within 4Å: Chain B: R.714, R.762 Ligand excluded by PLIP SO4.38: 2 residues within 4Å: Chain B: R.286, K.289 Ligand excluded by PLIP SO4.39: 6 residues within 4Å: Chain B: L.535, H.536, S.537, T.538, M.566 Ligands: NAG.33 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain B: S.85, K.86, S.87 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain B: Q.474, K.498, E.521 Ligand excluded by PLIP SO4.42: 5 residues within 4Å: Chain B: K.396, Q.397, F.398, K.399, R.400 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain B: K.471, Y.472, R.523 Ligand excluded by PLIP SO4.44: 6 residues within 4Å: Chain B: P.60, H.64, R.99, S.100, G.103, L.104 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain A: T.810 Chain B: I.41, P.42, T.43, R.65 Ligand excluded by PLIP SO4.46: 3 residues within 4Å: Chain B: R.335, A.336, S.337 Ligand excluded by PLIP

2 x QCX: (3S)-3-({5-amino-1-[(2-methoxy-4-{[(oxan-4-yl)amino]methyl}phenyl)methyl]-1H-pyrazolo[4,3-d]pyrimidin-7-yl}amino)hexan-1-ol(Non-covalent)

QCX.27: 6 residues within 4Å: Chain A: T.510, D.533, L.535, G.562, I.563, T.564 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.535 Hydrogen bonds: A:T.564, A:T.564 Salt bridges: A:D.533 QCX.31: 6 residues within 4Å: Chain B: T.510, D.533, L.535, G.562, I.563, T.564 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.535 Hydrogen bonds: B:T.564, B:T.564 Salt bridges: B:D.533

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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