SMTL ID : 8s9h.1

Crystal structure of monkey TLR7 ectodomain with compound 14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.524 Hydrogen bonds: A:C.469, A:N.501, A:D.526, A:D.526 NAG.6: 8 residues within 4Å: Chain A: S.537, M.566, N.568, F.569, K.571, N.572, T.590, S.591 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.537, A:T.590 NAG.7: 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.8: 5 residues within 4Å: Chain A: N.391, S.393, M.394, K.396, H.493 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.391, A:K.396 Water bridges: A:N.391 NAG.9: 3 residues within 4Å: Chain A: Q.509, N.512, S.514 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.512, A:S.514 Water bridges: A:T.510, A:N.512 NAG.10: 4 residues within 4Å: Chain A: K.306, G.309, D.310, N.339 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.306 Water bridges: A:G.309, A:N.339 NAG.11: 6 residues within 4Å: Chain A: E.632, D.634, N.657, S.659, T.681, N.705 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.657 Water bridges: A:E.632 NAG.14: 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 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.524 Hydrogen bonds: B:C.469, B:N.501, B:D.526, B:D.526 Water bridges: B:S.468, B:Y.470 NAG.15: 8 residues within 4Å: Chain B: S.537, M.566, N.568, F.569, K.571, N.572, T.590, S.591 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.537, B:T.590 Water bridges: B:R.592, B:E.595 NAG.16: 4 residues within 4Å: Chain B: Q.509, N.512, S.514, E.515 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.512, B:N.512, B:S.514, B:E.515 Water bridges: B:Q.509 NAG.17: 5 residues within 4Å: Chain B: N.391, S.393, M.394, K.396, H.493 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.391, B:K.396 Water bridges: B:S.393, B:H.493 NAG.18: 4 residues within 4Å: Chain B: K.306, G.309, D.310, N.339 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.306 NAG.19: 7 residues within 4Å: Chain B: T.601, E.631, E.632, K.656, N.657, T.681, N.705 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.657, B:N.657, B:T.681, B:N.705 Water bridges: B:E.631, B:N.657 NAG.20: 3 residues within 4Å: Chain B: E.671, R.674, N.698 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.674, B:N.698

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

ZWV.12: 22 residues within 4Å: Chain A: T.510, D.533, L.535, H.536, G.562, I.563, T.564 Chain B: Y.242, N.243, F.327, F.329, E.330, L.331, Q.332, V.333, Y.334, G.357, V.359, T.384, F.386, K.410 Ligands: SO4.13 15 PLIP interactions: 5 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:T.564, A:T.564, B:Y.242, B:Q.332 Water bridges: A:T.510, A:D.533, B:Y.242 Salt bridges: A:D.533 Hydrophobic interactions: B:F.329, B:F.329, B:Y.334, B:V.359, B:F.386 pi-Stacking: B:F.386, B:F.386 ZWV.21: 23 residues within 4Å: Chain A: Y.242, N.243, F.327, F.329, E.330, L.331, Q.332, V.333, Y.334, G.357, V.359, T.384, F.386, K.410 Chain B: T.510, D.533, L.535, H.536, G.562, I.563, T.564, H.565 Ligands: SO4.22 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.329, A:F.329, A:Y.334, A:V.359, A:F.386 Hydrogen bonds: A:Y.242, B:T.564, B:T.564 Water bridges: A:Y.242 pi-Stacking: A:F.386, A:F.386 Salt bridges: B:D.533

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

SO4.13: 5 residues within 4Å: Chain A: N.512, H.536, S.537, T.538 Ligands: ZWV.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.537, A:T.538 Water bridges: A:H.536 Salt bridges: A:H.536 SO4.22: 4 residues within 4Å: Chain B: L.535, H.536, S.537 Ligands: ZWV.21 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.535 Water bridges: B:S.537 Salt bridges: B:H.536

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, L. et al., Identification and Optimization of Small Molecule Pyrazolopyrimidine TLR7 Agonists for Applications 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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