SMTL ID : 7ytp.1

TLR7 in complex with an inhibitor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

6 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.179, Y.180, P.184, C.185, Y.186, V.187, S.188, N.211 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 8 residues within 4Å: Chain A: S.486, C.487, D.495, S.497, K.498, N.519, Y.542, D.544 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: I.44, N.65, V.88, E.89, K.126, S.127 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.126 NAG-NAG.4: 8 residues within 4Å: Chain B: C.179, Y.180, P.184, C.185, Y.186, V.187, S.188, N.211 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain B: S.486, C.487, S.497, K.498, N.519, Y.542, D.544 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: I.44, N.65, V.88, E.89, K.126, S.127 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:K.126

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

NAG.7: 3 residues within 4Å: Chain A: L.36, P.60, N.62 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain A: S.555, N.586, K.589, N.590 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.589 Hydrogen bonds: A:S.555, A:S.555, A:N.586 NAG.9: 4 residues within 4Å: Chain A: N.409, S.411, K.414, H.511 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.409, A:K.414, A:K.414 NAG.10: 4 residues within 4Å: Chain A: K.324, G.327, D.328, N.357 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.324, A:N.357 NAG.11: 4 residues within 4Å: Chain A: E.650, K.674, N.675, T.699 No protein-ligand interaction detected (PLIP) NAG.13: 3 residues within 4Å: Chain B: L.36, P.60, N.62 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.62 NAG.14: 4 residues within 4Å: Chain B: S.555, N.586, K.589, N.590 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.589 Hydrogen bonds: B:S.555, B:S.555, B:N.586 NAG.15: 3 residues within 4Å: Chain B: N.409, S.411, K.414 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.409, B:K.414, B:K.414 NAG.16: 4 residues within 4Å: Chain B: K.324, G.327, D.328, N.357 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.324, B:N.357 NAG.17: 5 residues within 4Å: Chain B: K.674, N.675, E.698, T.699, N.723 No protein-ligand interaction detected (PLIP)

2 x JRI: (2R,6R)-4-(8-cyanoquinolin-5-yl)-N-[(3S,4R)-4-fluoranylpyrrolidin-3-yl]-6-methyl-morpholine-2-carboxamide(Non-covalent)

JRI.12: 11 residues within 4Å: Chain A: F.347, E.348, L.349, Q.350, V.351, V.377, T.402, F.404 Chain B: F.502, F.503, S.526 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:F.502, B:F.503, A:F.347, A:F.347, A:L.349, A:V.377, A:T.402 pi-Stacking: B:F.503 Hydrogen bonds: A:Q.350, A:Q.350, A:V.351 JRI.18: 14 residues within 4Å: Chain A: F.502, F.503, L.524, S.526 Chain B: Y.260, N.261, F.347, E.348, L.349, Q.350, V.351, V.377, T.402, F.404 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.260, B:F.347, B:V.377, B:V.377, B:T.402, A:F.502, A:F.503 Hydrogen bonds: B:Q.350, B:V.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., TLR7 in complex with an inhibitor. To Be Published

Release Date

2023-11-15

Peptides

Toll-like receptor 7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Toll-like receptor 7