SMTL ID : 7tjo.3 (3 other biounits)

HIV-1 gp120 complex with CJF-II-197-S

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.07 Å

Oligo State

monomer

Ligands

1 x I6Q: N~1~-[(1R,2R)-5-{[(3R)-3-aminopyrrolidin-1-yl]methyl}-2-(carbamimidamidomethyl)-2,3-dihydro-1H-inden-1-yl]-N~2~-(4-chloro-3-fluorophenyl)ethanediamide(Non-covalent)

I6Q.1: 19 residues within 4Å: Chain A: V.139, S.140, T.141, E.237, I.238, S.242, F.243, N.244, F.249, I.288, N.289, M.290, W.291, E.293, V.294, G.295, G.338, G.339, M.341 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.238, A:F.249, A:I.288 Hydrogen bonds: A:N.289, A:M.290, A:G.295, A:G.339 pi-Stacking: A:W.291 Halogen bonds: A:S.242

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

NAG.2: 6 residues within 4Å: Chain A: N.118, T.120, P.122, S.158, L.161, H.220 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118, A:T.120 Water bridges: A:E.159 NAG.3: 6 residues within 4Å: Chain A: P.96, L.145, N.146, C.309, N.310, S.311 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:S.311 Water bridges: A:T.308, A:N.310 NAG.4: 7 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, E.174, K.212, E.216 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.152, A:I.154, A:E.174, A:K.212, A:E.216 NAG.5: 5 residues within 4Å: Chain A: N.202, S.204, N.275, G.276, T.277 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.204, A:N.275 NAG.6: 5 residues within 4Å: Chain A: E.203, S.204, N.207, Y.267, H.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.269 NAG.7: 5 residues within 4Å: Chain A: L.236, T.239, T.240, N.253, S.255 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.236, A:T.240 Hydrogen bonds: A:N.253, A:S.255 NAG.8: 6 residues within 4Å: Chain A: P.230, D.256, N.259, T.270, G.271, R.272 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.256, A:N.259, A:R.272, A:R.272 NAG.9: 2 residues within 4Å: Chain A: N.160, T.162 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain A: S.175, N.310, N.312 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaplain, C. et al., Structural and Functional Characterization of Indane-Core CD4-Mimetic Compounds Substituted with Heterocyclic Amines. ACS Medicinal Chemistry Letters (2023)

Release Date

2023-01-25

Peptides

Glycoprotein 120: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Glycoprotein 120

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