SMTL ID : 4dkr.1 (1 other biounit)

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-169

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.118, T.120, I.156, S.158, H.220 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.118 Water bridges: A:N.118, A:S.158, A:S.158 NAG.2: 3 residues within 4Å: Chain A: D.114, K.115, N.125 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.114 Hydrogen bonds: A:K.115, A:N.125 NAG.3: 9 residues within 4Å: Chain A: P.96, K.136, L.145, N.146, N.244, C.306, V.307, S.308 Ligands: NAG.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:S.308 Water bridges: A:K.136, A:N.244, A:V.307 NAG.4: 3 residues within 4Å: Chain A: N.160, T.162, N.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.160 Water bridges: A:N.163 NAG.5: 5 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.216 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.154, A:N.173, A:K.216, A:K.216 NAG.6: 4 residues within 4Å: Chain A: N.179, Y.198, E.200, V.307 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.307 Hydrogen bonds: A:N.179, A:Y.198, A:Y.198 Water bridges: A:T.181, A:T.181, A:N.305 NAG.7: 3 residues within 4Å: Chain A: N.202, T.204, K.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.202 NAG.8: 2 residues within 4Å: Chain A: N.222, N.223 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.223 Water bridges: A:N.223 NAG.9: 3 residues within 4Å: Chain A: T.239, N.253, T.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.253, A:T.255 Water bridges: A:T.239, A:N.253 NAG.10: 4 residues within 4Å: Chain A: T.255, Q.256, N.259, T.261 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.255, A:Q.256 NAG.11: 4 residues within 4Å: Chain A: N.146, S.175, N.309 Ligands: NAG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.175, A:N.309 Water bridges: A:S.175

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.12: 7 residues within 4Å: Chain A: L.9, C.11, H.29, A.30, Q.60, D.64, Y.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.60 Salt bridges: A:D.64, A:D.64

1 x 0LJ: N-[(1R,2R)-2-carbamimidamido-2,3-dihydro-1H-inden-1-yl]-N'-(4-chloro-3-fluorophenyl)ethanediamide(Non-covalent)

0LJ.13: 15 residues within 4Å: Chain A: V.139, S.140, T.141, D.235, E.237, I.238, S.242, F.243, F.249, I.285, N.286, M.287, W.288, G.290, G.334 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.141, A:E.237, A:F.249, A:I.285, A:W.288 Hydrogen bonds: A:N.286, A:G.334 Water bridges: A:D.235, A:D.235 Salt bridges: A:D.235 pi-Stacking: A:W.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lalonde, J.M. et al., Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule HIV-1 Entry Inhibitors. J.Med.Chem. (2012)

Release Date

2012-05-02

Peptides

HIV-1 gp120 core: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HIV-1 gp120 core

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