SMTL ID : 4dko.2 (1 other biounit)

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with TS-II-224

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 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, S.158, L.161, H.220 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.161 NAG.2: 4 residues within 4Å: Chain A: H.42, N.113, K.115, N.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.42, A:K.115 NAG.3: 9 residues within 4Å: Chain A: K.136, V.138, L.145, N.146, R.246, C.306, V.307, S.308 Ligands: NAG.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.138, A:L.145 Hydrogen bonds: A:K.136, A:N.146, A:R.246, A:S.308 Water bridges: A:R.246 NAG.4: 3 residues within 4Å: Chain A: N.160, T.162, N.163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.160, A:N.160, A:T.162, A:N.163 NAG.5: 6 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212, K.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.154 NAG.6: 6 residues within 4Å: Chain A: N.179, T.181, Y.198, E.200, K.303, N.305 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.179, A:E.200, A:K.303 Water bridges: A:T.181, A:E.200, A:N.305 NAG.7: 3 residues within 4Å: Chain A: N.202, T.204, K.205 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.202, A:K.205 NAG.8: 3 residues within 4Å: Chain A: E.219, N.222, N.223 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain A: T.239, M.240, N.253, T.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.253, A:T.255 NAG.10: 2 residues within 4Å: Chain A: N.259, C.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.259 Water bridges: A:N.259 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 Water bridges: A:K.174, A:K.174

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 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.64, A:D.64

1 x 0LM: N-(4-chloro-3-fluorophenyl)-N'-(1,2,2,6,6-pentamethylpiperidin-4-yl)ethanediamide(Non-covalent)

0LM.13: 14 residues within 4Å: Chain A: V.139, S.140, T.141, E.237, I.238, S.242, F.243, N.244, N.286, W.288, G.290, G.334, N.335, I.336 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.141, A:E.237 Hydrogen bonds: A:N.286, A:G.334 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
C

HIV-1 gp120 core

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