SMTL ID : 4dkq.1

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with DMJ-I-228

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.118, T.120, I.156, H.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.118 Water bridges: A:N.118 NAG.2: 2 residues within 4Å: Chain A: N.113, N.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.125 Water bridges: A:N.113 NAG.3: 9 residues within 4Å: Chain A: P.96, L.145, N.146, N.244, R.246, C.306, V.307, S.308 Ligands: NAG.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:N.146, A:R.246, A:S.308 Water bridges: 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: 6 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, Q.212, K.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.153, A:I.154, A:N.173 NAG.6: 4 residues within 4Å: Chain A: N.179, T.181, Y.198, E.200 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.179, A:Y.198, A:Y.198 NAG.7: 4 residues within 4Å: Chain A: N.202, K.205, G.273, T.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.205 NAG.8: 2 residues within 4Å: Chain A: E.215, N.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.215 NAG.9: 2 residues within 4Å: Chain A: N.253, T.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.253, A:T.255 NAG.10: 4 residues within 4Å: Chain A: T.255, Q.256, N.259, C.262 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.256 Hydrogen bonds: A:N.259 NAG.11: 4 residues within 4Å: Chain A: N.146, S.175, N.309 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.175, A:N.309

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

0LK.13: 17 residues within 4Å: Chain A: V.139, S.140, T.141, D.235, E.237, I.238, S.242, F.243, N.244, F.249, I.285, N.286, M.287, W.288, G.290, G.334, N.335 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.141, A:E.237, A:F.249, A:I.285, A:W.288, A:N.335 Hydrogen bonds: A:N.286, A:G.334 Water bridges: A:D.235, A:D.235, A:N.286, A:M.287, A:G.290 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

clade A/E 93TH057 HIV-1 gp120 core: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

clade A/E 93TH057 HIV-1 gp120 core

Related Entries With Identical Sequence