SMTL ID : 4i54.1 (1 other biounit)

Crystal structure of clade A/E 93TH057 HIV-1 gp120 H375S core in complex with DMJ-II-121

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x 1C1: amino({[(1R,2R)-1-({[(4-chloro-3-fluorophenyl)amino](oxo)acetyl}amino)-2,3-dihydro-1H-inden-2-yl]methyl}amino)methanimi nium(Non-covalent)

1C1.1: 17 residues within 4Å: Chain A: V.139, S.140, T.141, E.237, S.242, F.243, N.244, F.249, I.285, N.286, M.287, W.288, G.290, T.291, G.292, G.333, 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:M.287, A:T.291, A:G.292, A:G.334 pi-Stacking: A:W.288

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

EPE.2: 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

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

NAG.3: 5 residues within 4Å: Chain A: N.118, T.120, I.156, S.158, H.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.118, A:T.120, A:T.120 NAG.4: 10 residues within 4Å: Chain A: D.95, P.96, V.138, L.145, N.146, N.244, R.246, C.306, V.307, S.308 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:N.146, A:R.246, A:R.246, A:S.308 NAG.5: 3 residues within 4Å: Chain A: N.160, T.162, N.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.160 NAG.6: 6 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.174, K.216 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.174 Hydrogen bonds: A:I.154, A:N.173, A:K.216, A:K.216 NAG.7: 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:E.200 NAG.8: 3 residues within 4Å: Chain A: N.202, T.204, K.205 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain A: N.222, N.223 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.223 NAG.10: 4 residues within 4Å: Chain A: T.239, M.240, N.253, T.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lalonde, J.M. et al., Structure-Based Design and Synthesis of an HIV-1 Entry Inhibitor Exploiting X-Ray and Thermodynamic Characterization. ACS Med Chem Lett (2013)

Release Date

2013-05-29

Peptides

HIV-1 glycoprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HIV-1 glycoprotein

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