SMTL ID : 8fa0.1

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-14208, an HIV-1 gp120 antagonist

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

8 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, L.161 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118 Water bridges: A:N.118 NAG.2: 2 residues within 4Å: Chain A: N.113, N.125 No protein-ligand interaction detected (PLIP) NAG.3: 10 residues within 4Å: Chain A: D.95, P.96, L.145, N.146, F.243, N.244, R.246, C.306, V.307, S.308 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.145, A:F.243 Hydrogen bonds: A:D.95, A:N.146, A:R.246, A:S.308 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, A:T.162 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:I.154 Water bridges: A:N.173, A:Q.212 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:T.181, A:Y.198 NAG.7: 4 residues within 4Å: Chain A: N.202, T.204, K.205, K.208 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.202, A:K.208, A:K.208 Water bridges: A:K.205 NAG.8: 2 residues within 4Å: Chain A: N.253, T.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.253

2 x XKR: N-{(1S)-2-amino-1-[4,5-bis(hydroxymethyl)-1,3-thiazol-2-yl]ethyl}-5-(4-chloro-3,5-difluorophenyl)-1H-pyrrole-2-carboxamide(Non-covalent)

XKR.9: 15 residues within 4Å: Chain A: V.139, S.140, T.141, D.235, E.237, S.242, F.243, F.249, I.285, N.286, M.287, W.288, G.334, I.336 Ligands: XKR.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.141, A:E.237, A:E.237, A:W.288 Hydrogen bonds: A:D.235, A:D.235, A:N.286 pi-Stacking: A:W.288 XKR.10: 11 residues within 4Å: Chain A: V.77, L.79, V.84, N.286, M.287, G.292, Q.293, A.294, M.295 Ligands: XKR.9, EPE.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.84, A:V.84 Hydrogen bonds: A:N.286, A:G.292, A:Q.293, A:Q.293

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

EPE.11: 3 residues within 4Å: Chain A: S.83, V.84 Ligands: XKR.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.83, A:S.83 Salt bridges: A:K.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Curreli, F. et al., Antiviral Activity and Crystal Structures of HIV-1 gp120 Antagonists. Int J Mol Sci (2022)

Release Date

2023-01-11

Peptides

HIV-1 gp120 core: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HIV-1 gp120 core

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