SMTL ID : 5u6e.1 (1 other biounit)

Crystal structure of clade A/E HIV-1 gp120 core in complex with NBD-14010

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: N.118, T.120, I.156, S.158, L.161, H.220 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118 NAG.2: 4 residues within 4Å: Chain A: N.113, 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: D.95, P.96, L.145, N.146, R.246, C.306, V.307, S.308 Ligands: NAG.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.145 Hydrogen bonds: A:N.146, A:R.246, A:S.308 Water bridges: A:R.246, 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:E.153, A:I.154 NAG.6: 5 residues within 4Å: Chain A: N.179, T.181, 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: 2 residues within 4Å: Chain A: N.202, K.205 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.205 Water bridges: 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: 3 residues within 4Å: Chain A: M.240, N.253, T.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.253, A:T.255 NAG.10: 6 residues within 4Å: Chain A: N.146, G.147, L.149, S.175, N.309 Ligands: NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.175 Water bridges: A:S.175 NAG.11: 2 residues within 4Å: Chain A: T.162, N.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.322

1 x 82M: N-{(1S)-2-amino-1-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl]ethyl}-5-(4-chloro-3-fluorophenyl)-1H-pyrrole-2-carboxamide(Non-covalent)

82M.12: 18 residues within 4Å: Chain A: V.139, S.140, T.141, D.235, E.237, S.242, F.243, N.244, F.249, Y.251, I.285, N.286, M.287, W.288, Q.289, G.290, G.334, I.336 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.141, A:E.237 Hydrogen bonds: A:D.235, A:D.235, A:N.286 Water bridges: A:N.286, A:N.286, A:W.288, A:G.290, A:G.334

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

EPE.13: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Curreli, F. et al., Synthesis, Antiviral Potency, in Vitro ADMET, and X-ray Structure of Potent CD4 Mimics as Entry Inhibitors That Target the Phe43 Cavity of HIV-1 gp120. J. Med. Chem. (2017)

Release Date

2017-03-22

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

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