SMTL ID : 5f4p.1

HIV-1 gp120 complex with BNM-III-170

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 5 residues within 4Å: Chain A: N.113, P.117, I.151, S.153, L.156 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.156 Hydrogen bonds: A:N.113 NAG.2: 8 residues within 4Å: Chain A: D.90, L.140, N.141, N.239, C.304, N.305, S.306 Chain B: K.11 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.140 Hydrogen bonds: A:S.306, B:K.11 NAG.3: 3 residues within 4Å: Chain A: N.155, T.157, N.158 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.155 Hydrogen bonds: A:N.155, A:N.158 NAG.4: 6 residues within 4Å: Chain A: E.147, E.148, N.168, K.207 Chain B: N.172, N.305 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.168, A:K.207, B:N.172 NAG.5: 3 residues within 4Å: Chain A: T.234, N.248, S.250 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.248, A:S.250 NAG.6: 6 residues within 4Å: Chain A: P.225, D.251, N.254, T.265, G.266, R.267 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.225 Hydrogen bonds: A:D.251, A:N.254, A:R.267 NAG.9: 3 residues within 4Å: Chain B: N.113, L.156, H.215 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.156 Hydrogen bonds: B:N.113 NAG.10: 7 residues within 4Å: Chain B: D.90, P.91, L.140, N.141, C.304, N.305, S.306 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.140 Hydrogen bonds: B:N.141, B:S.306 NAG.11: 1 residues within 4Å: Chain B: N.155 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.155 NAG.12: 5 residues within 4Å: Chain B: E.147, E.148, N.168, E.169, K.207 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.168, B:E.169 NAG.13: 3 residues within 4Å: Chain B: T.234, N.248, S.250 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.248, B:S.250 NAG.14: 4 residues within 4Å: Chain B: P.225, D.251, N.254, R.267 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.225 Hydrogen bonds: B:N.254, B:R.267

2 x 5VG: ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide(Non-covalent)

5VG.7: 19 residues within 4Å: Chain A: V.134, S.135, T.136, E.232, I.233, S.237, F.238, N.239, F.244, I.283, N.284, M.285, W.286, E.288, V.289, G.290, G.331, G.332, M.334 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.136, A:E.232, A:I.233, A:F.244, A:I.283 Hydrogen bonds: A:N.284, A:E.288, A:G.290, A:G.331, A:G.332 Halogen bonds: A:S.237 5VG.8: 19 residues within 4Å: Chain B: V.134, S.135, T.136, E.232, I.233, S.237, F.238, N.239, F.244, I.283, N.284, M.285, W.286, E.288, V.289, G.290, G.331, G.332, M.334 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:E.232, B:I.233, B:F.244, B:I.283 Hydrogen bonds: B:N.284, B:E.288, B:G.290, B:G.332 Halogen bonds: B:S.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Melillo, B. et al., Small-Molecule CD4-Mimics: Structure-Based Optimization of HIV-1 Entry Inhibition. Acs Med.Chem.Lett. (2016)

Release Date

2016-03-30

Peptides

ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C

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