SMTL ID : 5f4r.1

HIV-1 gp120 complex with BNW-IV-147

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 4 residues within 4Å: Chain A: N.284, G.290, R.291 Ligands: 5VF.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.284, A:R.291 FMT.9: 4 residues within 4Å: Chain B: N.284, G.290, R.291 Ligands: 5VF.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.284, B:R.291

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

NAG.2: 5 residues within 4Å: Chain A: N.113, T.115, P.117, S.153, L.156 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.156 Hydrogen bonds: A:N.113, A:T.115 NAG.3: 8 residues within 4Å: Chain A: D.90, K.131, L.140, N.141, C.304, N.305, S.306 Chain B: K.11 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.140 Hydrogen bonds: A:K.131, A:S.306, B:K.11, B:K.11 NAG.4: 2 residues within 4Å: Chain A: N.155, T.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.155 NAG.5: 6 residues within 4Å: Chain A: E.147, E.148, I.149, N.168, E.211 Chain B: N.305 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.147 Hydrogen bonds: A:I.149, A:N.168, A:E.211, A:E.211 NAG.6: 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.7: 4 residues within 4Å: Chain A: P.225, N.254, T.265, R.267 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.225 Hydrogen bonds: A:N.254 NAG.10: 5 residues within 4Å: Chain B: N.113, T.115, I.151, L.156, H.215 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.156 Hydrogen bonds: B:N.113 NAG.11: 8 residues within 4Å: Chain B: D.90, K.131, L.140, N.141, N.239, C.304, N.305, S.306 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.140 Hydrogen bonds: B:K.131, B:N.141, B:S.306 NAG.12: 2 residues within 4Å: Chain B: N.155, T.157 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.155 Hydrogen bonds: B:N.155 NAG.13: 6 residues within 4Å: Chain B: E.147, E.148, I.149, N.168, K.207, E.211 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:E.147 Hydrogen bonds: B:I.149, B:N.168, B:E.211, B:E.211 NAG.14: 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.15: 4 residues within 4Å: Chain B: P.225, D.251, N.254, T.265 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.225 Hydrogen bonds: B:N.254

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

5VF.8: 18 residues within 4Å: Chain A: 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.332, M.334 Ligands: FMT.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.136, A:E.232, A:E.232, A:I.233, A:F.244, A:I.283 Hydrogen bonds: A:D.230, A:N.284, A:N.284, A:M.285, A:E.288, A:G.290, A:G.332 Halogen bonds: A:S.237 5VF.16: 18 residues within 4Å: Chain B: 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.332, M.334 Ligands: FMT.9 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.136, B:E.232, B:I.233, B:F.244, B:I.283 Hydrogen bonds: B:N.284, B:N.284, B:M.285, 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
A

B
C

ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C

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