Structure of PDB 5f4p Chain D Binding Site BS01

Receptor Information

>5f4p Chain D (length=335) Species: 11676 (Human immunodeficiency virus 1)

KTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKN
DMVEQMHEDIISLWDESLKPCVKLTGGSAITQACPKVSFDPIPLHYCAPA
GFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEII
IRSENLTNNAKTIIVHLNESVNIVCTRPNNIRQAHCNINESKWNNTLQKV
GEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYR
NGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNI
TGLLLLRDDTETFRPGGGDMRDNWRSELYKYKVVE

Ligand information

• Ligand ID: 5VG
• InChI: InChI=1S/C21H24ClFN6O2/c1-26-9-11-2-4-15-12(6-11)7-13(10-27-21(24)25)18(15)29-20(31)19(30)28-14-3-5-16(22)17(23)8-14/h2-6,8,13,18,26H,7,9-10H2,1H3,(H,28,30)(H,29,31)(H4,24,25,27)/t13-,18-/m1/s1
• InChIKey: ZUJVWZRAMJMXLF-FZKQIMNGSA-N
• SMILES:
  CACTVS 3.385: CNCc1ccc2[C@H](NC(=O)C(=O)Nc3ccc(Cl)c(F)c3)[C@@H](CNC(N)=N)Cc2c1
  OpenEye OEToolkits 2.0.4: CNCc1ccc2c(c1)CC(C2NC(=O)C(=O)Nc3ccc(c(c3)F)Cl)CNC(=N)N
  OpenEye OEToolkits 2.0.4: [H]/N=C(/N)\NC[C@H]1Cc2cc(ccc2[C@@H]1NC(=O)C(=O)Nc3ccc(c(c3)F)Cl)CNC
  CACTVS 3.385: CNCc1ccc2[CH](NC(=O)C(=O)Nc3ccc(Cl)c(F)c3)[CH](CNC(N)=N)Cc2c1
• Formula: C21 H24 Cl F N6 O2
• Name: ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide
• ChEMBL: CHEMBL4803962
• ZINC: ZINC000584905343
• PDB chain: 5f4p Chain D Residue 507

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5f4p Small-Molecule CD4-Mimics: Structure-Based Optimization of HIV-1 Entry Inhibition.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): E370 I371 S375 F376 F382 N425 M426 W427 E429 G431 G473 M475
• Binding residue (residue number reindexed from 1): E224 I225 S229 F230 F236 N276 M277 W278 E280 G282 G318 M320
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.33,Kd=0.047uM

Gene Ontology

Cellular Component

• GO:0019031 viral envelope

External links

• PDB: RCSB:5f4p, PDBe:5f4p, PDBj:5f4p
• PDBsum: 5f4p
• PubMed: 26985324
• UniProt: C6G099