Structure of PDB 5f4l Chain A Binding Site BS01

Receptor Information

>5f4l Chain A (length=336) Species: 11676 (Human immunodeficiency virus 1)

KTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKN
DMVEQMHEDIISLWDESLKPCVKLTGGSAITQACPKVSFDPIPLHYCAPA
GFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEII
IRSENLTNNAKTIIVHLNESVNIVCTRPNNIRQAHCNINESKWNNTLQKV
GEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYR
NGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNI
TGLLLLRDDTETFRPGGGDMRDNWRSELYKYKVVEI

Ligand information

• Ligand ID: 5VE
• InChI: InChI=1S/C21H24ClFN6O2/c1-26-9-11-2-3-12-7-13(10-27-21(24)25)18(15(12)6-11)29-20(31)19(30)28-14-4-5-16(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: XFJPCFZRCFHOOP-FZKQIMNGSA-N
• SMILES:
  OpenEye OEToolkits 2.0.4: CNCc1ccc2c(c1)C(C(C2)CNC(=N)N)NC(=O)C(=O)Nc3ccc(c(c3)F)Cl
  CACTVS 3.385: CNCc1ccc2C[C@H](CNC(N)=N)[C@@H](NC(=O)C(=O)Nc3ccc(Cl)c(F)c3)c2c1
  CACTVS 3.385: CNCc1ccc2C[CH](CNC(N)=N)[CH](NC(=O)C(=O)Nc3ccc(Cl)c(F)c3)c2c1
  OpenEye OEToolkits 2.0.4: [H]/N=C(/N)\NC[C@H]1Cc2ccc(cc2[C@@H]1NC(=O)C(=O)Nc3ccc(c(c3)F)Cl)CNC
• Formula: C21 H24 Cl F N6 O2
• Name: ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-6-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide
• ChEMBL: CHEMBL4802887
• ZINC: ZINC000584905329
• PDB chain: 5f4l Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5f4l Small-Molecule CD4-Mimics: Structure-Based Optimization of HIV-1 Entry Inhibition.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): S256 E370 S375 F376 F382 N425 M426 W427 G473 M475
• Binding residue (residue number reindexed from 1): S135 E224 S229 F230 F236 N276 M277 W278 G318 M320
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.62,Kd=0.024uM

Gene Ontology

Cellular Component

• GO:0019031 viral envelope

External links

• PDB: RCSB:5f4l, PDBe:5f4l, PDBj:5f4l
• PDBsum: 5f4l
• PubMed: 26985324
• UniProt: C6G099