Structure of PDB 4dkr Chain C Binding Site BS01

Receptor Information

>4dkr Chain C (length=339) Species: 11686 (Human immunodeficiency virus type 1 (BRU ISOLATE))

VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENF
NMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIH
YCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLA
EEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGDIRKAYCEINGTKW
NKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQ
LFNNTCINGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGIL
LTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE

Ligand information

• Ligand ID: 0LJ
• InChI: InChI=1S/C18H17ClFN5O2/c19-12-6-5-10(8-13(12)20)23-16(26)17(27)25-15-11-4-2-1-3-9(11)7-14(15)24-18(21)22/h1-6,8,14-15H,7H2,(H,23,26)(H,25,27)(H4,21,22,24)/t14-,15-/m1/s1
• InChIKey: ICNIHLCRBSFIFO-HUUCEWRRSA-N
• SMILES:
  CACTVS 3.370: NC(=N)N[CH]1Cc2ccccc2[CH]1NC(=O)C(=O)Nc3ccc(Cl)c(F)c3
  OpenEye OEToolkits 1.7.6: [H]/N=C(/N)\N[C@@H]1Cc2ccccc2[C@H]1NC(=O)C(=O)Nc3ccc(c(c3)F)Cl
  OpenEye OEToolkits 1.7.6: c1ccc2c(c1)CC(C2NC(=O)C(=O)Nc3ccc(c(c3)F)Cl)NC(=N)N
  CACTVS 3.370: NC(=N)N[C@@H]1Cc2ccccc2[C@H]1NC(=O)C(=O)Nc3ccc(Cl)c(F)c3
  ACDLabs 12.01: Clc1ccc(cc1F)NC(=O)C(=O)NC3c2ccccc2CC3NC(=[N@H])N
• Formula: C18 H17 Cl F N5 O2
• Name: N-[(1R,2R)-2-carbamimidamido-2,3-dihydro-1H-inden-1-yl]-N'-(4-chloro-3-fluorophenyl)ethanediamide
• ChEMBL: CHEMBL2219814
• ZINC: ZINC000095556243
• PDB chain: 4dkr Chain C Residue 513

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4dkr Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule HIV-1 Entry Inhibitors.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): S256 E370 I371 S375 F376 N425 W427 G473
• Binding residue (residue number reindexed from 1): S140 E231 I232 S236 F237 N272 W274 G320
• Annotation score: 1
• Binding affinity: MOAD: Kd=0.3uM

Gene Ontology

Cellular Component

• GO:0019031 viral envelope

External links

• PDB: RCSB:4dkr, PDBe:4dkr, PDBj:4dkr
• PDBsum: 4dkr
• PubMed: 22497421
• UniProt: Q0ED31