Structure of PDB 2q54 Chain A Binding Site BS01

Receptor Information

>2q54 Chain A (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: MU1
• InChI: InChI=1S/C37H44N4O7/c1-23(2)34(38-25(4)43)36(46)39-29(18-26-12-7-5-8-13-26)21-32(44)31(19-27-14-9-6-10-15-27)40-35(45)33-22-41(37(47)48-33)30-17-11-16-28(20-30)24(3)42/h5-17,20,23,29,31-34,44H,18-19,21-22H2,1-4H3,(H,38,43)(H,39,46)(H,40,45)/t29-,31-,32-,33-,34-/m0/s1
• InChIKey: CZPLKLADANMGQQ-JUZBSFEJSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C)[C@@H](C(=O)N[C@@H](Cc1ccccc1)C[C@@H]([C@H](Cc2ccccc2)NC(=O)[C@@H]3CN(C(=O)O3)c4cccc(c4)C(=O)C)O)NC(=O)C
  ACDLabs 10.04: O=C4OC(C(=O)NC(Cc1ccccc1)C(O)CC(NC(=O)C(NC(=O)C)C(C)C)Cc2ccccc2)CN4c3cccc(C(=O)C)c3
  CACTVS 3.341: CC(C)[C@H](NC(C)=O)C(=O)N[C@H](C[C@H](O)[C@H](Cc1ccccc1)NC(=O)[C@@H]2CN(C(=O)O2)c3cccc(c3)C(C)=O)Cc4ccccc4
  OpenEye OEToolkits 1.5.0: CC(C)C(C(=O)NC(Cc1ccccc1)CC(C(Cc2ccccc2)NC(=O)C3CN(C(=O)O3)c4cccc(c4)C(=O)C)O)NC(=O)C
  CACTVS 3.341: CC(C)[CH](NC(C)=O)C(=O)N[CH](C[CH](O)[CH](Cc1ccccc1)NC(=O)[CH]2CN(C(=O)O2)c3cccc(c3)C(C)=O)Cc4ccccc4
• Formula: C37 H44 N4 O7
• Name: N~2~-ACETYL-N-[(1S,3S,4S)-4-({[(5S)-3-(3-ACETYLPHENYL)-2-OXO-1,3-OXAZOLIDIN-5-YL]CARBONYL}AMINO)-1-BENZYL-3-HYDROXY-5-PHENYLPENTYL]-L-VALINAMIDE
• ChEMBL: CHEMBL388901
• ZINC: ZINC000024909856
• PDB chain: 2q54 Chain B Residue 200

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2q54 Design and Synthesis of HIV-1 Protease Inhibitors Incorporating Oxazolidinones as P2/P2' Ligands in Pseudosymmetric Dipeptide Isosteres.
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): D25 G27 A28 D29 G48 G49 I50 P81 I84
• Binding residue (residue number reindexed from 1): D25 G27 A28 D29 G48 G49 I50 P81 I84
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=9.01,Ki=0.98nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D25 T26 G27
• Catalytic site (residue number reindexed from 1): D25 T26 G27

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:2q54, PDBe:2q54, PDBj:2q54
• PDBsum: 2q54
• PubMed: 17696512
• UniProt: O38710