Structure of PDB 3dcr Chain A Binding Site BS01

Receptor Information

>3dcr Chain A (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEELNLPGCWKPKLIGGI
GGFIKVRQYDQIPVEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligand information

• Ligand ID: KVS
• InChI: InChI=1S/C36H68N10O10/c1-7-10-13-23(31(51)44-25(16-17-27(37)49)32(52)43-24(30(38)50)14-12-18-41-35(39)40)19-36(55,56)26(15-11-8-2)45-33(53)28(20(4)9-3)46-34(54)29(21(5)47)42-22(6)48/h20-21,23-26,28-29,47,55-56H,7-19H2,1-6H3,(H2,37,49)(H2,38,50)(H,42,48)(H,43,52)(H,44,51)(H,45,53)(H,46,54)(H4,39,40,41)/t20-,21+,23+,24-,25-,26-,28-,29-/m0/s1
• InChIKey: GHZIZWOGRIROFP-WZGNFWQUSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: [H]/N=C(\N)/NCCC[C@@H](C(=O)N)NC(=O)[C@H](CCC(=O)N)NC(=O)[C@H](CCCC)CC([C@H](CCCC)NC(=O)[C@H]([C@@H](C)CC)NC(=O)[C@H]([C@@H](C)O)NC(=O)C)(O)O
  CACTVS 3.385: CCCC[C@H](CC(O)(O)[C@H](CCCC)NC(=O)[C@@H](NC(=O)[C@@H](NC(C)=O)[C@@H](C)O)[C@@H](C)CC)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CCCNC(N)=N)C(N)=O
  ACDLabs 12.01: C(=O)(C)NC(C(NC(C(=O)NC(C(O)(CC(C(NC(C(NC(C(N)=O)CCCN/C(N)=N)=O)CCC(N)=O)=O)CCCC)O)CCCC)C(C)CC)=O)C(C)O
  CACTVS 3.385: CCCC[CH](CC(O)(O)[CH](CCCC)NC(=O)[CH](NC(=O)[CH](NC(C)=O)[CH](C)O)[CH](C)CC)C(=O)N[CH](CCC(N)=O)C(=O)N[CH](CCCNC(N)=N)C(N)=O
  OpenEye OEToolkits 1.7.6: CCCCC(CC(C(CCCC)NC(=O)C(C(C)CC)NC(=O)C(C(C)O)NC(=O)C)(O)O)C(=O)NC(CCC(=O)N)C(=O)NC(CCCNC(=N)N)C(=O)N
• Formula: C36 H68 N10 O10
• Name: N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-acetyl-L-threonyl)amino]-3-methylpent-4-enoyl}amino)-2-butyl-4,4-dihydroxynonanoyl]-L-glutaminyl-L-argininamide
• PDB chain: 3dcr Chain B Residue 101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3dcr Crystal structure of chemically synthesized HIV-1 protease and a ketomethylene isostere inhibitor based on the p2/NC cleavage site
• Resolution: 1.4 Å
• Binding residue (original residue number in PDB): R8 D25 G27 A28 D29 G48 I84
• Binding residue (residue number reindexed from 1): R8 D25 G27 A28 D29 G48 I84
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.20,IC50=6.3nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D25 T26 G27
• Catalytic site (residue number reindexed from 1): D25 T26 G27
• Enzyme Commision number: 3.4.23.16: HIV-1 retropepsin.

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:3dcr, PDBe:3dcr, PDBj:3dcr
• PDBsum: 3dcr
• PubMed: 18657969
• UniProt: O38732