Structure of PDB 3hdk Chain A Binding Site BS01

Receptor Information

>3hdk Chain A (length=99) Species: 11685 (HIV-1 M:B_ARV2/SF2)

PQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEELNLPGCWKPKLIGGI
AGFIKVRQYDQIPVEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligand information

• Ligand ID: 2NC
• InChI: InChI=1S/C35H67N11O8/c1-7-10-13-23(43-33(53)28(20(4)9-3)46-34(54)29(21(5)47)42-22(6)48)19-41-25(14-11-8-2)31(51)45-26(16-17-27(36)49)32(52)44-24(30(37)50)15-12-18-40-35(38)39/h20-21,23-26,28-29,41,47H,7-19H2,1-6H3,(H2,36,49)(H2,37,50)(H,42,48)(H,43,53)(H,44,52)(H,45,51)(H,46,54)(H4,38,39,40)/p+1/t20-,21+,23-,24-,25-,26-,28-,29-/m0/s1
• InChIKey: MQPXOVRKKPPKFZ-QYKDHROSSA-O
• SMILES:
  OpenEye OEToolkits 1.7.5: CCCCC(CNC(CCCC)C(=O)NC(CCC(=O)N)C(=O)NC(CCCNC(=[NH2+])N)C(=O)N)NC(=O)C(C(C)CC)NC(=O)C(C(C)O)NC(=O)C
  CACTVS 3.385: CCCC[CH](CN[CH](CCCC)C(=O)N[CH](CCC(N)=O)C(=O)N[CH](CCCNC(N)=[NH2+])C(N)=O)NC(=O)[CH](NC(=O)[CH](NC(C)=O)[CH](C)O)[CH](C)CC
  ACDLabs 12.01: O=C(NC(C(=O)NC(CCCC)CNC(C(=O)NC(C(=O)NC(C(=O)N)CCCNC(=[NH2+])\\N)CCC(=O)N)CCCC)C(C)CC)C(NC(=O)C)C(O)C
  CACTVS 3.385: CCCC[C@@H](CN[C@@H](CCCC)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CCCNC(N)=[NH2+])C(N)=O)NC(=O)[C@@H](NC(=O)[C@@H](NC(C)=O)[C@@H](C)O)[C@@H](C)CC
  OpenEye OEToolkits 1.7.5: CCCC[C@@H](CN[C@@H](CCCC)C(=O)N[C@@H](CCC(=O)N)C(=O)N[C@@H](CCCNC(=[NH2+])N)C(=O)N)NC(=O)[C@H]([C@@H](C)CC)NC(=O)[C@H]([C@@H](C)O)NC(=O)C
• Formula: C35 H68 N11 O8
• Name: N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide;
  p2/NC
• PDB chain: 3hdk Chain B Residue 0

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3hdk Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): R8 D25 G27 A28 D29 G48 I50
• Binding residue (residue number reindexed from 1): R8 D25 G27 A28 D29 G48 I50
• Annotation score: 1

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: 2.7.7.-
  2.7.7.49: RNA-directed DNA polymerase.
  2.7.7.7: DNA-directed DNA polymerase.
  3.1.-.-
  3.1.13.2: exoribonuclease H.
  3.1.26.13: retroviral ribonuclease H.
  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:3hdk, PDBe:3hdk, PDBj:3hdk
• PDBsum: 3hdk
• PubMed: 22158985
• UniProt: P03369|POL_HV1A2 Gag-Pol polyprotein (Gene Name=gag-pol)