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Structure of PDB 1a94 Chain B Binding Site BS01

Receptor Information

>1a94 Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWEPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligand information

• Ligand ID: 0Q4
• InChI: InChI=1S/C40H69N11O8/c1-7-8-16-29(34(42)54)49-35(55)25(6)47-37(57)30(17-18-32(52)53)50-38(58)31(21-26-13-10-9-11-14-26)46-22-27(20-23(2)3)48-39(59)33(24(4)5)51-36(56)28(41)15-12-19-45-40(43)44/h9-11,13-14,23-25,27-31,33,46H,7-8,12,15-22,41H2,1-6H3,(H2,42,54)(H,47,57)(H,48,59)(H,49,55)(H,50,58)(H,51,56)(H,52,53)(H4,43,44,45)/p+1/t25-,27-,28-,29-,30-,31-,33-/m0/s1
• InChIKey: SGWAZUZKMXHYMB-UQGDEETHSA-O
• SMILES:
  OpenEye OEToolkits 1.7.0: CCCCC(C(=O)N)NC(=O)C(C)NC(=O)C(CCC(=O)O)NC(=O)C(Cc1ccccc1)NCC(CC(C)C)NC(=O)C(C(C)C)NC(=O)C(CCCNC(=[NH2+])N)N
  ACDLabs 12.01: O=C(N)C(NC(=O)C(NC(=O)C(NC(=O)C(NCC(NC(=O)C(NC(=O)C(N)CCCNC(=[NH2+])\N)C(C)C)CC(C)C)Cc1ccccc1)CCC(=O)O)C)CCCC
  OpenEye OEToolkits 1.7.0: CCCC[C@@H](C(=O)N)NC(=O)[C@H](C)NC(=O)[C@H](CCC(=O)O)NC(=O)[C@H](Cc1ccccc1)NC[C@H](CC(C)C)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CCCNC(=[NH2+])N)N
  CACTVS 3.370: CCCC[CH](NC(=O)[CH](C)NC(=O)[CH](CCC(O)=O)NC(=O)[CH](Cc1ccccc1)NC[CH](CC(C)C)NC(=O)[CH](NC(=O)[CH](N)CCCNC(N)=[NH2+])C(C)C)C(N)=O
  CACTVS 3.370: CCCC[C@H](NC(=O)[C@H](C)NC(=O)[C@H](CCC(O)=O)NC(=O)[C@H](Cc1ccccc1)NC[C@H](CC(C)C)NC(=O)[C@@H](NC(=O)[C@@H](N)CCCNC(N)=[NH2+])C(C)C)C(N)=O
• Formula: C40 H70 N11 O8
• Name: N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl-L-alanyl-L-norleucinamide;
  Inhibitor analogues of CA-p2
• PDB chain: 1a94 Chain A Residue 100

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1a94 Structural basis for specificity of retroviral proteases.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): D25 G27 A28 D29 G48 V82 I84
• Binding residue (residue number reindexed from 1): D25 G27 A28 D29 G48 V82 I84
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.85,Ki=14nM

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:1a94, PDBe:1a94, PDBj:1a94
• PDBsum: 1a94
• PubMed: 9521772
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)

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