Structure of PDB 1gnm Chain A Binding Site BS02

Receptor Information

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

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPDNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: U0E
• InChI: InChI=1S/C28H52N8O6/c1-16(2)19(15-23(38)22(34-17(3)37)14-18-8-5-4-6-9-18)26(41)36-21(11-12-24(29)39)27(42)35-20(25(30)40)10-7-13-33-28(31)32/h16,18-23,38H,4-15H2,1-3H3,(H2,29,39)(H2,30,40)(H,34,37)(H,35,42)(H,36,41)(H4,31,32,33)/t19-,20-,21-,22-,23-/m0/s1
• InChIKey: XTOQWMLQBSGKOK-VUBDRERZSA-N
• SMILES:
  CACTVS 3.341: CC(C)[CH](C[CH](O)[CH](CC1CCCCC1)NC(C)=O)C(=O)N[CH](CCC(N)=O)C(=O)N[CH](CCCNC(N)=N)C(N)=O
  OpenEye OEToolkits 1.5.0: CC(C)C(CC(C(CC1CCCCC1)NC(=O)C)O)C(=O)NC(CCC(=O)N)C(=O)NC(CCCNC(=N)N)C(=O)N
  OpenEye OEToolkits 1.5.0: CC(C)[C@H](C[C@@H]([C@H](CC1CCCCC1)NC(=O)C)O)C(=O)N[C@@H](CCC(=O)N)C(=O)N[C@@H](CCCNC(=N)N)C(=O)N
  CACTVS 3.341: CC(C)[C@H](C[C@H](O)[C@H](CC1CCCCC1)NC(C)=O)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CCCNC(N)=N)C(N)=O
  ACDLabs 10.04: O=C(N)C(NC(=O)C(NC(=O)C(C(C)C)CC(O)C(NC(=O)C)CC1CCCCC1)CCC(=O)N)CCCNC(=[N@H])N
• Formula: C28 H52 N8 O6
• Name: N-[[1-[N-ACETAMIDYL]-[1-CYCLOHEXYLMETHYL-2-HYDROXY-4-ISOPROPYL]-BUT-4-YL]-CARBONYL]-GLUTAMINYL-ARGINYL-AMIDE
• PDB chain: 1gnm Chain A Residue 101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1gnm Crystal structures of complexes of a peptidic inhibitor with wild-type and two mutant HIV-1 proteases.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): D25 G27 A28 D29 D30 I47 G48 G49 I50 P81 I84
• Binding residue (residue number reindexed from 1): D25 G27 A28 D29 D30 I47 G48 G49 I50 P81 I84
• Annotation score: 1
• Binding affinity: MOAD: Ki=560nM
  PDBbind-CN: -logKd/Ki=6.25,Ki=560nM

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:1gnm, PDBe:1gnm, PDBj:1gnm
• PDBsum: 1gnm
• PubMed: 8718851
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)