Structure of PDB 6dj1 Chain A Binding Site BS01

Receptor Information

>6dj1 Chain A (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligand information

• Ligand ID: AB1
• InChI: InChI=1S/C37H48N4O5/c1-25(2)34(41-20-12-19-38-37(41)45)36(44)39-30(21-28-15-7-5-8-16-28)23-32(42)31(22-29-17-9-6-10-18-29)40-33(43)24-46-35-26(3)13-11-14-27(35)4/h5-11,13-18,25,30-32,34,42H,12,19-24H2,1-4H3,(H,38,45)(H,39,44)(H,40,43)/t30-,31-,32-,34-/m0/s1
• InChIKey: KJHKTHWMRKYKJE-SUGCFTRWSA-N
• SMILES:
  ACDLabs 10.04: O=C(NC(Cc1ccccc1)C(O)CC(NC(=O)C(N2C(=O)NCCC2)C(C)C)Cc3ccccc3)COc4c(cccc4C)C
  OpenEye OEToolkits 1.5.0: Cc1cccc(c1OCC(=O)N[C@@H](Cc2ccccc2)[C@H](C[C@H](Cc3ccccc3)NC(=O)[C@H](C(C)C)N4CCCNC4=O)O)C
  CACTVS 3.341: CC(C)[C@H](N1CCCNC1=O)C(=O)N[C@H](C[C@H](O)[C@H](Cc2ccccc2)NC(=O)COc3c(C)cccc3C)Cc4ccccc4
  CACTVS 3.341: CC(C)[CH](N1CCCNC1=O)C(=O)N[CH](C[CH](O)[CH](Cc2ccccc2)NC(=O)COc3c(C)cccc3C)Cc4ccccc4
  OpenEye OEToolkits 1.5.0: Cc1cccc(c1OCC(=O)NC(Cc2ccccc2)C(CC(Cc3ccccc3)NC(=O)C(C(C)C)N4CCCNC4=O)O)C
• Formula: C37 H48 N4 O5
• Name: N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE;
  ABT-378;
  LOPINAVIR
• ChEMBL: CHEMBL729
• DrugBank: DB01601
• ZINC: ZINC000003951740
• PDB chain: 6dj1 Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6dj1 Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap-Core Interface of HIV-1 Protease.
• Resolution: 1.26 Å
• Binding residue (original residue number in PDB): D25 G27 A28 D29 G48 G49 I84
• Binding residue (residue number reindexed from 1): D25 G27 A28 D29 G48 G49 I84
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=10.51,Ki=0.031nM

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:6dj1, PDBe:6dj1, PDBj:6dj1
• PDBsum: 6dj1
• PubMed: 30288468
• UniProt: P04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)