Structure of PDB 4zip Chain A Binding Site BS01

Receptor Information

>4zip Chain A (length=99) Species: 11678 (Human immunodeficiency virus type 1 BH10)

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligand information

• Ligand ID: G64
• InChI: InChI=1S/C37H46N4O7S/c1-24(2)21-41(49(45,46)32-15-13-31(47-7)14-16-32)23-35(42)33(19-28-11-9-8-10-12-28)39-36(43)29-17-25(3)18-30(20-29)37(44)40(6)22-34-26(4)48-27(5)38-34/h8-18,20,24,33,35,42H,19,21-23H2,1-7H3,(H,39,43)/t33-,35+/m0/s1
• InChIKey: VYTQZAGDUBREEP-QWOOXDRHSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: Cc1cc(cc(c1)C(=O)N(C)Cc2c(oc(n2)C)C)C(=O)NC(Cc3ccccc3)C(CN(CC(C)C)S(=O)(=O)c4ccc(cc4)OC)O
  ACDLabs 12.01: c4(ccc(S(=O)(N(CC(O)C(NC(=O)c1cc(C)cc(c1)C(=O)N(C)Cc2nc(oc2C)C)Cc3ccccc3)CC(C)C)=O)cc4)OC
  CACTVS 3.385: COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[CH](O)[CH](Cc2ccccc2)NC(=O)c3cc(C)cc(c3)C(=O)N(C)Cc4nc(C)oc4C
  OpenEye OEToolkits 1.9.2: Cc1cc(cc(c1)C(=O)N(C)Cc2c(oc(n2)C)C)C(=O)N[C@@H](Cc3ccccc3)[C@@H](CN(CC(C)C)S(=O)(=O)c4ccc(cc4)OC)O
  CACTVS 3.385: COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[C@@H](O)[C@H](Cc2ccccc2)NC(=O)c3cc(C)cc(c3)C(=O)N(C)Cc4nc(C)oc4C
• Formula: C37 H46 N4 O7 S
• Name: N-[(2,5-dimethyl-1,3-oxazol-4-yl)methyl]-N'-[(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]-N,5-dimethylbenzene-1,3-dicarboxamide
• ChEMBL: CHEMBL3627880
• ZINC: ZINC000068203929
• PDB chain: 4zip Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4zip Structure-based design, synthesis, X-ray studies, and biological evaluation of novel HIV-1 protease inhibitors containing isophthalamide-derived P2-ligands.
• Resolution: 1.11 Å
• Binding residue (original residue number in PDB): R8 D25 A28 D30 V82
• Binding residue (residue number reindexed from 1): R8 D25 A28 D30 V82
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=9.68,Ki=0.21nM

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:4zip, PDBe:4zip, PDBj:4zip
• PDBsum: 4zip
• PubMed: 26096678
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)