Structure of PDB 4cpx Chain B Binding Site BS01

Receptor Information

>4cpx Chain B (length=99) Species: 12721 (Human immunodeficiency virus)

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPTNVIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: J3W
• InChI: InChI=1S/C40H53N5O6S/c1-27(2)33-35(46)41-22-8-7-11-28-13-15-29(16-14-28)25-40(50,37(48)42-33)21-10-23-45(44-36(47)34(39(3,4)5)43-38(49)51-6)26-30-17-19-31(20-18-30)32-12-9-24-52-32/h7-9,12-20,24,27,33-34,50H,10-11,21-23,25-26H2,1-6H3,(H,41,46)(H,42,48)(H,43,49)(H,44,47)/b8-7-/t33-,34+,40+/m0/s1
• InChIKey: NERZJFGHXSDKOR-SDGWMEQNSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CC(C)C1C(=O)NCC=CCc2ccc(cc2)CC(C(=O)N1)(CCCN(Cc3ccc(cc3)c4cccs4)NC(=O)C(C(C)(C)C)NC(=O)OC)O
  CACTVS 3.385: COC(=O)N[C@H](C(=O)NN(CCC[C@@]1(O)Cc2ccc(C\C=C/CNC(=O)[C@@H](NC1=O)C(C)C)cc2)Cc3ccc(cc3)c4sccc4)C(C)(C)C
  OpenEye OEToolkits 2.0.6: CC(C)[C@H]1C(=O)NC/C=C\Cc2ccc(cc2)C[C@@](C(=O)N1)(CCCN(Cc3ccc(cc3)c4cccs4)NC(=O)[C@H](C(C)(C)C)NC(=O)OC)O
  CACTVS 3.385: COC(=O)N[CH](C(=O)NN(CCC[C]1(O)Cc2ccc(CC=CCNC(=O)[CH](NC1=O)C(C)C)cc2)Cc3ccc(cc3)c4sccc4)C(C)(C)C
• Formula: C40 H53 N5 O6 S
• Name: methyl ~{N}-[(2~{S})-3,3-dimethyl-1-[2-[3-[(3~{R},6~{S},10~{Z})-3-oxidanyl-4,7-bis(oxidanylidene)-6-propan-2-yl-5,8-diazabicyclo[11.2.2]heptadeca-1(16),10,13(17),14-tetraen-3-yl]propyl]-2-[(4-thiophen-2-ylphenyl)methyl]hydrazinyl]-1-oxidanylidene-butan-2-yl]carbamate
• PDB chain: 4cpx Chain A Residue 1101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4cpx Synthesis of P1'-functionalized macrocyclic transition-state mimicking HIV-1 protease inhibitors encompassing a tertiary alcohol.
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): L123 D125 G127 D129 G148 G149
• Binding residue (residue number reindexed from 1): L23 D25 G27 D29 G48 G49
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D125 T126 G127
• 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:4cpx, PDBe:4cpx, PDBj:4cpx
• PDBsum: 4cpx
• PubMed: 25054811
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)