Structure of PDB 4cpr Chain B Binding Site BS01

Receptor Information

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

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPTNVIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: 378
• InChI: InChI=1S/C42H57N5O6S/c1-9-13-30-15-17-31(18-16-30)27-42(52,39(50)44-35(29(3)4)37(48)43-24-10-2)23-12-25-47(46-38(49)36(41(5,6)7)45-40(51)53-8)28-32-19-21-33(22-20-32)34-14-11-26-54-34/h9-11,14-22,26,29,35-36,52H,1-2,12-13,23-25,27-28H2,3-8H3,(H,43,48)(H,44,50)(H,45,51)(H,46,49)/t35-,36+,42+/m0/s1
• InChIKey: IBNVZQRVRDNWIL-FCSANXPSSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)[C@@H](C(=O)NCC=C)NC(=O)[C@@](CCCN(Cc1ccc(cc1)c2cccs2)NC(=O)[C@H](C(C)(C)C)NC(=O)OC)(Cc3ccc(cc3)CC=C)O
  OpenEye OEToolkits 2.0.7: CC(C)C(C(=O)NCC=C)NC(=O)C(CCCN(Cc1ccc(cc1)c2cccs2)NC(=O)C(C(C)(C)C)NC(=O)OC)(Cc3ccc(cc3)CC=C)O
  CACTVS 3.385: COC(=O)N[CH](C(=O)NN(CCC[C](O)(Cc1ccc(CC=C)cc1)C(=O)N[CH](C(C)C)C(=O)NCC=C)Cc2ccc(cc2)c3sccc3)C(C)(C)C
  CACTVS 3.385: COC(=O)N[C@H](C(=O)NN(CCC[C@@](O)(Cc1ccc(CC=C)cc1)C(=O)N[C@@H](C(C)C)C(=O)NCC=C)Cc2ccc(cc2)c3sccc3)C(C)(C)C
• Formula: C42 H57 N5 O6 S
• Name: methyl ~{N}-[(2~{S})-3,3-dimethyl-1-[2-[(4~{R})-5-[[(2~{S})-3-methyl-1-oxidanylidene-1-(prop-2-enylamino)butan-2-yl]amino]-4-oxidanyl-5-oxidanylidene-4-[(4-prop-2-enylphenyl)methyl]pentyl]-2-[(4-thiophen-2-ylphenyl)methyl]hydrazinyl]-1-oxidanylidene-butan-2-yl]carbamate
• PDB chain: 4cpr Chain A Residue 1101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4cpr Synthesis of P1'-Functionalized Macrocyclic Transition-State Mimicking HIV-1 Protease Inhibitors Encompassing a Tertiary Alcohol.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): R108 D125 G127 A128 D129 G148 G149 F153 P181 T182
• Binding residue (residue number reindexed from 1): R8 D25 G27 A28 D29 G48 G49 F53 P81 T82
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.46,Ki=35nM

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:4cpr, PDBe:4cpr, PDBj:4cpr
• PDBsum: 4cpr
• PubMed: 25054811
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)