Structure of PDB 1zsr Chain B Binding Site BS01

Receptor Information

>1zsr Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: 0ZT
• InChI: InChI=1S/C38H49N5O8/c1-38(2,3)51-37(50)43-29(21-25-13-7-4-8-14-25)32(44)24-40-31(23-27-17-11-6-12-18-27)36(49)41-28(19-20-33(45)46)35(48)42-30(34(39)47)22-26-15-9-5-10-16-26/h4-18,28-32,40,44H,19-24H2,1-3H3,(H2,39,47)(H,41,49)(H,42,48)(H,43,50)(H,45,46)/t28-,29-,30-,31-,32-/m0/s1
• InChIKey: MPMUDVMRFYJRLP-XDIGFQIYSA-N
• SMILES:
  CACTVS 3.370: CC(C)(C)OC(=O)N[CH](Cc1ccccc1)[CH](O)CN[CH](Cc2ccccc2)C(=O)N[CH](CCC(O)=O)C(=O)N[CH](Cc3ccccc3)C(N)=O
  CACTVS 3.370: CC(C)(C)OC(=O)N[C@@H](Cc1ccccc1)[C@@H](O)CN[C@@H](Cc2ccccc2)C(=O)N[C@@H](CCC(O)=O)C(=O)N[C@@H](Cc3ccccc3)C(N)=O
  ACDLabs 12.01: O=C(N)C(NC(=O)C(NC(=O)C(NCC(O)C(NC(=O)OC(C)(C)C)Cc1ccccc1)Cc2ccccc2)CCC(=O)O)Cc3ccccc3
  OpenEye OEToolkits 1.7.0: CC(C)(C)OC(=O)NC(Cc1ccccc1)C(CNC(Cc2ccccc2)C(=O)NC(CCC(=O)O)C(=O)NC(Cc3ccccc3)C(=O)N)O
  OpenEye OEToolkits 1.7.0: CC(C)(C)OC(=O)N[C@@H](Cc1ccccc1)[C@H](CN[C@@H](Cc2ccccc2)C(=O)N[C@@H](CCC(=O)O)C(=O)N[C@@H](Cc3ccccc3)C(=O)N)O
• Formula: C38 H49 N5 O8
• Name: N-{(2S,3S)-3-[(tert-butoxycarbonyl)amino]-2-hydroxy-4-phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl-L-phenylalaninamide
• ChEMBL: CHEMBL386563
• ZINC: ZINC000033360308
• PDB chain: 1zsr Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1zsr On the role of the R configuration of the reaction-intermediate isostere in HIV-1 protease-inhibitor binding: X-ray structure at 2.0 A resolution.
• Resolution: 2.06 Å
• Binding residue (original residue number in PDB): D125 G127 G148 P181 V182 I184
• Binding residue (residue number reindexed from 1): D25 G27 G48 P81 V82 I84
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=9.82,Ki=0.15nM

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:1zsr, PDBe:1zsr, PDBj:1zsr
• PDBsum: 1zsr
• PubMed: 16627941
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)