Structure of PDB 2xye Chain B Binding Site BS01

Receptor Information

>2xye Chain B (length=99) Species: 11683 (Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE))

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPTNVIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: CXG
• InChI: InChI=1S/C40H55N5O6/c1-38(2,3)32(34(46)41-7)42-36(48)40(50,26-28-16-11-9-12-17-28)24-15-25-45(44-35(47)33(39(4,5)6)43-37(49)51-8)27-29-20-22-31(23-21-29)30-18-13-10-14-19-30/h9-14,16-23,32-33,50H,15,24-27H2,1-8H3,(H,41,46)(H,42,48)(H,43,49)(H,44,47)/t32-,33-,40-/m1/s1
• InChIKey: TXYBNSUGKNIMSP-UBNGCCFSSA-N
• SMILES:
  CACTVS 3.352: CNC(=O)[C@@H](NC(=O)[C@@](O)(CCCN(Cc1ccc(cc1)c2ccccc2)NC(=O)[C@@H](NC(=O)OC)C(C)(C)C)Cc3ccccc3)C(C)(C)C
  OpenEye OEToolkits 1.6.1: CC(C)(C)[C@@H](C(=O)NC)NC(=O)[C@@](CCC[N@](Cc1ccc(cc1)c2ccccc2)NC(=O)[C@H](C(C)(C)C)NC(=O)OC)(Cc3ccccc3)O
  OpenEye OEToolkits 1.6.1: CC(C)(C)C(C(=O)NC)NC(=O)C(CCCN(Cc1ccc(cc1)c2ccccc2)NC(=O)C(C(C)(C)C)NC(=O)OC)(Cc3ccccc3)O
  CACTVS 3.352: CNC(=O)[CH](NC(=O)[C](O)(CCCN(Cc1ccc(cc1)c2ccccc2)NC(=O)[CH](NC(=O)OC)C(C)(C)C)Cc3ccccc3)C(C)(C)C
• Formula: C40 H55 N5 O6
• Name: METHYL N-[(2S)-1-[2-[(4R)-5-[[(2S)-3,3-DIMETHYL-1-METHYLAMINO-1-OXO-BUTAN-2-YL]AMINO]-4-HYDROXY-5-OXO-4-(PHENYLMETHYL)PENTYL]-2-[(4-PHENYLPHENYL)METHYL]HYDRAZINYL]-3,3-DIMETHYL-1-OXO-BUTAN-2-YL]CARBAMATE
• ChEMBL: CHEMBL3221307
• ZINC: ZINC000098208771
• PDB chain: 2xye Chain B Residue 1200

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2xye HIV-1 Protease Inhibitors with a Tertiary Alcohol Containing Transition-State Mimic and Various P2 and P1' Substituents
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): L123 D125 G127 A128 D129 G148 G149 I150 F153 P181 T182
• Binding residue (residue number reindexed from 1): L23 D25 G27 A28 D29 G48 G49 I50 F53 P81 T82
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.34,Ki=4.6nM

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:2xye, PDBe:2xye, PDBj:2xye
• PDBsum: 2xye
• UniProt: P12499|POL_HV1Z2 Gag-Pol polyprotein (Gene Name=gag-pol)