Structure of PDB 2wl0 Chain B Binding Site BS01

Receptor Information

>2wl0 Chain B (length=99) Species: 11683 (Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE))

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPTNVIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: 5AH
• InChI: InChI=1S/C40H47N5O6/c1-39(2,3)35(43-38(49)51-4)36(47)44-45(26-28-17-19-29(20-18-28)32-16-10-11-22-41-32)23-21-40(50,25-27-12-6-5-7-13-27)37(48)42-34-31-15-9-8-14-30(31)24-33(34)46/h5-20,22,33-35,46,50H,21,23-26H2,1-4H3,(H,42,48)(H,43,49)(H,44,47)/t33-,34+,35-,40-/m1/s1
• InChIKey: AWOPQBWUWCOWJO-UKVDXBKXSA-N
• SMILES:
  ACDLabs 10.04: O=C(NC2c1ccccc1CC2O)C(O)(Cc3ccccc3)CCN(NC(=O)C(NC(=O)OC)C(C)(C)C)Cc5ccc(c4ncccc4)cc5
  CACTVS 3.352: COC(=O)N[CH](C(=O)NN(CC[C](O)(Cc1ccccc1)C(=O)N[CH]2[CH](O)Cc3ccccc23)Cc4ccc(cc4)c5ccccn5)C(C)(C)C
  OpenEye OEToolkits 1.6.1: CC(C)(C)[C@@H](C(=O)N[N@](CC[C@@](Cc1ccccc1)(C(=O)N[C@H]2c3ccccc3C[C@H]2O)O)Cc4ccc(cc4)c5ccccn5)NC(=O)OC
  CACTVS 3.352: COC(=O)N[C@H](C(=O)NN(CC[C@@](O)(Cc1ccccc1)C(=O)N[C@@H]2[C@H](O)Cc3ccccc23)Cc4ccc(cc4)c5ccccn5)C(C)(C)C
  OpenEye OEToolkits 1.6.1: CC(C)(C)C(C(=O)NN(CCC(Cc1ccccc1)(C(=O)NC2c3ccccc3CC2O)O)Cc4ccc(cc4)c5ccccn5)NC(=O)OC
• Formula: C40 H47 N5 O6
• Name: METHYL [(1S)-1-({2-[(3S)-3-BENZYL-3-HYDROXY-4-{[(1S,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YL]AMINO}-4-OXOBUTYL]-2-(4-PYRIDIN-2-YLBENZYL)HYDRAZINO}CARBONYL)-2,2-DIMETHYLPROPYL]CARBAMATE
• ChEMBL: CHEMBL583370
• ZINC: ZINC000049722966
• PDB chain: 2wl0 Chain A Residue 1100

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2wl0 HIV-1 Protease Inhibitors with a Transition-State Mimic Comprising a Tertiary Alcohol: Improved Antiviral Activity in Cells.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): L123 D125 G127 A128 D129 G148 G149 I150 P181 T182
• Binding residue (residue number reindexed from 1): L23 D25 G27 A28 D29 G48 G49 I50 P81 T82
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.80,Ki=16nM

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:2wl0, PDBe:2wl0, PDBj:2wl0
• PDBsum: 2wl0
• PubMed: 19961222
• UniProt: P12499|POL_HV1Z2 Gag-Pol polyprotein (Gene Name=gag-pol)