Structure of PDB 1bwb Chain A Binding Site BS01

Receptor Information

>1bwb Chain A (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPFNVIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: 146
• InChI: InChI=1S/C49H44N8O5/c58-43-41(27-31-13-3-1-4-14-31)56(29-33-17-11-19-35(25-33)45(60)54-47-50-37-21-7-8-22-38(37)51-47)49(62)57(42(44(43)59)28-32-15-5-2-6-16-32)30-34-18-12-20-36(26-34)46(61)55-48-52-39-23-9-10-24-40(39)53-48/h1-26,41-44,58-59H,27-30H2,(H2,50,51,54,60)(H2,52,53,55,61)/t41-,42-,43+,44+/m1/s1
• InChIKey: UWSVAGUSMAEUKO-QHQGJXSCSA-N
• SMILES:
  CACTVS 3.341: O[C@@H]1[C@@H](O)[C@@H](Cc2ccccc2)N(Cc3cccc(c3)C(=O)Nc4[nH]c5ccccc5n4)C(=O)N(Cc6cccc(c6)C(=O)Nc7[nH]c8ccccc8n7)[C@@H]1Cc9ccccc9
  CACTVS 3.341: O[CH]1[CH](O)[CH](Cc2ccccc2)N(Cc3cccc(c3)C(=O)Nc4[nH]c5ccccc5n4)C(=O)N(Cc6cccc(c6)C(=O)Nc7[nH]c8ccccc8n7)[CH]1Cc9ccccc9
  ACDLabs 10.04: O=C(Nc1nc2ccccc2n1)c3cc(ccc3)CN5C(=O)N(C(Cc4ccccc4)C(O)C(O)C5Cc6ccccc6)Cc7cccc(c7)C(=O)Nc9nc8ccccc8n9
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)CC2C(C(C(N(C(=O)N2Cc3cccc(c3)C(=O)Nc4[nH]c5ccccc5n4)Cc6cccc(c6)C(=O)Nc7[nH]c8ccccc8n7)Cc9ccccc9)O)O
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)C[C@@H]2[C@@H]([C@H]([C@H](N(C(=O)N2Cc3cccc(c3)C(=O)Nc4[nH]c5ccccc5n4)Cc6cccc(c6)C(=O)Nc7[nH]c8ccccc8n7)Cc9ccccc9)O)O
• Formula: C49 H44 N8 O5
• Name: [4R-(4ALPHA,5ALPHA,6ALPHA,7ALPHA)]-3,3'-{{TETRAHYDRO-5,6-DIHYDROXY-2-OXO-4,7-BIS(PHENYLMETHYL)-1H-1,3-DIAZEPINE-1,3(2H)-DIYL]BIS(METHYLENE)]BIS[N-1H-BENZIMIDAZOL-2-YLBENZAMIDE];
  SD146
• ChEMBL: CHEMBL11266
• DrugBank: DB02729
• ZINC: ZINC000085548773
• PDB chain: 1bwb Chain B Residue 641

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1bwb Counteracting HIV-1 protease drug resistance: structural analysis of mutant proteases complexed with XV638 and SD146, cyclic urea amides with broad specificities.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): D25 G27 A28 D30 V32 K45 I47 G48 I50 P81
• Binding residue (residue number reindexed from 1): D25 G27 A28 D30 V32 K45 I47 G48 I50 P81
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.42,Ki=3.8nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D25 T26 G27
• 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:1bwb, PDBe:1bwb, PDBj:1bwb
• PDBsum: 1bwb
• PubMed: 9790666
• UniProt: P04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)