Structure of PDB 1sdu Chain B Binding Site BS01

Receptor Information

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

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLMTQIGATLNF

Ligand information

• Ligand ID: MK1
• InChI: InChI=1S/C36H47N5O4/c1-36(2,3)39-35(45)31-24-40(22-26-12-9-15-37-21-26)16-17-41(31)23-29(42)19-28(18-25-10-5-4-6-11-25)34(44)38-33-30-14-8-7-13-27(30)20-32(33)43/h4-15,21,28-29,31-33,42-43H,16-20,22-24H2,1-3H3,(H,38,44)(H,39,45)/t28-,29+,31+,32-,33+/m1/s1
• InChIKey: CBVCZFGXHXORBI-PXQQMZJSSA-N
• SMILES:
  CACTVS 3.341: CC(C)(C)NC(=O)[C@@H]1CN(CCN1C[C@@H](O)C[C@@H](Cc2ccccc2)C(=O)N[C@@H]3[C@H](O)Cc4ccccc34)Cc5cccnc5
  ACDLabs 10.04: O=C(NC2c1ccccc1CC2O)C(Cc3ccccc3)CC(O)CN5C(C(=O)NC(C)(C)C)CN(Cc4cnccc4)CC5
  CACTVS 3.341: CC(C)(C)NC(=O)[CH]1CN(CCN1C[CH](O)C[CH](Cc2ccccc2)C(=O)N[CH]3[CH](O)Cc4ccccc34)Cc5cccnc5
  OpenEye OEToolkits 1.5.0: CC(C)(C)NC(=O)C1CN(CCN1CC(CC(Cc2ccccc2)C(=O)NC3c4ccccc4CC3O)O)Cc5cccnc5
  OpenEye OEToolkits 1.5.0: CC(C)(C)NC(=O)[C@@H]1C[N@@](CC[N@]1C[C@H](C[C@@H](Cc2ccccc2)C(=O)N[C@H]3c4ccccc4C[C@H]3O)O)Cc5cccnc5
• Formula: C36 H47 N5 O4
• Name: N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE;
  INDINAVIR
• ChEMBL: CHEMBL115
• DrugBank: DB00224
• ZINC: ZINC000022448696
• PDB chain: 1sdu Chain B Residue 902

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1sdu Crystal structures of HIV protease V82A and L90M mutants reveal changes in the indinavir-binding site
• Resolution: 1.25 Å
• Binding residue (original residue number in PDB): R108 D125 G127 A128 D129 D130 I147 G148 P181
• Binding residue (residue number reindexed from 1): R8 D25 G27 A28 D29 D30 I47 G48 P81
• Annotation score: 1
• Binding affinity: MOAD: Ki=86pM
  PDBbind-CN: -logKd/Ki=10.07,Ki=86pM

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:1sdu, PDBe:1sdu, PDBj:1sdu
• PDBsum: 1sdu
• PubMed: 15066177
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)