Structure of PDB 2i4d Chain B Binding Site BS01

Receptor Information

>2i4d Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGMTLNF

Ligand information

• Ligand ID: QFI
• InChI: InChI=1S/C29H41N2O12PS/c1-19(2)15-31(45(37,38)23-10-8-21(39-3)9-11-23)16-26(32)25(14-20-4-6-22(7-5-20)42-18-44(34,35)36)30-29(33)43-27-17-41-28-24(27)12-13-40-28/h4-11,19,24-28,32H,12-18H2,1-3H3,(H,30,33)(H2,34,35,36)/t24-,25-,26+,27-,28+/m0/s1
• InChIKey: VGMTVMSJTCIQMF-AJIIGFCHSA-N
• SMILES:
  CACTVS 3.341: COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[CH](O)[CH](Cc2ccc(OC[P](O)(O)=O)cc2)NC(=O)O[CH]3CO[CH]4OCC[CH]34
  ACDLabs 10.04: O=S(=O)(c1ccc(OC)cc1)N(CC(C)C)CC(O)C(NC(=O)OC2COC3OCCC23)Cc4ccc(OCP(=O)(O)O)cc4
  CACTVS 3.341: COc1ccc(cc1)[S](=O)(=O)N(CC(C)C)C[C@@H](O)[C@H](Cc2ccc(OC[P](O)(O)=O)cc2)NC(=O)O[C@H]3CO[C@H]4OCC[C@@H]34
  OpenEye OEToolkits 1.5.0: CC(C)CN(CC(C(Cc1ccc(cc1)OCP(=O)(O)O)NC(=O)OC2COC3C2CCO3)O)S(=O)(=O)c4ccc(cc4)OC
  OpenEye OEToolkits 1.5.0: CC(C)C[N@@](C[C@H]([C@H](Cc1ccc(cc1)OCP(=O)(O)O)NC(=O)O[C@H]2CO[C@@H]3[C@H]2CCO3)O)S(=O)(=O)c4ccc(cc4)OC
• Formula: C29 H41 N2 O12 P S
• Name: ({4-[(2S,3R)-2-({[(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YLOXY]CARBONYL}AMINO)-3-HYDROXY-4-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}BUTYL]PHENOXY}METHYL)PHOSPHONIC ACID
• ChEMBL: CHEMBL1235561
• ZINC: ZINC000024854015
• PDB chain: 2i4d Chain B Residue 300

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2i4d Suppression of HIV-1 Protease Inhibitor Resistance by Phosphonate-mediated Solvent Anchoring.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): D225 G227 A228 D229 D230 G248 G249 I250 F253
• Binding residue (residue number reindexed from 1): D25 G27 A28 D29 D30 G48 G49 I50 F53
• Annotation score: 1
• Binding affinity: MOAD: Ki=2.1pM
  PDBbind-CN: -logKd/Ki=11.68,Ki=2.1pM

Enzymatic activity

• Catalytic site (original residue number in PDB): D225 T226 G227
• Catalytic site (residue number reindexed from 1): D25 T26 G27
• Enzyme Commision number: 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:2i4d, PDBe:2i4d, PDBj:2i4d
• PDBsum: 2i4d
• PubMed: 16979654
• UniProt: Q5RZ08