Structure of PDB 3kdc Chain B Binding Site BS01

Receptor Information

>3kdc Chain B (length=99) Species: 11686 (Human immunodeficiency virus type 1 (BRU ISOLATE))

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: JZP
• InChI: InChI=1S/C33H35Cl2N3O6S/c1-33(2)30(31(42)37-27-21-12-7-6-11-20(21)16-25(27)39)38(18-45-33)32(43)28(41)24(15-19-9-4-3-5-10-19)36-26(40)17-44-29-22(34)13-8-14-23(29)35/h3-14,24-25,27-28,30,39,41H,15-18H2,1-2H3,(H,36,40)(H,37,42)/t24-,25+,27-,28-,30+/m0/s1
• InChIKey: XMAMZSZKRBFNLW-UPZHSWQNSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: CC1([C@H](N(CS1)C(=O)[C@H]([C@H](Cc2ccccc2)NC(=O)COc3c(cccc3Cl)Cl)O)C(=O)N[C@H]4c5ccccc5C[C@H]4O)C
  ACDLabs 12.01: O=C(NC2c1ccccc1CC2O)C5N(C(=O)C(O)C(NC(=O)COc3c(Cl)cccc3Cl)Cc4ccccc4)CSC5(C)C
  OpenEye OEToolkits 1.7.0: CC1(C(N(CS1)C(=O)C(C(Cc2ccccc2)NC(=O)COc3c(cccc3Cl)Cl)O)C(=O)NC4c5ccccc5CC4O)C
  CACTVS 3.370: CC1(C)SCN([CH]1C(=O)N[CH]2[CH](O)Cc3ccccc23)C(=O)[CH](O)[CH](Cc4ccccc4)NC(=O)COc5c(Cl)cccc5Cl
  CACTVS 3.370: CC1(C)SCN([C@@H]1C(=O)N[C@@H]2[C@H](O)Cc3ccccc23)C(=O)[C@@H](O)[C@H](Cc4ccccc4)NC(=O)COc5c(Cl)cccc5Cl
• Formula: C33 H35 Cl2 N3 O6 S
• Name: (4R)-3-[(2S,3S)-3-{[(2,6-dichlorophenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide;
  KNI-10074
• ChEMBL: CHEMBL510300
• ZINC: ZINC000049899614
• PDB chain: 3kdc Chain A Residue 100

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3kdc How much binding affinity can be gained by filling a cavity?
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): D25 G27 A28 D29 D30 G48 G49 I50
• Binding residue (residue number reindexed from 1): D25 G27 A28 D29 D30 G48 G49 I50
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=9.28,Kd=0.52nM

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:3kdc, PDBe:3kdc, PDBj:3kdc
• PDBsum: 3kdc
• PubMed: 20028396
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)