Structure of PDB 2pk6 Chain A Binding Site BS01

Receptor Information

>2pk6 Chain A (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligand information

• Ligand ID: O33
• InChI: InChI=1S/C40H45N5O7S2/c1-40(2)36(38(50)44-34-28-14-8-7-12-25(28)19-31(34)46)45(23-54-40)39(51)35(48)29(18-24-10-5-4-6-11-24)43-37(49)30(22-53-3)42-33(47)21-52-32-15-9-13-26-20-41-17-16-27(26)32/h4-17,20,29-31,34-36,46,48H,18-19,21-23H2,1-3H3,(H,42,47)(H,43,49)(H,44,50)/t29-,30-,31+,34-,35-,36+/m0/s1
• InChIKey: NLPSIHQYIUXYOW-SHJYOGRKSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: CC1([C@H](N(CS1)C(=O)[C@H]([C@H](Cc2ccccc2)NC(=O)[C@H](CSC)NC(=O)COc3cccc4c3ccnc4)O)C(=O)N[C@H]5c6ccccc6C[C@H]5O)C
  CACTVS 3.370: CSC[C@H](NC(=O)COc1cccc2cnccc12)C(=O)N[C@@H](Cc3ccccc3)[C@H](O)C(=O)N4CSC(C)(C)[C@H]4C(=O)N[C@@H]5[C@H](O)Cc6ccccc56
  CACTVS 3.370: CSC[CH](NC(=O)COc1cccc2cnccc12)C(=O)N[CH](Cc3ccccc3)[CH](O)C(=O)N4CSC(C)(C)[CH]4C(=O)N[CH]5[CH](O)Cc6ccccc56
  ACDLabs 12.01: O=C(NC2c1ccccc1CC2O)C6N(C(=O)C(O)C(NC(=O)C(NC(=O)COc4c3ccncc3ccc4)CSC)Cc5ccccc5)CSC6(C)C
  OpenEye OEToolkits 1.7.0: CC1(C(N(CS1)C(=O)C(C(Cc2ccccc2)NC(=O)C(CSC)NC(=O)COc3cccc4c3ccnc4)O)C(=O)NC5c6ccccc6CC5O)C
• Formula: C40 H45 N5 O7 S2
• Name: (4R)-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-3-[(2S,3S)-2-hydroxy-3-({N-[(isoquinolin-5-yloxy)acetyl]-S-methyl- L-cysteinyl}amino)-4-phenylbutanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide;
  KNI-10033
• ChEMBL: CHEMBL440965
• ZINC: ZINC000095614822
• PDB chain: 2pk6 Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2pk6 Compensating enthalpic and entropic changes hinder binding affinity optimization.
• Resolution: 1.45 Å
• Binding residue (original residue number in PDB): R8 D25 G27 A28 D29 D30 V32 I47 G48 I50 P81 V82 I84
• Binding residue (residue number reindexed from 1): R8 D25 G27 A28 D29 D30 V32 I47 G48 I50 P81 V82 I84
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=10.89,Kd=13pM

Enzymatic activity

• Catalytic site (original residue number in PDB): D25 T26 G27
• Catalytic site (residue number reindexed from 1): D25 T26 G27

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:2pk6, PDBe:2pk6, PDBj:2pk6
• PDBsum: 2pk6
• PubMed: 17581235
• UniProt: Q9Q2G8