Structure of PDB 2pk5 Chain B Binding Site BS01

Receptor Information
>2pk5 Chain B (length=99) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF
Ligand information
Ligand ID075
InChIInChI=1S/C40H45N5O9S2/c1-40(2)36(38(50)44-34-28-14-8-7-12-25(28)19-31(34)46)45(23-55-40)39(51)35(48)29(18-24-10-5-4-6-11-24)43-37(49)30(22-56(3,52)53)42-33(47)21-54-32-15-9-13-26-20-41-17-16-27(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
InChIKeyGNSJNHNIJIEWNZ-SHJYOGRKSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NC2c1ccccc1CC2O)C6N(C(=O)C(O)C(NC(=O)C(NC(=O)COc4c3ccncc3ccc4)CS(=O)(=O)C)Cc5ccccc5)CSC6(C)C
OpenEye OEToolkits 1.7.0CC1([C@H](N(CS1)C(=O)[C@H]([C@H](Cc2ccccc2)NC(=O)[C@H](CS(=O)(=O)C)NC(=O)COc3cccc4c3ccnc4)O)C(=O)N[C@H]5c6ccccc6C[C@H]5O)C
CACTVS 3.370CC1(C)SCN([CH]1C(=O)N[CH]2[CH](O)Cc3ccccc23)C(=O)[CH](O)[CH](Cc4ccccc4)NC(=O)[CH](C[S](C)(=O)=O)NC(=O)COc5cccc6cnccc56
CACTVS 3.370CC1(C)SCN([C@@H]1C(=O)N[C@@H]2[C@H](O)Cc3ccccc23)C(=O)[C@@H](O)[C@H](Cc4ccccc4)NC(=O)[C@H](C[S](C)(=O)=O)NC(=O)COc5cccc6cnccc56
OpenEye OEToolkits 1.7.0CC1(C(N(CS1)C(=O)C(C(Cc2ccccc2)NC(=O)C(CS(=O)(=O)C)NC(=O)COc3cccc4c3ccnc4)O)C(=O)NC5c6ccccc6CC5O)C
FormulaC40 H45 N5 O9 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]-3-(methyl sulfonyl)-L-alanyl}amino)-4-phenylbutanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide;
KNI-10075
ChEMBL
DrugBank
ZINCZINC000096933695
PDB chain2pk5 Chain A Residue 900 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2pk5 Compensating enthalpic and entropic changes hinder binding affinity optimization.
Resolution1.9 Å
Binding residue
(original residue number in PDB)
D25 G27 A28 D29 D30 I47 G48 G49 I50
Binding residue
(residue number reindexed from 1)
D25 G27 A28 D29 D30 I47 G48 G49 I50
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=10.70,Kd=20pM
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 ?
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function

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Biological Process
External links
PDB RCSB:2pk5, PDBe:2pk5, PDBj:2pk5
PDBsum2pk5
PubMed17581235
UniProtQ9J2P7

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