Structure of PDB 3sdi Chain L Binding Site BS01

Receptor Information
>3sdi Chain L (length=222) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QFNPYGDNGGTILGIAGEDFAVLAGDTRNITDYSINSRYEPKVFDCGDNI
VMSANGFAADGDALVKRFKNSVKWYHFDHNDKKLSINSAARNIQHLLYGK
RFFPYYVHTIIAGLDEDGKGAVYSFDPVGSYEREQCRAGGAAASLIMPFL
DNQVNFKNQYEPGTNGKVKKPLKYLSVEEVIKLVRDSFTSATERHIQVGD
GLEILIVTKDGVRKEFYELKRD
Ligand information
Ligand ID3SD
InChIInChI=1S/C32H41N5O5/c1-21-11-13-24(14-12-21)19-33-29(39)25(16-15-23-9-7-6-8-10-23)35-30(40)26(18-28(38)34-20-32(3,4)5)36-31(41)27-17-22(2)42-37-27/h6-14,17,25-26H,15-16,18-20H2,1-5H3,(H,33,39)(H,34,38)(H,35,40)(H,36,41)/t25-,26-/m0/s1
InChIKeyKVWOEKNSWWTEAJ-UIOOFZCWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2Cc1ccc(cc1)CNC(=O)C(CCc2ccccc2)NC(=O)C(CC(=O)NCC(C)(C)C)NC(=O)c3cc(on3)C
OpenEye OEToolkits 1.7.2Cc1ccc(cc1)CNC(=O)[C@H](CCc2ccccc2)NC(=O)[C@H](CC(=O)NCC(C)(C)C)NC(=O)c3cc(on3)C
CACTVS 3.370Cc1onc(c1)C(=O)N[CH](CC(=O)NCC(C)(C)C)C(=O)N[CH](CCc2ccccc2)C(=O)NCc3ccc(C)cc3
CACTVS 3.370Cc1onc(c1)C(=O)N[C@@H](CC(=O)NCC(C)(C)C)C(=O)N[C@@H](CCc2ccccc2)C(=O)NCc3ccc(C)cc3
ACDLabs 12.01O=C(NC(C(=O)NC(C(=O)NCc1ccc(cc1)C)CCc2ccccc2)CC(=O)NCC(C)(C)C)c3noc(c3)C
FormulaC32 H41 N5 O5
NameN~4~-(2,2-dimethylpropyl)-N~1~-{(2S)-1-[(4-methylbenzyl)amino]-1-oxo-4-phenylbutan-2-yl}-N~2~-[(5-methyl-1,2-oxazol-3-yl)carbonyl]-L-aspartamide
ChEMBL
DrugBank
ZINCZINC000098208465
PDB chain3sdi Chain K Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3sdi Optimization of a series of dipeptides with a P3 threonine residue as non-covalent inhibitors of the chymotrypsin-like activity of the human 20S proteasome.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		D114 P115 S118
Binding residue
(residue number reindexed from 1)		D126 P127 S130
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.33,IC50=4.7nM
Enzymatic activity
Enzyme Commision number 3.4.25.1: proteasome endopeptidase complex.
Gene Ontology
Molecular Function
GO:0003674 molecular_function
GO:0005515 protein binding
Biological Process
GO:0010499 proteasomal ubiquitin-independent protein catabolic process
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0051603 proteolysis involved in protein catabolic process
Cellular Component
GO:0000502 proteasome complex
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005839 proteasome core complex
GO:0019774 proteasome core complex, beta-subunit complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3sdi, PDBe:3sdi, PDBj:3sdi
PDBsum3sdi
PubMed20875739
UniProtP23724|PSB6_YEAST Proteasome subunit beta type-6 (Gene Name=PRE7)

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