Structure of PDB 3sdi Chain K Binding Site BS02

Receptor Information
>3sdi Chain K (length=212) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TTTLAFRFQGGIIVAVDSRATAGNWVASQTVKKVIEINPFLLGTMAGGAA
DCQFWETWLGSQCRLHELREKERISVAAASKILSNLVYQYKGAGLSMGTM
ICGYTRKEGPTIYYVDSDGTRLKGDIFCVGSGQTFAYGVLDSNYKWDLSV
EDALYLGKRSILAAAHRDAYSGGSVNLYHVTEDGWIYHGNHDVGELFWKV
KEEEGSFNNVIG
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
Global viewLocal viewStructure summary

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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)		A20 T21 A27 K33 M45 G47 G48 A49
Binding residue
(residue number reindexed from 1)		A20 T21 A27 K33 M45 G47 G48 A49
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.33,IC50=4.7nM
Enzymatic activity
Catalytic site (original residue number in PDB) T1 D17 R19 K33 G47 S129 D166 S169
Catalytic site (residue number reindexed from 1) T1 D17 R19 K33 G47 S131 D168 S171
Enzyme Commision number 3.4.25.1: proteasome endopeptidase complex.
Gene Ontology
Molecular Function
GO:0004298 threonine-type endopeptidase activity
Biological Process
GO:0051603 proteolysis involved in protein catabolic process
Cellular Component
GO:0005839 proteasome core 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
UniProtP30656|PSB5_YEAST Proteasome subunit beta type-5 (Gene Name=PRE2)

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