Structure of PDB 3sdk Chain Y Binding Site BS01

Receptor Information
>3sdk Chain Y (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 IDP3N
InChIInChI=1S/C32H38N6O5/c1-20-11-13-23(14-12-20)19-33-28(39)24(16-15-22-9-7-6-8-10-22)34-29(40)25(35-30(41)26-17-21(2)42-37-26)18-27-36-31(38-43-27)32(3,4)5/h6-14,17,24-25H,15-16,18-19H2,1-5H3,(H,33,39)(H,34,40)(H,35,41)/t24-,25-/m0/s1
InChIKeyOHMJOYZRJHYMAE-DQEYMECFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2Cc1ccc(cc1)CNC(=O)[C@H](CCc2ccccc2)NC(=O)[C@H](Cc3nc(no3)C(C)(C)C)NC(=O)c4cc(on4)C
CACTVS 3.370Cc1onc(c1)C(=O)N[C@@H](Cc2onc(n2)C(C)(C)C)C(=O)N[C@@H](CCc3ccccc3)C(=O)NCc4ccc(C)cc4
OpenEye OEToolkits 1.7.2Cc1ccc(cc1)CNC(=O)C(CCc2ccccc2)NC(=O)C(Cc3nc(no3)C(C)(C)C)NC(=O)c4cc(on4)C
CACTVS 3.370Cc1onc(c1)C(=O)N[CH](Cc2onc(n2)C(C)(C)C)C(=O)N[CH](CCc3ccccc3)C(=O)NCc4ccc(C)cc4
ACDLabs 12.01O=C(NCc1ccc(cc1)C)C(NC(=O)C(NC(=O)c2noc(c2)C)Cc3nc(no3)C(C)(C)C)CCc4ccccc4
FormulaC32 H38 N6 O5
NameN-[(2S)-3-(3-tert-butyl-1,2,4-oxadiazol-5-yl)-1-({(2S)-1-[(4-methylbenzyl)amino]-1-oxo-4-phenylbutan-2-yl}amino)-1-oxopropan-2-yl]-5-methyl-1,2-oxazole-3-carboxamide
ChEMBLCHEMBL3218845
DrugBank
ZINCZINC000098209284
PDB chain3sdk Chain Y Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3sdk 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.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		A20 T21 A27 V31 K33 G47 G48 A49 S96
Binding residue
(residue number reindexed from 1)		A20 T21 A27 V31 K33 G47 G48 A49 S96
Annotation score1
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:3sdk, PDBe:3sdk, PDBj:3sdk
PDBsum3sdk
PubMed20875739
UniProtP30656|PSB5_YEAST Proteasome subunit beta type-5 (Gene Name=PRE2)

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