Structure of PDB 3gpj Chain I Binding Site BS01

Receptor Information
>3gpj Chain I (length=204) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDPSSINGGIVVAMTGKDCVAIACDLRLGSQSLGVSNKFEKIFHYGHVFL
GITGLATDVTTLNEMFRYKTNLYKLKEERAIEPETFTQLVSSSLYERRFG
PYFVGPVVAGINSKSGKPFIAGFDLIGCIDEAKDFIVSGTASDQLFGMCE
SLYEPNLEPEDLFETISQALLNAADRDALSGWGAVVYIIKKDEVVKRYLK
MRQD
Ligand information
Ligand IDSY2
InChIInChI=1S/C24H41N5O6/c1-13(2)16-10-11-18(30)25-12-8-7-9-17(21(31)26-16)27-22(32)19(14(3)4)28-24(35)29-20(15(5)6)23(33)34/h10-11,13-17,19-20H,7-9,12H2,1-6H3,(H,25,30)(H,26,31)(H,27,32)(H,33,34)(H2,28,29,35)/t16-,17+,19+,20+/m1/s1
InChIKeyAIMDTYKFJMYVNG-UMGGQSCQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)[CH]1NC(=O)[CH](CCCCNC(=O)C=C1)NC(=O)[CH](NC(=O)N[CH](C(C)C)C(O)=O)C(C)C
ACDLabs 10.04O=C(O)C(NC(=O)NC(C(=O)NC1C(=O)NC(C=CC(=O)NCCCC1)C(C)C)C(C)C)C(C)C
OpenEye OEToolkits 1.5.0CC(C)[C@H]1C=CC(=O)NCCCC[C@@H](C(=O)N1)NC(=O)[C@H](C(C)C)NC(=O)N[C@@H](C(C)C)C(=O)O
CACTVS 3.341CC(C)[C@@H]/1NC(=O)[C@H](CCCCNC(=O)\C=C/1)NC(=O)[C@@H](NC(=O)N[C@@H](C(C)C)C(O)=O)C(C)C
OpenEye OEToolkits 1.5.0CC(C)C1C=CC(=O)NCCCCC(C(=O)N1)NC(=O)C(C(C)C)NC(=O)NC(C(C)C)C(=O)O
FormulaC24 H41 N5 O6
NameN-{[(1S)-2-methyl-1-{[(5S,8S)-5-(1-methylethyl)-2,7-dioxo-1,6-diazacyclododec-3-en-8-yl]carbamoyl}propyl]carbamoyl}-L-valine;
Syringolin B
ChEMBL
DrugBank
ZINCZINC000263620236
PDB chain3gpj Chain H Residue 7710 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3gpj Synthetic and structural studies on syringolin A and B reveal critical determinants of selectivity and potency of proteasome inhibition
Resolution2.7 Å
Binding residue
(original residue number in PDB)		D114 I116 C118
Binding residue
(residue number reindexed from 1)		D124 I126 C128
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.11,Ki=7.8uM
Enzymatic activity
Enzyme Commision number 3.4.25.1: proteasome endopeptidase complex.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0061133 endopeptidase activator activity
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3gpj, PDBe:3gpj, PDBj:3gpj
PDBsum3gpj
PubMed19359491
UniProtP25451|PSB3_YEAST Proteasome subunit beta type-3 (Gene Name=PUP3)

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