Structure of PDB 3gpj Chain H Binding Site BS01

Receptor Information
>3gpj Chain H (length=222) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TTIVGVKFNNGVVIAADTRSTQGPIVADKNCAKLHRISPKIWCAGAGTAA
DTEAVTQLIGSNIELHSLYTSREPRVVSALQMLKQHLFKYQGHIGAYLIV
AGVDPTGSHLFSIHAHGSTDVGYYLSLGSGSLAAMAVLESHWKQDLTKEE
AIKLASDAIQAGIWNDLGSGSNVDVCVMEIGKDAEYLRNYLTPNVREEKQ
KSYKFPRGTTAVLKESIVNICD
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)		T1 T21 Q22 K33 G47 A49
Binding residue
(residue number reindexed from 1)		T1 T21 Q22 K33 G47 A49
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.11,Ki=7.8uM
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 S129 D166 S169
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:3gpj, PDBe:3gpj, PDBj:3gpj
PDBsum3gpj
PubMed19359491
UniProtP25043|PSB2_YEAST Proteasome subunit beta type-2 (Gene Name=PUP1)

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