Structure of PDB 5sdc Chain B Binding Site BS01

Receptor Information
>5sdc Chain B (length=695) Species: 837 (Porphyromonas gingivalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EGMWLMQQLGRKYAQMKERGLKMKEYDLYNPNGTSLKDAVVLFDGGCTGE
VVSDRGLVLTNHHCGYDMIQAHSTLEHNYLENGFWAMREADELPNKDISV
VFIDKIEDVTDYVKKELKAIKDPNSMDYLSPKYLQKLADKKAGKNFSAKN
PGLSVEIKAFYGGNLYLMFTKKTYTDVRLVGAPPSSIGKFGADTDNWIWP
RHTGDFSIFRIYADKNGNPAPYSEDNVPLKPKRFFNISLGGVQENDYAMI
MGFPGTTHRYFTASEVDEWKSIDNDIRIRMRDIRQGVMLREMLADPQIKI
MYSAKYAASQNAYKRAIGANWAIKTRGLRQNKQAMQDRLIAWGAKQGTPR
YEEAVHEIDATVAKRADLRRRYWMIEEGIIRGIEFARSPIPTEDETKALQ
ASARKEAIDKIRTRYSKFANKDYSAEVDKKVAVAMLTEYLKEIPYENLPL
HLRLVKDRFAGDVQAYVDDIFARSVFGSEAQFDAFAAVPSVEKLAEDPMV
LFASSVFDEYRKLYNELRPYDDPILRAQRTYIAGLLEMDGDQDQFPDANL
TLRFTYGQVKGYSPRDNVYYGHQTTLDGVMEKEDPDNWEFVVDPKLKAVY
ERKDFGRYADRSGRMPVAFCATTHTTGGNSGSPVMNANGELIGLNFDRNW
EGVGGDIQYLADYQRSIIVDIRYVLLVIDKVGGCQRLLDEMNIVP
Ligand information
Ligand IDLDV
InChIInChI=1S/C15H20N2/c1-12-6-8-17(9-7-12)11-13-10-16-15-5-3-2-4-14(13)15/h2-5,10,12,16H,6-9,11H2,1H3
InChIKeyDGCGMYNLCDVYMB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1CCN(CC1)Cc2c[nH]c3c2cccc3
CACTVS 3.385CC1CCN(CC1)Cc2c[nH]c3ccccc23
ACDLabs 12.01N1(CCC(CC1)C)Cc3c2c(cccc2)nc3
FormulaC15 H20 N2
Name3-[(4-methylpiperidin-1-yl)methyl]-1H-indole
ChEMBLCHEMBL57478
DrugBank
ZINCZINC000000142608
PDB chain5sdc Chain B Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5sdc PanDDA analysis group deposition
Resolution1.928 Å
Binding residue
(original residue number in PDB)		C69 H85 N218 F671 D672
Binding residue
(residue number reindexed from 1)		C47 H63 N196 F646 D647
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.14.-
Gene Ontology
Molecular Function
GO:0004177 aminopeptidase activity
GO:0008236 serine-type peptidase activity
GO:0008239 dipeptidyl-peptidase activity
GO:0042277 peptide binding
GO:0070009 serine-type aminopeptidase activity
Biological Process
GO:0006508 proteolysis
GO:0043171 peptide catabolic process
GO:0048588 developmental cell growth
Cellular Component
GO:0009986 cell surface

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5sdc, PDBe:5sdc, PDBj:5sdc
PDBsum5sdc
PubMed
UniProtB2RID1|DPP11_PORG3 Asp/Glu-specific dipeptidyl-peptidase (Gene Name=dpp11)

[Back to BioLiP]