Structure of PDB 6jtc Chain B Binding Site BS01

Receptor Information
>6jtc Chain B (length=699) Species: 431947 (Porphyromonas gingivalis ATCC 33277) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DEGMWLMQQLGRKYAQMKERGLKMKEYDLYNPNGTSLKDAVVLFDGGCTG
EVVSDRGLVLTNHHCGYDMIQAHSTLEHNYLENGFWAMREADELPNKDIS
VVFIDKIEDVTDYVKKELKAIKDPNSMDYLSPKYLQKLADKKAGKNFSAK
NPGLSVEIKAFYGGNLYLMFTKKTYTDVRLVGAPPSSIGKFGADTDNWIW
PRHTGDFSIFRIYADKNGNPAPYSEDNVPLKPKRFFNISLGGVQENDYAM
IMGFPGTTHRYFTASEVDEWKSIDNDIRIRMRDIRQGVMLREMLADPQIK
IMYSAKYAASQNAYKRAIGANWAIKTRGLRQNKQAMQDRLIAWGAKQGTP
RYEEAVHEIDATVAKRADLRRRYWMIEEGIIRGIEFARSPIPTEDETKAL
QGNDASARKEAIDKIRTRYSKFANKDYSAEVDKKVAVAMLTEYLKEIPYE
NLPLHLRLVKDRFAGDVQAYVDDIFARSVFGSEAQFDAFAAVPSVEKLAE
DPMVLFASSVFDEYRKLYNELRPYDDPILRAQRTYIAGLLEMDGDQDQFP
DANLTLRFTYGQVKGYSPRDNVYYGHQTTLDGVMEKEDPDNWEFVVDPKL
KAVYERKDFGRYADRSGRMPVAFCATTHTTGGNSGSPVMNANGELIGLNF
DRNWEGVGGDIQYLADYQRSIIVDIRYVLLVIDKVGGCQRLLDEMNIVP
Ligand information
Ligand IDC8O
InChIInChI=1S/C9H11N3O4/c10-3-4-11-8-2-1-6(12(15)16)5-7(8)9(13)14/h1-2,5,11H,3-4,10H2,(H,13,14)
InChIKeyPGIQBPZLZVDGHP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc(c(cc1[N+](=O)[O-])C(=O)O)NCCN
CACTVS 3.385NCCNc1ccc(cc1C(O)=O)[N+]([O-])=O
FormulaC9 H11 N3 O4
Name2-(2-azanylethylamino)-5-nitro-benzoic acid
ChEMBL
DrugBank
ZINCZINC000004313545
PDB chain6jtc 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]
PDB6jtc Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase.
Resolution2.39 Å
Binding residue
(original residue number in PDB)		N218 W219 T650 T651 G652 N654 S655 N670 F671 D672 R673
Binding residue
(residue number reindexed from 1)		N197 W198 T629 T630 G631 N633 S634 N649 F650 D651 R652
Annotation score1
Binding affinityMOAD: Ki=8.45uM
Enzymatic activity
Enzyme Commision number 3.4.14.-
Gene Ontology
Molecular Function
GO:0008239 dipeptidyl-peptidase activity
GO:0070009 serine-type aminopeptidase activity

View graph for
Molecular Function
External links
PDB RCSB:6jtc, PDBe:6jtc, PDBj:6jtc
PDBsum6jtc
PubMed31537874
UniProtB2RID1|DPP11_PORG3 Asp/Glu-specific dipeptidyl-peptidase (Gene Name=dpp11)

[Back to BioLiP]