Structure of PDB 3wmc Chain A Binding Site BS01

Receptor Information
>3wmc Chain A (length=572) Species: 93504 (Ostrinia furnacalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EDVVWRWSCDNGKCVKLKNDPRSSEPALSLEACKMFCNEYGLLWPRPTGE
ADLGNFLSKINLNSIEVKILKKGATDDLMEAAAKRFKEQVSLAIPRGSTP
KLTGKAVDVYLVNENPNEKAFSLEMDESYGLRVSPSGADRVNATITANSF
FGMRHGLETLSQLFVFDDIRDHLLMVRDVNISDKPVYPYRGILLDTARNY
YSIESIKRTIEAMAAVKLNTLHWHITDSQSFPFVTTKRPNLYKFGALSPQ
KVYTKAAIREVVRFGLERGVRVLPEFDAPAHVGEGWQDTDLTVCFKAEPW
KSYCVEPPCGQLNPTKDELYQYLEDIYSDMAEVFDTTDIFHMGGDEVSEA
CWNSSDSIQNFMMQNRWDLDKESFLKLWNYFQQKAQDKAYKAFGKKLPLI
LWTSTLTNYKHIDDYLNKDDYIIQVWTTGVDPQIKGLLEKGYRLIMSNYD
ALYFDCGYGAWVGAGNNWCSPYIGWQKVYDNSPAVIALEHRDQVLGGEAA
LWSEQSDTSTLDGRLWPRAAALAERLWAEPATSWQDAEYRMLHIRERFVR
MGIQAESLQPEWCYQNEGYCYS
Ligand information
Ligand IDNF6
InChIInChI=1S/C20H21N5O2S/c1-12-22-23-17(28-12)11-21-9-10-25-19(26)14-6-4-5-13-16(24(2)3)8-7-15(18(13)14)20(25)27/h4-8,21H,9-11H2,1-3H3
InChIKeyMZVBLDCRQKXSHR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C3c1c2c(c(N(C)C)cc1)cccc2C(=O)N3CCNCc4nnc(s4)C
OpenEye OEToolkits 1.7.6Cc1nnc(s1)CNCCN2C(=O)c3cccc4c3c(ccc4N(C)C)C2=O
CACTVS 3.385CN(C)c1ccc2C(=O)N(CCNCc3sc(C)nn3)C(=O)c4cccc1c24
FormulaC20 H21 N5 O2 S
Name6-(dimethylamino)-2-(2-{[(5-methyl-1,3,4-thiadiazol-2-yl)methyl]amino}ethyl)-1H-benzo[de]isoquinoline-1,3(2H)-dione
ChEMBLCHEMBL4544229
DrugBank
ZINCZINC000224698099
PDB chain3wmc Chain A Residue 601 [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]
PDB3wmc A crystal structure-guided rational design switching non-carbohydrate inhibitors' specificity between two beta-GlcNAcase homologs
Resolution2.095 Å
Binding residue
(original residue number in PDB)		V327 D367 E368 W424 W448 Y475 W490 W524
Binding residue
(residue number reindexed from 1)		V305 D345 E346 W402 W426 Y453 W468 W502
Annotation score1
Binding affinityMOAD: Ki=0.31uM
PDBbind-CN: -logKd/Ki=6.51,Ki=0.31uM
Enzymatic activity
Catalytic site (original residue number in PDB) D367 E368
Catalytic site (residue number reindexed from 1) D345 E346
Enzyme Commision number 3.2.1.52: beta-N-acetylhexosaminidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004563 beta-N-acetylhexosaminidase activity
GO:0016231 beta-N-acetylglucosaminidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0000272 polysaccharide catabolic process
GO:0005975 carbohydrate metabolic process
GO:0006032 chitin catabolic process
GO:0006517 protein deglycosylation
GO:0006689 ganglioside catabolic process
GO:0030203 glycosaminoglycan metabolic process
Cellular Component
GO:0005764 lysosome
GO:0005886 plasma membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3wmc, PDBe:3wmc, PDBj:3wmc
PDBsum3wmc
PubMed25155420
UniProtQ06GJ0|HEXC_OSTFU Chitooligosaccharidolytic beta-N-acetylglucosaminidase

[Back to BioLiP]