Structure of PDB 2vqt Chain A Binding Site BS01

Receptor Information
>2vqt Chain A (length=836) Species: 818 (Bacteroides thetaiotaomicron) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NDTSEVMLLDTGWEFSQSGTEKWMPATVPGTVHQDLISHELLPNPFYGMN
EKKIQWVENEDWEYRTSFIVSEEQLNRDGIQLIFEGLDTYADVYLNGSLL
LKADNMFVGYTLPVKSVLRKGENHLYIYFHSPIRQTLPQYASNGFNYPAD
NDHHEKHLSVFSRKAPYSYGWDWGIRMVTSGVWRPVTLRFYDIATISDYY
VRQLSLTDENARLSNELIVNQIVPQKIPAEVRVNVSLNGTTVTEVKQQVT
LQPGINHITLPAEVTNPVRWMPNGWGTPTLYDFSAQIACGRIVAEQSHRI
GLRTIRVVNEKDKDGESFYFEVNGIPMFAKGANYIPQDALLPNVTTERYQ
TLFRDMKEANMNMVRIWGGGTYENNLFYDLADENGILVWQDFMFACTPYP
SDPTFLKRVEAEAVYNIRRLRNHASLAMWCGNNEILEALKYWGFEKKFTP
EVYQGLMHGYDKLFRELLPSTVKEFDSDRFYVHSSPYLANWGRPESWGTG
DSHNWGVWYGKKPFESLDTDLPRFMSEFGFQSFPEMKTIAAFAAPEDYQI
ESEVMNAHQKSSIGNSLIRTYMERDYIIPESFEDFVYVGLVLQGQGMRHG
LEAHRRNRPYCMGTLYWQLNDSWPVVSWSSIDYYGNWKALHYQAKRAFAP
VLINPIQQNDSLSVYLISDRLDTMEQMTLEMKVVDFDGKTLGKKIQVHSL
EVPANTSKCVYRAKLDGWLTPEDCRRSFLKLILKDKSGHQVAESVHFFRK
TKDLQLPPTSVSYQMKQTDGKCELTLFSSMLAKDIFIETPLQGARYSDNF
FDLLPGERKKVIITSPRIKKGEELPVNIKHIRETYK
Ligand information
Ligand ID15A
InChIInChI=1S/C8H17N3O4/c9-1-2-10-8-7(15)6(14)5(13)4(3-12)11-8/h4-7,12-15H,1-3,9H2,(H,10,11)/t4-,5-,6+,7+/m1/s1
InChIKeyZLIQDFHJGBHZAQ-JWXFUTCRSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NCCN=C1N[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1O
CACTVS 3.341NCCN=C1N[CH](CO)[CH](O)[CH](O)[CH]1O
ACDLabs 10.04OC1C(O)C(O)C(=N/CCN)/NC1CO
OpenEye OEToolkits 1.5.0C(CN=C1C(C(C(C(N1)CO)O)O)O)N
OpenEye OEToolkits 1.5.0C(C/N=C\1/[C@H]([C@H]([C@@H]([C@H](N1)CO)O)O)O)N
FormulaC8 H17 N3 O4
Name(2Z,3R,4S,5R,6R)-2-[(2-aminoethyl)imino]-6-(hydroxymethyl)piperidine-3,4,5-triol
ChEMBLCHEMBL1213402
DrugBank
ZINCZINC000016052635
PDB chain2vqt Chain A Residue 1865 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2vqt Structural and Biochemical Evidence for a Boat-Like Transition State in Beta-Mannosidases.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		W198 D199 W200 W395 N461 E462 W533 Y537 E555 W645 W656
Binding residue
(residue number reindexed from 1)		W171 D172 W173 W367 N433 E434 W505 Y509 E527 W617 W628
Annotation score1
Binding affinityMOAD: Ki=1uM
PDBbind-CN: -logKd/Ki=6.00,Ki=1.0uM
Enzymatic activity
Enzyme Commision number 3.2.1.25: beta-mannosidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004567 beta-mannosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006516 glycoprotein catabolic process
Cellular Component
GO:0005576 extracellular region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2vqt, PDBe:2vqt, PDBj:2vqt
PDBsum2vqt
PubMed18408714
UniProtQ8AAK6

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