Structure of PDB 2vr4 Chain B Binding Site BS01

Receptor Information
>2vr4 Chain B (length=841) Species: 226186 (Bacteroides thetaiotaomicron VPI-5482) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GNDTSEVMLLDTGWEFSQSGTEKWMPATVPGTVHQDLISHELLPNPFYGM
NEKKIQWVENEDWEYRTSFIVSEEQLNRDGIQLIFEGLDTYADVYLNGSL
LLKADNMFVGYTLPVKSVLRKGENHLYIYFHSPIRQTLPQYASNGFNYPA
DNDHHEKHLSVFSRKAPYSYGWDWGIRMVTSGVWRPVTLRFYDIATISDY
YVRQLSLTDENARLSNELIVNQIVPQKIPAEVRVNVSLNGTTVTEVKQQV
TLQPGINHITLPAEVTNPVRWMPNGWGTPTLYDFSAQIACGDRIVAEQSH
RIGLRTIRVVNEKDKDGESFYFEVNGIPMFAKGANYIPQDALLPNVTTER
YQTLFRDMKEANMNMVRIWGGGTYENNLFYDLADENGILVWQDFMFACTP
YPSDPTFLKRVEAEAVYNIRRLRNHASLAMWCGNNEILEALKYWGFEKKF
TPEVYQGLMHGYDKLFRELLPSTVKEFDSDRFYVHSSPYLANWGRPESWG
TGDSHNWGVWYGKKPFESLDTDLPRFMSEFGFQSFPEMKTIAAFAAPEDY
QIESEVMNAHQKSSIGNSLIRTYMERDYIIPESFEDFVYVGLVLQGQGMR
HGLEAHRRNRPYCMGTLYWQLNDSWPVVSWSSIDYYGNWKALHYQAKRAF
APVLINPIQQNDSLSVYLISDRLDTMEQMTLEMKVVDFDGKTLGKKIQVH
SLEVPANTSKCVYRAKLDGWLTPEDCRRSFLKLILKDKSGHQVAESVHFF
RKTKDLQLPPTSVSYQMKQTDGKCELTLFSSMLAKDIFIETPLQGARYSD
NFFDLLPGERKKVIITSPRIKKGEELPVNIKHIRETYKEHH
Ligand information
Ligand ID17B
InChIInChI=1S/C10H21N3O4/c11-3-1-2-4-12-10-9(17)8(16)7(15)6(5-14)13-10/h6-9,14-17H,1-5,11H2,(H,12,13)/t6-,7-,8+,9+/m1/s1
InChIKeyZLLQXILWWIGNJJ-HXFLIBJXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(CC/N=C\1/[C@H]([C@H]([C@@H]([C@H](N1)CO)O)O)O)CN
ACDLabs 10.04OC1C(O)C(O)C(=N/CCCCN)/NC1CO
CACTVS 3.341NCCCCN=C1N[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1O
CACTVS 3.341NCCCCN=C1N[CH](CO)[CH](O)[CH](O)[CH]1O
OpenEye OEToolkits 1.5.0C(CCN=C1C(C(C(C(N1)CO)O)O)O)CN
FormulaC10 H21 N3 O4
Name(2Z,3R,4S,5R,6R)-2-[(4-aminobutyl)imino]-6-(hydroxymethyl)piperidine-3,4,5-triol
ChEMBLCHEMBL1213438
DrugBank
ZINCZINC000016052636
PDB chain2vr4 Chain B Residue 1869 [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]
PDB2vr4 Structural and Biochemical Evidence for a Boat-Like Transition State in Beta-Mannosidases.
Resolution1.8 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)		W172 D173 W174 W369 N435 E436 W507 Y511 E529 W619 W630
Annotation score1
Binding affinityMOAD: Ki=2.1uM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2vr4, PDBe:2vr4, PDBj:2vr4
PDBsum2vr4
PubMed18408714
UniProtQ8AAK6

[Back to BioLiP]