Structure of PDB 2vr4 Chain A Binding Site BS01

Receptor Information
>2vr4 Chain A (length=836) Species: 226186 (Bacteroides thetaiotaomicron VPI-5482) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NDTSEVMLLDTGWEFSQSGTEKWMPATVPGTVHQDLISHELLPNPFYGMN
EKKIQWVENEDWEYRTSFIVSEEQLNRDGIQLIFEGLDTYADVYLNGSLL
LKADNMFVGYTLPVKSVLRKGENHLYIYFHSPIRQTLPQYASNGFNYPAD
NDHHEKHLSVFSRKAPYSYGWDWGIRMVTSGVWRPVTLRFYDIATISDYY
VRQLSLTDENARLSNELIVNQIVPQKIPAEVRVNVSLNGTTVTEVKQQVT
LQPGINHITLPAEVTNPVRWMPNGWGTPTLYDFSAQIACGDRIVAEQSHR
IGLRTIRVVNEKDKDGESFYFEVNGIPMFAKGANYIPQDALLPNVTTERY
QTLFRDMKEANMNMVRIWGGGTYENNLFYDLADENGILVWQDFMFACTPY
PSDPTFLKRVEAEAVYNIRRLRNHASLAMWCGNNEILEALKYWGFEKKFT
PEVYQGLMHGYDKLFRELLPSTVKEFDSDRFYVHSSPYLANWGRPESWGT
GDSHNWGVWYGKKPFESLDTDLPRFMSEFGFQSFPEMKTIAAFAAPEDYQ
IESEVMNAHQKSSIGNSLIRTYMERDYIIPESFEDFVYVGLVLQGQGMRH
GLEAHRRNRPYCMGTLYWQLNDSWPVVSWSSIDYYGNWKALHYQAKRAFA
PVLINPIQQNDSLSVYLISDRLDTMEQMTLEMKVVDFDGKTLGKKIQVHS
LEVPANTSKCVYRAKLDGWLTPEDCRRSFLKLILKDKSGHQVAESVHFFR
KTKDLQLPPTSVSYQMKQTDGKCELTLFSSMLAKDIFIETPLQGARYSDN
FFDLLPGERKKVIITSPRIKKGELPVNIKHIRETYK
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 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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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)		W171 D172 W173 W368 N434 E435 W506 Y510 E528 W618 W629
Annotation score1
Binding affinityMOAD: Ki=2.1uM
PDBbind-CN: -logKd/Ki=5.68,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

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

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