Structure of PDB 4ad2 Chain A Binding Site BS02

Receptor Information
>4ad2 Chain A (length=345) Species: 657309 (Bacteroides xylanisolvens XB1A) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TELDYDTFCFYYDWYGSEAIDGQYRHWAHAIAPDPNGGSGQNPGTIPGTQ
ESIASNFYPQLGRYSSSDPNILTKHMDMFVMARTGVLALTWWNEQDETEA
KRIGLILDAADKKKIKVCFHLEPYPSRNVQNLRENIVKLITRYGNHPAFY
RKDGKPLFFIYDSYLIEPSEWEKLLSPGGSITIRNTAYDALMIGLWTSSP
TVQRPFILNAHFDGFYTYFAATGFTYGSTPTNWVSMQKWAKENGKIFIPS
VGPGYIDTRIRPWNGSVIRTRTDGQYYDAMYRKAIEAGVSAISITSFNEW
HEGSQIEPAVPYTSSEFTYLDYENREPDYYLTRTAYWVGKFRESK
Ligand information
Ligand IDIFM
InChIInChI=1S/C6H13NO3/c8-3-4-1-7-2-5(9)6(4)10/h4-10H,1-3H2/t4-,5-,6-/m1/s1
InChIKeyQPYJXFZUIJOGNX-HSUXUTPPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[CH]1CNC[CH](O)[CH]1O
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H]([C@@H](CN1)O)O)CO
ACDLabs 10.04OC1C(CO)CNCC1O
CACTVS 3.341OC[C@H]1CNC[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C1C(C(C(CN1)O)O)CO
FormulaC6 H13 N O3
Name5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE;
Afegostat;
isofagomine;
(3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL
ChEMBLCHEMBL206468
DrugBankDB04545
ZINCZINC000003813668
PDB chain4ad2 Chain A Residue 501 [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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PDB4ad2 Structural and Mechanistic Insight Into N-Glycan Processing by Endo-Alpha-Mannosidase.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y46 W126 H154 E156 Y195 Y252 E333 E336
Binding residue
(residue number reindexed from 1)		Y12 W92 H120 E122 Y161 Y218 E299 E302
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.20,Kd=625nM
Enzymatic activity
Enzyme Commision number 3.2.1.130: glycoprotein endo-alpha-1,2-mannosidase.
Gene Ontology
Molecular Function
GO:0004559 alpha-mannosidase activity
GO:0016787 hydrolase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Cellular Component
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:4ad2, PDBe:4ad2, PDBj:4ad2
PDBsum4ad2
PubMed22219371
UniProtD6D1V7

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