Structure of PDB 5lyr Chain A Binding Site BS02

Receptor Information
>5lyr Chain A (length=349) Species: 657309 (Bacteroides xylanisolvens XB1A) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NNLGTELDYDTFCFYYDWYGSEAIDGQYRHWAHAIAPDPNGGSGQNPGTI
PGTQESIASNFYPQLGRYSSSDPNILTKHMDMFVMARTGVLALTWWNEQD
ETEAKRIGLILDAADKKKIKVCFHLEPYPSRNVQNLRENIVKLITRYGNH
PAFYRKDGKPLFFIYDSYLIEPSEWEKLLSPGGSITIRNTAYDALMIGLW
TSSPTVQRPFILNAHFDGFYTYFAATGFTYGSTPTNWVSMQKWAKENGKI
FIPSVGPGYIDTRIRPWNGSVIRTRTDGQYYDAMYRKAIEAGVSAISITS
FNEWHEGSQIEPAVPYTSSEFTYLDYENREPDYYLTRTAYWVGKFRESK
Ligand information
Ligand IDMNM
InChIInChI=1S/C6H13NO4/c8-2-3-1-7-6(11)5(10)4(3)9/h3-11H,1-2H2/t3-,4-,5+,6+/m1/s1
InChIKeyBHOYFRIRWXBNHP-ZXXMMSQZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C(C(C(C(N1)O)O)O)CO
CACTVS 3.341OC[CH]1CN[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1CN[C@@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H]([C@@H]([C@@H](N1)O)O)O)CO
ACDLabs 10.04OC1C(CNC(O)C1O)CO
FormulaC6 H13 N O4
Name(2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-HYDROXYMETHYL-PIPERIDINE
ChEMBL
DrugBank
ZINC
PDB chain5lyr Chain A Residue 404 [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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PDB5lyr Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-alpha-1,2-Mannanase.
Resolution1.14 Å
Binding residue
(original residue number in PDB)		Y46 W126 H154 E156 Y195 Y252 E333 E336
Binding residue
(residue number reindexed from 1)		Y16 W96 H124 E126 Y165 Y222 E303 E306
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.89,Kd=0.013uM
Enzymatic activity
Enzyme Commision number ?
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:5lyr, PDBe:5lyr, PDBj:5lyr
PDBsum5lyr
PubMed27992199
UniProtD6D1V7

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