Structure of PDB 5n0f Chain A Binding Site BS01

Receptor Information
>5n0f Chain A (length=332) Species: 1397 (Niallia circulans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDFWVEAELWELVMDAYQH
TSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDDIMWWAMGSARAYQ
ITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTKNACINFPA
AQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRIEIEHGAVP
DATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLVDSNGVLNY
EGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWLAFNIEMAW
SHQNSDHIVDGNWAGGTYESWSSAAAVQALNG
Ligand information
Ligand ID7K2
InChIInChI=1S/C12H23NO7S/c14-3-7-9(17)10(18)11(19)12(20-7)21-4-5-1-13-2-6(15)8(5)16/h5-19H,1-4H2/t5-,6-,7-,8-,9-,10+,11+,12-/m1/s1
InChIKeyKDPQETHZRPVZAI-TYMLGRTHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C1C(C(C(CN1)O)O)CSC2C(C(C(C(O2)CO)O)O)O
CACTVS 3.385OC[C@H]1O[C@H](SC[C@H]2CNC[C@@H](O)[C@@H]2O)[C@@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 2.0.6C1[C@@H]([C@H]([C@@H](CN1)O)O)CS[C@@H]2[C@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O
CACTVS 3.385OC[CH]1O[CH](SC[CH]2CNC[CH](O)[CH]2O)[CH](O)[CH](O)[CH]1O
FormulaC12 H23 N O7 S
Name[(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-alpha-D-mannopyranoside;
(2~{R},3~{S},4~{S},5~{S},6~{R})-2-[[(3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)piperidin-3-yl]methylsulfanyl]-6-(hydroxymethy l)oxane-3,4,5-triol;
isofagomine-thiol-alpha-D-mannopyranoside;
[(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-alpha-D-mannoside;
[(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-D-mannoside;
[(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-mannoside
ChEMBL
DrugBank
ZINC
PDB chain5n0f Chain A Residue 401 [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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PDB5n0f An atypical interaction explains the high-affinity of a non-hydrolyzable S-linked 1,6-alpha-mannanase inhibitor.
Resolution1.69 Å
Binding residue
(original residue number in PDB)
F122 D124 D125 W172 C183 D228 Y243 D294
Binding residue
(residue number reindexed from 1)
F84 D86 D87 W134 C145 D190 Y205 D256
Annotation score1
Binding affinityMOAD: Kd=0.9uM
PDBbind-CN: -logKd/Ki=6.05,Kd=0.90uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Biological Process
External links
PDB RCSB:5n0f, PDBe:5n0f, PDBj:5n0f
PDBsum5n0f
PubMed28766587
UniProtQ9Z4P9

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