Structure of PDB 4j28 Chain B Binding Site BS01

Receptor Information
>4j28 Chain B (length=438) Species: 226186 (Bacteroides thetaiotaomicron VPI-5482) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EIPLKYGATNEGKRQDPAMQKFRDNRLGAFIHWGLYAIPGGEWNGKVYGG
AAEWLKSWAKVPADEWLKLMDQWNPTKFDAKKWAKMAKEMGTKYVKITTK
HHEGFCLWPSKYTKYTVANTPYKRDILGELVKAYNDEGIDVHFYFSVMDW
SNPDYRYDIKSKEDSIAFSRFLEFTDNQLKELATRYPTVKDFWFDGTWDA
SVKKNGWWTAHAEQMLKELVPGVAINSRLRADDKGKRHFDSNGRLMGDYE
SGYERRLPDPVKDLKVTQWDWEACMTIPENQWGYHKDWSLSYVKTPIEVI
DRIVHAVSMGGNMVVNFGPQADGDFRPEEKAMATAIGKWMNRYGKAVYAC
DYAGFEKQDWGYYTRGKNDEVYMVVFNQPYSERLIVKTPKGITVEKATLL
TTGEDITVVETTRNEYNVSVPKKNPGEPYVIQLKVRAA
Ligand information
Ligand IDEAT
InChIInChI=1S/C12H15N3O2/c1-6-10(16)11(17)9(13-6)12-14-7-4-2-3-5-8(7)15-12/h2-6,9-11,13,16-17H,1H3,(H,14,15)/t6-,9+,10+,11-/m0/s1
InChIKeyWKDUAKZZRFRSAE-HCPDIIQCSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01OC3C(c2nc1ccccc1n2)NC(C)C3O
OpenEye OEToolkits 1.7.6CC1C(C(C(N1)c2[nH]c3ccccc3n2)O)O
OpenEye OEToolkits 1.7.6C[C@H]1[C@H]([C@H]([C@@H](N1)c2[nH]c3ccccc3n2)O)O
CACTVS 3.370C[CH]1N[CH]([CH](O)[CH]1O)c2[nH]c3ccccc3n2
CACTVS 3.370C[C@@H]1N[C@H]([C@H](O)[C@@H]1O)c2[nH]c3ccccc3n2
FormulaC12 H15 N3 O2
Name(2S,3S,4R,5S)-2-(1H-benzimidazol-2-yl)-5-methylpyrrolidine-3,4-diol
ChEMBLCHEMBL2407928
DrugBank
ZINC
PDB chain4j28 Chain B 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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PDB4j28 Three dimensional structure of a bacterial alpha-l-fucosidase with a 5-membered iminocyclitol inhibitor.
Resolution1.73 Å
Binding residue
(original residue number in PDB)		H66 E87 W88 H135 Y178 D229 W232 W316
Binding residue
(residue number reindexed from 1)		H32 E53 W54 H101 Y144 D195 W198 W282
Annotation score1
Binding affinityMOAD: Ki=2uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004560 alpha-L-fucosidase activity
GO:0016787 hydrolase activity
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006004 fucose metabolic process
GO:0016139 glycoside catabolic process
Cellular Component
GO:0005764 lysosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4j28, PDBe:4j28, PDBj:4j28
PDBsum4j28
PubMed23830696
UniProtQ8A3I4

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