Structure of PDB 6ld0 Chain A Binding Site BS01

Receptor Information
>6ld0 Chain A (length=620) Species: 401473 (Bifidobacterium dentium Bd1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NGMLYPQSNDSRIVFPLDGVWDFRTAGEDSYPAEWADAPLPEPLPMAVPG
SYNDQNDELNLRAHYGWVVYQRSFAVPSRLVAGQRMILRFDAATHAADVY
LNGQLLGSHFGGFLPFEFDVTSALHAGENLLTVAVDNRIGSSTLPVGNDA
GTAFMGSDNANVPAVAEAKKHARRQNLPNFDFFNFAGLNRHVELYTTPAD
AYIADIAITTERLDHIAGDACTAANALIAYDVTFGGDGRQVRISILDGEG
TVVAGVTADIERTAKASGEIAIRDAKLWNPGAAYLYTAVAELLPSRIIDA
YRQTFGIRTVEVSGTTFLINGKPFYFKGFGKHEDSYFHGRGTDDVLNVKD
VSLIHWLHANSFRTSHYPYAESMYDLCDREGIVIIDEVPAVGMSWLQYAN
PLVAERHREAIRGMIARDKNHPCIVMWSIANEPGLDGDGERPRQAYDYFR
PLYELAHASDPQNRPVTLVCCQNDYTTDITERTMDVVCINRYYGWYNLSG
DLDAACHALNIELDFWENIGKPVMFTEYGADTIEGIHGTHGEMFSEEFQR
DYYARINAEIDKRPWFIGEQLWNFADFATFQGIIRVEGNRKGILTRDRQP
KMAAHWLRERWAGIPDYGYK
Ligand information
Ligand IDE8X
InChIInChI=1S/C12H23NO4/c1-2-3-4-5-6-8-10(12(16)17)11(15)9(14)7-13-8/h8-11,13-15H,2-7H2,1H3,(H,16,17)/t8-,9+,10-,11-/m0/s1
InChIKeyRRWNAAJMVJWKAM-VLEAKVRGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCC[C@@H]1NC[C@@H](O)[C@H](O)[C@H]1C(O)=O
OpenEye OEToolkits 2.0.7CCCCCC[C@H]1[C@@H]([C@H]([C@@H](CN1)O)O)C(=O)O
CACTVS 3.385CCCCCC[CH]1NC[CH](O)[CH](O)[CH]1C(O)=O
OpenEye OEToolkits 2.0.7CCCCCCC1C(C(C(CN1)O)O)C(=O)O
FormulaC12 H23 N O4
Name(2~{S},3~{S},4~{R},5~{R})-2-hexyl-4,5-bis(oxidanyl)piperidine-3-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6ld0 Chain A Residue 701 [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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PDB6ld0 Entropy-driven binding of gut bacterial beta-glucuronidase inhibitors ameliorates irinotecan-induced toxicity.
Resolution1.901 Å
Binding residue
(original residue number in PDB)		D179 H413 E479 Q519 Y539 Y543 E574 W619 R632 N636 K638
Binding residue
(residue number reindexed from 1)		D181 H366 E432 Q472 Y492 Y496 E527 W572 R585 N589 K591
Annotation score1
Enzymatic activity
Enzyme Commision number 3.2.1.31: beta-glucuronidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004565 beta-galactosidase activity
GO:0004566 beta-glucuronidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0030246 carbohydrate binding
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6ld0, PDBe:6ld0, PDBj:6ld0
PDBsum6ld0
PubMed33664385
UniProtD2Q7B1

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