Structure of PDB 4woz Chain F Binding Site BS01

Receptor Information
>4woz Chain F (length=290) Species: 1496 (Clostridioides difficile) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDMKGIYSALLVSFDKEGNINEKGLRQIIRHNIDVCKVDGLYVGGSTGEN
FMLSTDEKKRIFEIAKDEVKEEIKLIAQVGSVNLKEAVELAKFTTDLGYD
AISAVTPFYYKFDFEEIKHYYNTIINSVDNRLIIYSIPFLTGVDMSLDQF
GELFENEKIIGVKFTAADFYLLERMRKTFPNKLIFAGFDEMMLPATVLGV
DGAIGSTFNVNGVRARQIFELTKNEKISEALEVQHVTNDLITDILGNGLY
QTIKLLLEEQGVEAGYCRQPMKEATDEMKSRAKEIYRKYF
Ligand information
Ligand IDMN9
InChIInChI=1S/C8H15NO6/c1-4(12)9-5(2-10)7(14)8(15)6(13)3-11/h2,5-8,11,13-15H,3H2,1H3,(H,9,12)/t5-,6-,7-,8-/m1/s1
InChIKeyMBLBDJOUHNCFQT-WCTZXXKLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1CC(=O)NC(C=O)C(C(C(CO)O)O)O
CACTVS 3.352CC(=O)N[CH](C=O)[CH](O)[CH](O)[CH](O)CO
ACDLabs 10.04O=CC(NC(=O)C)C(O)C(O)C(O)CO
OpenEye OEToolkits 1.6.1CC(=O)N[C@H](C=O)[C@H]([C@@H]([C@@H](CO)O)O)O
CACTVS 3.352CC(=O)N[C@H](C=O)[C@@H](O)[C@H](O)[C@H](O)CO
FormulaC8 H15 N O6
Name2-(ACETYLAMINO)-2-DEOXY-D-MANNOSE
ChEMBL
DrugBankDB12536
ZINCZINC000002020190
PDB chain4woz Chain F Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4woz Crystal Structures of CdNal from Clostridium difficile in complex with mannosamine
Resolution1.96 Å
Binding residue
(original residue number in PDB)		L159 Y182 L183
Binding residue
(residue number reindexed from 1)		L147 Y170 L171
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) S58 Y121 Y147 L152 K175 I216
Catalytic site (residue number reindexed from 1) S46 Y109 Y135 L140 K163 I204
Enzyme Commision number 4.1.3.3: N-acetylneuraminate lyase.
Gene Ontology
Molecular Function
GO:0008747 N-acetylneuraminate lyase activity
GO:0016829 lyase activity
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0019262 N-acetylneuraminate catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4woz, PDBe:4woz, PDBj:4woz
PDBsum4woz
PubMed
UniProtD5Q364

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