Structure of PDB 5a69 Chain A Binding Site BS01

Receptor Information
>5a69 Chain A (length=585) Species: 170187 (Streptococcus pneumoniae TIGR4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RFTGLSLKQTQAIEVLKHISLPVEVAVTQSDQASISIEGEEGHYQLTYRK
PHQLYRALSLLVTVLADKVEIEEQAAYEDLAYMVDCSRNAVLNVASAKQM
IEILALMGYSTFELYMEDTYQIEGQPYFGYFRGAYSAEELQEIEAYAQQF
DVTFVPCIQTLAHLSAFVKWGVKEVQELRDVEDILLIGEEKVYDLIDGMF
ATLSKLKTRKVNIGMDEAHLVGLGRYLILNRLLMCQHLERVLDIADKYGF
HCQMWSDMFDRVTLVYWDYYQDSEEKYNRNFRNHHKIDLAFAGGAWKWIG
FTPHNHFSRLVAIEANKACRANQIKEVIVTGWGDNGGETAQFSILPSLQI
WAELSYRNDLDGLSAHFKTNTGLTVEDFMQIDLANLLPDLPGNLSGINPN
RYVFYQDILCPILDQHMTPEQDKPHFAQAAETLANIKEKAGNYAYLFETQ
AQLNAILSSKVDVGRRIRQAYQADDKESLQQIARQELPELRSQIEDFHAL
FSHQWLKENKVFGLDTVDIRMGGLLQRIKRAESRIEVYLAGQLDRIDELE
VEILPFTDFYADKDFAATTANQWHTIATASTIYTT
Ligand information
Ligand IDOGN
InChIInChI=1S/C15H19N3O7/c1-8(20)16-11-13(22)12(21)10(7-19)24-14(11)18-25-15(23)17-9-5-3-2-4-6-9/h2-6,10-13,19,21-22H,7H2,1H3,(H,16,20)(H,17,23)/b18-14-/t10-,11-,12+,13-/m1/s1
InChIKeyPBLNJFVQMUMOJY-UYZOWNTJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CC(=O)NC1C(C(C(OC1=NOC(=O)Nc2ccccc2)CO)O)O
OpenEye OEToolkits 1.7.2CC(=O)N[C@@H]\1[C@H]([C@H]([C@H](O/C1=N\OC(=O)Nc2ccccc2)CO)O)O
CACTVS 3.370CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)OC1=NOC(=O)Nc2ccccc2
ACDLabs 12.01O=C(O\N=C1/OC(CO)C(O)C(O)C1NC(=O)C)Nc2ccccc2
CACTVS 3.370CC(=O)N[C@@H]\1[C@@H](O)[C@@H](O)[C@@H](CO)OC\1=N\OC(=O)Nc2ccccc2
FormulaC15 H19 N3 O7
Name[(Z)-[(3R,4R,5R,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-ylidene]amino] N-phenylcarbamate;
Gal-PUGNAc
ChEMBL
DrugBank
ZINCZINC000044154749
PDB chain5a69 Chain A Residue 1627 [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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PDB5a69 A Second beta-Hexosaminidase Encoded in the Streptococcus pneumoniae Genome Provides an Expanded Biochemical Ability to Degrade Host Glycans.
Resolution2.2 Å
Binding residue
(original residue number in PDB)
R94 D222 E223 W266 W306 Y308 Y309 W339 W373 D375
Binding residue
(residue number reindexed from 1)
R88 D216 E217 W255 W267 Y269 Y270 W298 W332 D334
Annotation score1
Binding affinityMOAD: Ki=1.1nM
PDBbind-CN: -logKd/Ki=8.96,Ki=1.1nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004563 beta-N-acetylhexosaminidase activity
GO:0015929 hexosaminidase activity
GO:0016787 hydrolase activity
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:5a69, PDBe:5a69, PDBj:5a69
PDBsum5a69
PubMed26491009
UniProtA0A0H2US73

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