Structure of PDB 1now Chain A Binding Site BS01

Receptor Information
>1now Chain A (length=480) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALWPLPLSVKMTPNLLHLAPENFYISHSPNSTAGPSCTLLEEAFRRYHGY
IFGTQVQQLLVSITLQSECDAFPNISSDESYTLLVKEPVAVLKANRVWGA
LRGLETFSQLVYQDSYGTFTINESTIIDSPRFSHRGILIDTSRHYLPVKI
ILKTLDAMAFNKFNVLHWHIVDDQSFPYQSITFPELSNKGSYSLSHVYTP
NDVRMVIEYARLRGIRVLPEFDTPGHTLSWGKGQKDLLTPCYSLDSFGPI
NPTLNTTYSFLTTFFKEISEVFPDQFIHLGGDEVEFKCWESNPKIQDFMR
QKGFGTDFKKLESFYIQKVLDIIATINKGSIVWQEVFDDKAKLAPGTIVE
VWKDSAYPEELSRVTASGFPVILSAPWYLDLISYGQDWRKYYKVEPLDFG
GTQKQKQLFIGGEACLWGEYVDATNLTPRLWPRASAVGERLWSSKDVRDM
DDAYDRLTRHRCRMVERGIAAQPLYAGYCN
Ligand information
Ligand IDIFG
InChIInChI=1S/C8H16N2O4/c1-4(12)10-8-7(14)6(13)5(3-11)2-9-8/h5-9,11,13-14H,2-3H2,1H3,(H,10,12)/t5-,6+,7+,8-/m1/s1
InChIKeyIWVRQJNSUOIUFV-VGRMVHKJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=O)NC1C(C(C(CN1)CO)O)O
ACDLabs 10.04O=C(NC1NCC(CO)C(O)C1O)C
CACTVS 3.341CC(=O)N[C@H]1NC[C@H](CO)[C@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0CC(=O)N[C@@H]1[C@H]([C@H]([C@H](CN1)CO)O)O
CACTVS 3.341CC(=O)N[CH]1NC[CH](CO)[CH](O)[CH]1O
FormulaC8 H16 N2 O4
Name(2R,3R,4S,5R)-2-ACETAMIDO-3,4-DIHYDROXY-5-HYDROXYMETHYL-PIPERIDINE
ChEMBL
DrugBankDB03861
ZINC
PDB chain1now Chain A Residue 557 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1now Crystal structure of Human beta-hexosaminidase B: Understanding the molecular basis of Sandhoff and Tay-Sachs disease
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R211 D354 E355 W405 W424 Y450 D452 W489 E491
Binding residue
(residue number reindexed from 1)		R143 D282 E283 W333 W352 Y378 D380 W417 E419
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) D354 E355
Catalytic site (residue number reindexed from 1) D282 E283
Enzyme Commision number 3.2.1.52: beta-N-acetylhexosaminidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004563 beta-N-acetylhexosaminidase activity
GO:0005515 protein binding
GO:0008375 acetylglucosaminyltransferase activity
GO:0015929 hexosaminidase activity
GO:0016787 hydrolase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0042802 identical protein binding
Biological Process
GO:0001501 skeletal system development
GO:0005975 carbohydrate metabolic process
GO:0006629 lipid metabolic process
GO:0006687 glycosphingolipid metabolic process
GO:0006689 ganglioside catabolic process
GO:0006874 intracellular calcium ion homeostasis
GO:0007040 lysosome organization
GO:0007338 single fertilization
GO:0007341 penetration of zona pellucida
GO:0007605 sensory perception of sound
GO:0007626 locomotory behavior
GO:0008049 male courtship behavior
GO:0008360 regulation of cell shape
GO:0008654 phospholipid biosynthetic process
GO:0009313 oligosaccharide catabolic process
GO:0019915 lipid storage
GO:0019953 sexual reproduction
GO:0030203 glycosaminoglycan metabolic process
GO:0030207 chondroitin sulfate catabolic process
GO:0030209 dermatan sulfate catabolic process
GO:0030214 hyaluronan catabolic process
GO:0042552 myelination
GO:0043615 astrocyte cell migration
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0048477 oogenesis
GO:0050885 neuromuscular process controlling balance
GO:0050905 neuromuscular process
GO:0051651 maintenance of location in cell
GO:0070050 neuron cellular homeostasis
GO:1901135 carbohydrate derivative metabolic process
Cellular Component
GO:0001669 acrosomal vesicle
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005764 lysosome
GO:0016020 membrane
GO:0031410 cytoplasmic vesicle
GO:0035578 azurophil granule lumen
GO:0042582 azurophil granule
GO:0043202 lysosomal lumen
GO:0060473 cortical granule
GO:0070062 extracellular exosome
GO:1905379 beta-N-acetylhexosaminidase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1now, PDBe:1now, PDBj:1now
PDBsum1now
PubMed12662933
UniProtP07686|HEXB_HUMAN Beta-hexosaminidase subunit beta (Gene Name=HEXB)

[Back to BioLiP]