Structure of PDB 3rik Chain B Binding Site BS01

Receptor Information
>3rik Chain B (length=497) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRME
LSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPA
QNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLP
EEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQ
PGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLG
FTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPE
AAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQ
SVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDS
PIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALM
HPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWHRQ
Ligand information
Ligand ID3RI
InChIInChI=1S/C8H17NO5/c10-2-1-9-3-5(11)7(13)8(14)6(12)4-9/h5-8,10-14H,1-4H2/t5-,6-,7+,8+/m0/s1
InChIKeyVWGJHYNWDXVPIU-RULNZFCNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1[C@@H]([C@H]([C@@H]([C@H](CN1CCO)O)O)O)O
CACTVS 3.370OCCN1C[CH](O)[CH](O)[CH](O)[CH](O)C1
ACDLabs 12.01OC1CN(CCO)CC(O)C(O)C1O
CACTVS 3.370OCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@@H](O)C1
OpenEye OEToolkits 1.7.0C1C(C(C(C(CN1CCO)O)O)O)O
FormulaC8 H17 N O5
Name(3S,4R,5R,6S)-1-(2-hydroxyethyl)azepane-3,4,5,6-tetrol
ChEMBL
DrugBank
ZINCZINC000039039661
PDB chain3rik 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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PDB3rik Binding of 3,4,5,6-tetrahydroxyazepanes to the acid-beta-glucosidase active site: implications for pharmacological chaperone design for Gaucher disease
Resolution2.48 Å
Binding residue
(original residue number in PDB)		D127 F128 W179 N234 E235 W312 Y313 E340 W381
Binding residue
(residue number reindexed from 1)		D127 F128 W179 N234 E235 W312 Y313 E340 W381
Annotation score1
Binding affinityMOAD: ic50=3.4mM
PDBbind-CN: -logKd/Ki=2.47,IC50=3.4mM
Enzymatic activity
Catalytic site (original residue number in PDB) E235 E340 C342 N370
Catalytic site (residue number reindexed from 1) E235 E340 C342 N370
Enzyme Commision number 2.4.1.-
3.2.1.-
3.2.1.45: glucosylceramidase.
3.2.1.46: galactosylceramidase.
Gene Ontology
Molecular Function
GO:0004336 galactosylceramidase activity
GO:0004348 glucosylceramidase activity
GO:0005102 signaling receptor binding
GO:0005124 scavenger receptor binding
GO:0005515 protein binding
GO:0008422 beta-glucosidase activity
GO:0016757 glycosyltransferase activity
GO:0016787 hydrolase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0046527 glucosyltransferase activity
GO:0050295 steryl-beta-glucosidase activity
Biological Process
GO:0006665 sphingolipid metabolic process
GO:0006678 glucosylceramide metabolic process
GO:0006680 glucosylceramide catabolic process
GO:0006914 autophagy
GO:0007005 mitochondrion organization
GO:0007040 lysosome organization
GO:0007417 central nervous system development
GO:0008203 cholesterol metabolic process
GO:0008340 determination of adult lifespan
GO:0009267 cellular response to starvation
GO:0009268 response to pH
GO:0014004 microglia differentiation
GO:0016241 regulation of macroautophagy
GO:0019882 antigen processing and presentation
GO:0019915 lipid storage
GO:0021694 cerebellar Purkinje cell layer formation
GO:0021859 pyramidal neuron differentiation
GO:0022904 respiratory electron transport chain
GO:0023021 termination of signal transduction
GO:0030259 lipid glycosylation
GO:0031175 neuron projection development
GO:0031333 negative regulation of protein-containing complex assembly
GO:0032006 regulation of TOR signaling
GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0032715 negative regulation of interleukin-6 production
GO:0033077 T cell differentiation in thymus
GO:0033574 response to testosterone
GO:0042391 regulation of membrane potential
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0043243 positive regulation of protein-containing complex disassembly
GO:0043407 negative regulation of MAP kinase activity
GO:0043524 negative regulation of neuron apoptotic process
GO:0043627 response to estrogen
GO:0046512 sphingosine biosynthetic process
GO:0046513 ceramide biosynthetic process
GO:0048469 cell maturation
GO:0048854 brain morphogenesis
GO:0048872 homeostasis of number of cells
GO:0050728 negative regulation of inflammatory response
GO:0050877 nervous system process
GO:0050905 neuromuscular process
GO:0051246 regulation of protein metabolic process
GO:0051248 negative regulation of protein metabolic process
GO:0051402 neuron apoptotic process
GO:0061436 establishment of skin barrier
GO:0061518 microglial cell proliferation
GO:0061744 motor behavior
GO:0071356 cellular response to tumor necrosis factor
GO:0071425 hematopoietic stem cell proliferation
GO:0071548 response to dexamethasone
GO:0072676 lymphocyte migration
GO:0097066 response to thyroid hormone
GO:0098773 skin epidermis development
GO:1901805 beta-glucoside catabolic process
GO:1903052 positive regulation of proteolysis involved in protein catabolic process
GO:1903061 positive regulation of protein lipidation
GO:1904457 positive regulation of neuronal action potential
GO:1905037 autophagosome organization
GO:1905165 regulation of lysosomal protein catabolic process
Cellular Component
GO:0005615 extracellular space
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0016020 membrane
GO:0043202 lysosomal lumen
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3rik, PDBe:3rik, PDBj:3rik
PDBsum3rik
PubMed22047104
UniProtP04062|GBA1_HUMAN Lysosomal acid glucosylceramidase (Gene Name=GBA1)

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