Structure of PDB 2xwd Chain A Binding Site BS01

Receptor Information
>2xwd Chain A (length=493) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FARPCIPKSFGYSSVVCVCNATYCDSFPALGTFSRYESTRSGRRMELSMG
PIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLL
LKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDT
KLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDI
YHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPE
HQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKY
VHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRL
GSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIV
DITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDG
SAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWHRQ
Ligand information
Ligand IDLGS
InChIInChI=1S/C15H28N2O5/c1-2-3-4-5-6-7-8-16-15-17-10(9-22-15)11(18)12(19)13(20)14(17)21/h10-14,18-21H,2-9H2,1H3/b16-15-/t10-,11-,12+,13-,14+/m1/s1
InChIKeyQJILQIWQVOAQBB-KRIYVDMXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1CCCCCCCC/N=C\1/N2[C@H](CO1)[C@H]([C@@H]([C@H]([C@@H]2O)O)O)O
ACDLabs 10.04N(=C1\OCC2N1C(O)C(O)C(O)C2O)\CCCCCCCC
CACTVS 3.352CCCCCCCCN=C1OC[CH]2[CH](O)[CH](O)[CH](O)[CH](O)N12
CACTVS 3.352CCCCCCCCN=C1OC[C@@H]2[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)N12
OpenEye OEToolkits 1.6.1CCCCCCCCN=C1N2C(CO1)C(C(C(C2O)O)O)O
FormulaC15 H28 N2 O5
Name(3Z,5S,6R,7S,8R,8aR)-3-(octylimino)hexahydro[1,3]oxazolo[3,4-a]pyridine-5,6,7,8-tetrol
ChEMBL
DrugBankDB08090
ZINCZINC000053683362
PDB chain2xwd Chain A Residue 610 [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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PDB2xwd Cyclodextrin-Mediated Crystallization of Acid Beta-Glucosidase in Complex with Amphiphilic Bicyclic Nojirimycin Analogues.
Resolution2.66 Å
Binding residue
(original residue number in PDB)		D127 F128 E235 Y313 E340 W381
Binding residue
(residue number reindexed from 1)		D123 F124 E231 Y309 E336 W377
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.96,Ki=0.11uM
Enzymatic activity
Catalytic site (original residue number in PDB) E235 E340 C342 N370
Catalytic site (residue number reindexed from 1) E231 E336 C338 N366
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:2xwd, PDBe:2xwd, PDBj:2xwd
PDBsum2xwd
PubMed21483943
UniProtP04062|GBA1_HUMAN Lysosomal acid glucosylceramidase (Gene Name=GBA1)

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