Structure of PDB 2wcg Chain B Binding Site BS01

Receptor Information
>2wcg Chain B (length=495) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FARPCIPKSFGYSSVVCVCNATYCDSFDPPALGTFSRYESTRSGRRMELS
MGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQN
LLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEE
DTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPG
DIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFT
PEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAA
KYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSV
RLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPI
IVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHP
DGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWHRQ
Ligand information
Ligand IDMT5
InChIInChI=1S/C15H29N3O4/c1-2-3-4-5-6-7-8-16-15-17-9-10-11(19)12(20)13(21)14(22)18(10)15/h10-14,19-22H,2-9H2,1H3,(H,16,17)/p+1/t10-,11-,12+,13-,14-/m1/s1
InChIKeyDGGJYTDCPYQDLL-RKQHYHRCSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1CCCCCCCC[NH+]=C1NCC2N1C(C(C(C2O)O)O)O
OpenEye OEToolkits 1.6.1CCCCCCCC\[NH+]=C\1/NC[C@H]2N1[C@@H]([C@@H]([C@H]([C@@H]2O)O)O)O
CACTVS 3.352CCCCCCCC[NH+]=C1NC[C@@H]2[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)N12
CACTVS 3.352CCCCCCCC[NH+]=C1NC[CH]2[CH](O)[CH](O)[CH](O)[CH](O)N12
ACDLabs 10.04OC2C1N(C(/NC1)=[NH+]\CCCCCCCC)C(O)C(O)C2O
FormulaC15 H30 N3 O4
NameN-[(3E,5R,6R,7S,8R,8AR)-5,6,7,8-TETRAHYDROXYHEXAHYDROIMIDAZO[1,5-A]PYRIDIN-3(2H)-YLIDENE]OCTAN-1-AMINIUM
ChEMBL
DrugBank
ZINC
PDB chain2wcg Chain B Residue 1508 [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]
PDB2wcg 6-Amino-6-Deoxy-5,6-Di-N-(N'-Octyliminomethylidene)Nojirimycin: Synthesis, Biological Evaluation, and Crystal Structure in Complex with Acid Beta-Glucosidase.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D127 F128 E235 Y313 E340 W381
Binding residue
(residue number reindexed from 1)		D125 F126 E233 Y311 E338 W379
Annotation score1
Binding affinityMOAD: Ki=0.42uM
Enzymatic activity
Catalytic site (original residue number in PDB) E235 E340 C342 N370
Catalytic site (residue number reindexed from 1) E233 E338 C340 N368
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2wcg, PDBe:2wcg, PDBj:2wcg
PDBsum2wcg
PubMed19437524
UniProtP04062|GBA1_HUMAN Lysosomal acid glucosylceramidase (Gene Name=GBA1)

[Back to BioLiP]