Structure of PDB 6z39 Chain AAA Binding Site BS01

Receptor Information
>6z39 Chain AAA (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 IDQ65
InChIInChI=1S/C26H37BF2N5O4/c1-13-9-15(3)33-20(13)18(21-14(2)10-16(4)34(21)27(33,28)29)8-6-5-7-17-11-32(31-30-17)12-19-22(35)23(36)24(37)26-25(19)38-26/h9,11,16,18-19,22-26,35-37H,5-8,10,12H2,1-4H3/t16-,18+,19-,22-,23+,24-,25-,26+/m1/s1
InChIKeyAJWVMTKRGUGWOR-QHKJSSTCSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH]1CC(=C2[CH](CCCCc3cn(C[CH]4[CH](O)[CH](O)[CH](O)[CH]5O[CH]45)nn3)c6n(c(C)cc6C)[B](F)(F)N12)C
CACTVS 3.385C[C@@H]1CC(=C2[C@@H](CCCCc3cn(C[C@@H]4[C@@H](O)[C@H](O)[C@@H](O)[C@@H]5O[C@H]45)nn3)c6n(c(C)cc6C)[B](F)(F)N12)C
OpenEye OEToolkits 2.0.7B1(n2c(cc(c2C(C3=C(CC(N31)C)C)CCCCc4cn(nn4)CC5C(C(C(C6C5O6)O)O)O)C)C)(F)F
OpenEye OEToolkits 2.0.7B1(n2c(cc(c2C(C3=C(C[C@H](N31)C)C)CCCCc4cn(nn4)C[C@@H]5[C@H]([C@@H]([C@H]([C@H]6[C@@H]5O6)O)O)O)C)C)(F)F
FormulaC26 H37 B F2 N5 O4
Name(1~{S},2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[4-[4-[(12~{R})-2,2-bis(fluoranyl)-4,6,10,12-tetramethyl-1,3-diaza-2$l^{4}-boratricyclo[7.3.0.0^{3,7}]dodeca-4,6,9-trien-8-yl]butyl]-1,2,3-triazol-1-yl]methyl]-7-oxabicyclo[4.1.0]heptane-2,3,4-triol
ChEMBL
DrugBank
ZINC
PDB chain6z39 Chain AAA Residue 504 [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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PDB6z39 Design, Synthesis and Structural Analysis of Glucocerebrosidase Imaging Agents.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		S237 Y244 P245 N396
Binding residue
(residue number reindexed from 1)		S237 Y244 P245 N396
Annotation score1
Enzymatic activity
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:6z39, PDBe:6z39, PDBj:6z39
PDBsum6z39
PubMed34570911
UniProtP04062|GBA1_HUMAN Lysosomal acid glucosylceramidase (Gene Name=GBA1)

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