Structure of PDB 2v3d Chain A Binding Site BS01

Receptor Information

>2v3d Chain A (length=495) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

EFARPCIPKSFGYSSVVCVCNATYCDSFDPALGTFSRYESTRSGRRMELS
MGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQN
LLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEE
DTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPG
DIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFT
PEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAA
KYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSV
RLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPI
IVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHP
DGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWHRQ

Ligand information

Ligand ID

NBV

InChI

InChI=1S/C10H21NO4/c1-2-3-4-11-5-8(13)10(15)9(14)7(11)6-12/h7-10,12-15H,2-6H2,1H3/t7-,8+,9-,10-/m1/s1

InChIKey

UQRORFVVSGFNRO-UTINFBMNSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	CCCCN1CC(C(C(C1CO)O)O)O
CACTVS 3.341	CCCCN1C[CH](O)[CH](O)[CH](O)[CH]1CO
ACDLabs 10.04	OCC1N(CCCC)CC(O)C(O)C1O
OpenEye OEToolkits 1.5.0	CCCC[N@@]1C[C@@H]([C@H]([C@@H]([C@H]1CO)O)O)O
CACTVS 3.341	CCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO

Formula

C10 H21 N O4

Name

(2R,3R,4R,5S)-1-BUTYL-2-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL

PDB chain

2v3d Chain A Residue 1503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	2v3d Crystal Structures of Complexes of N-Butyl- and N-Nonyl-Deoxynojirimycin Bound to Acid Beta-Glucosidase: Insights Into the Mechanism of Chemical Chaperone Action in Gaucher Disease.
Resolution	1.96 Å
Binding residue (original residue number in PDB)	D127 F128 W179 N234 E235 F246 Y313 E340 W381 N396
Binding residue (residue number reindexed from 1)	D125 F126 W177 N232 E233 F244 Y311 E338 W379 N394
Annotation score	1
Binding affinity	MOAD: Ki=116uM PDBbind-CN: -logKd/Ki=3.94,Ki=116uM BindingDB: IC50=400000nM,Ki=116000nM

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

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External links

PDB	RCSB:2v3d, PDBe:2v3d, PDBj:2v3d
PDBsum	2v3d
PubMed	17666401
UniProt	P04062\|GBA1_HUMAN Lysosomal acid glucosylceramidase (Gene Name=GBA1)

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