mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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	Gene Summary
	Ligand Binding Site Mutation Information
	Protein Structure Related Information
	Gene Expression and Gene-Gene Network
	Phenotype Information
	Pharmacological Information
	Conservation Information for LBS

Gene summary for PRKAB1

Gene summary

Basic gene Info.	Gene symbol	PRKAB1
	Gene name	protein kinase, AMP-activated, beta 1 non-catalytic subunit
	Synonyms	AMPK\|HAMPKb
	Cytomap	UCSC genome browser: 12q24.1-q24.3
	Type of gene	protein-coding
	RefGenes	NM_006253.4,
	Description	5'-AMP-activated protein kinase beta-1 subunit5'-AMP-activated protein kinase subunit beta-1AMP-activated protein kinase beta subunitAMPK beta -1 chainAMPK beta 1AMPK subunit beta-1AMPKbprotein kinase, AMP-activated, noncatalytic, beta-1
	Modification date	20141207
dbXrefs	MIM : 602740
	HGNC : HGNC
	Ensembl : ENSG00000111725
	HPRD : 04116
	Vega : OTTHUMG00000168954
Protein	UniProt: Q9Y478 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PRKAB1
	BioGPS: 5564
Pathway	NCI Pathway Interaction Database: PRKAB1
	KEGG: PRKAB1
	REACTOME: PRKAB1
	Pathway Commons: PRKAB1
Context	iHOP: PRKAB1
	ligand binding site mutation search in PubMed: PRKAB1
	UCL Cancer Institute: PRKAB1
Assigned class in mutLBSgeneDB	B: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID	GO Term	PubMed ID
GO:0006468	protein phosphorylation	17028174
GO:0010628	positive regulation of gene expression	17028174

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Ligand binding site mutations for PRKAB1

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
N111	N110S	HNSC	1
T106	P104H	LUAD	1

cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.

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Protein structure related information for PRKAB1

Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
(ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)

: nsSNV at non-LBS

: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.

LBS	AAchange of nsSNV	Relative stability change
T106	P104H	-1.4683665
N111	N110S	-0.73983042

(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for PRKAB1 from PDB

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Differential gene expression and gene-gene network for PRKAB1

Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)

* Left PPI network was created from samples with mutations in the LBS of PRKAB1 and the right PPI network was created from samples without mutations in the LBS of PRKAB1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.

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Phenotype information for PRKAB1

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0242656	Disease Progression	1	Biomarker
umls:C0038356	Stomach Neoplasms	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for PRKAB1

Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.

Gene-centered drug-gene interaction network

Drug information targeting mutLBSgene (Approved drugs only)

Drug status	DrugBank ID	Name	Type	Drug structure
Approved\|nutraceutical	DB00131	Adenosine monophosphate	Small molecule
Approved	DB00331	Metformin	Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PRKAB1 go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
C1V		3-[4-(2-HYDROXYPHENYL)PHENYL]-4-OXIDANYL-6- OXIDANYLIDENE-7H-THIENO[2,3-B]PYRIDINE-5- CARBONITRILE	4cff	D	T106
992		5-[[6-CHLORANYL-5-(1-METHYLINDOL-5-YL)-1H- BENZIMIDAZOL-2-YL]OXY]-2-METHYL-BENZOIC ACID	4cfe	B	T106 N111
992		5-[[6-CHLORANYL-5-(1-METHYLINDOL-5-YL)-1H- BENZIMIDAZOL-2-YL]OXY]-2-METHYL-BENZOIC ACID	4cfe	D	T106 N111
C1V		3-[4-(2-HYDROXYPHENYL)PHENYL]-4-OXIDANYL-6- OXIDANYLIDENE-7H-THIENO[2,3-B]PYRIDINE-5- CARBONITRILE	4cff	B	T106 N111

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Conservation information for LBS of PRKAB1

Multiple alignments for Q9Y478 in multiple species

LBS	AA sequence	# species	Species
N111	TRSHNNFVAIL	2	Homo sapiens, Bos taurus
N111	TRSQNNFVAIL	2	Mus musculus, Rattus norvegicus
N111	LLKSEDYTVLL	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R107	KLPLTRSHNNF	2	Homo sapiens, Bos taurus
R107	KLPLTRSQNNF	2	Mus musculus, Rattus norvegicus
R107	KKIQLLKSEDY	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R83	-PTVFRWTGGG	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R83	VPTIIRWRGGG	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S108	LPLTRSHNNFV	2	Homo sapiens, Bos taurus
S108	LPLTRSQNNFV	2	Mus musculus, Rattus norvegicus
S108	KIQLLKSEDYT	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T106	SKLPLTRSHNN	2	Homo sapiens, Bos taurus
T106	SKLPLTRSQNN	2	Mus musculus, Rattus norvegicus
T106	KKKIQLLKSED	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V113	SHNNFVAILDL	2	Homo sapiens, Bos taurus
V113	SQNNFVAILDL	2	Mus musculus, Rattus norvegicus
V113	KSEDYTVLLQL	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V81	---PTVFRWTG	4	Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
V81	PCVPTIIRWRG	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)