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 PKLR
Gene summary
Basic gene Info.Gene symbolPKLR
Gene namepyruvate kinase, liver and RBC
SynonymsPK1|PKL|PKR|PKRL|RPK
CytomapUCSC genome browser: 1q21
Type of geneprotein-coding
RefGenesNM_000298.5,
NM_181871.3,
DescriptionR-type/L-type pyruvate kinasepyruvate kinase 1pyruvate kinase PKLRpyruvate kinase isozyme R/Lpyruvate kinase isozymes L/Rpyruvate kinase isozymes R/Lpyruvate kinase type Lpyruvate kinase, liver and blood cellred cell/liver pyruvate kinase
Modification date20141207
dbXrefs MIM : 609712
HGNC : HGNC
Ensembl : ENSG00000143627
HPRD : 11841
Vega : OTTHUMG00000035875
ProteinUniProt: P30613
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PKLR
BioGPS: 5313
PathwayNCI Pathway Interaction Database: PKLR
KEGG: PKLR
REACTOME: PKLR
Pathway Commons: PKLR
ContextiHOP: PKLR
ligand binding site mutation search in PubMed: PKLR
UCL Cancer Institute: PKLR
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID


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Ligand binding site mutations for PKLR

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
F287R289WCOAD2
R532R531HBRCA1
F287R289QCOAD1
F287R289QHNSC1
A336A336ELUAD1
R479,T477G478CLUAD1
F287R289LOV1
M334G332DSKCM1
A336A336TUCEC1
R532R531CUCEC1
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 PKLR
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.
LBSAAchange of nsSNVRelative stability change
R532R531H-1.1524336
M334G332D-1.1264721
F287R289Q-1.0460525
A336A336T-0.88281985
R532R531C-0.83625456
F287R289W-0.76801805
A336A336E-0.63469532
F287R289L-0.45250388
R479G478C-0.21061508
T477G478C-0.21061508
(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 PKLR from PDB
PDB IDPDB titlePDB structure
2VGBHUMAN ERYTHROCYTE PYRUVATE KINASE

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Differential gene expression and gene-gene network for PKLR
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 PKLR and the right PPI network was created from samples without mutations in the LBS of PKLR. 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 PKLR
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0340968Pyruvate Kinase Deficiency of Red Cells11Biomarker, GeneticVariation
umls:C0011853Diabetes Mellitus, Experimental2Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

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Pharmacological information for PKLR
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 statusDrugBank IDNameTypeDrug structure
Approved|nutraceuticalDB00119Pyruvic acidSmall molecule
ExperimentalDB027262-Phosphoglycolic AcidSmall molecule
ExperimentalDB04551Fructose-1,6-DiphosphateSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PKLR go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
PGA2-PHOSPHOGLYCOLIC ACID2vgbAA336
PGA2-PHOSPHOGLYCOLIC ACID2vgbBA336
PGA2-PHOSPHOGLYCOLIC ACID2vgbCA336
PGA2-PHOSPHOGLYCOLIC ACID2vgbDA336
PGA2-PHOSPHOGLYCOLIC ACID2vgfAA336
PGA2-PHOSPHOGLYCOLIC ACID2vgfBA336
PGA2-PHOSPHOGLYCOLIC ACID2vgfCA336
PGA2-PHOSPHOGLYCOLIC ACID2vgfDA336
PGA2-PHOSPHOGLYCOLIC ACID2vggAA336
PGA2-PHOSPHOGLYCOLIC ACID2vggBA336
PGA2-PHOSPHOGLYCOLIC ACID2vggDA336
PGA2-PHOSPHOGLYCOLIC ACID2vgiAA336
PGA2-PHOSPHOGLYCOLIC ACID2vgiBA336
PGA2-PHOSPHOGLYCOLIC ACID2vgiCA336
PGA2-PHOSPHOGLYCOLIC ACID2vgiDA336
MNMANGANESE(2+)2vgbCF287
MNMANGANESE(2+)2vgfBF287
MNMANGANESE(2+)2vggAF287
MNMANGANESE(2+)2vggBF287
MNMANGANESE(2+)2vggCF287
MNMANGANESE(2+)2vggDF287
MNMANGANESE(2+)2vgiAF287
MNMANGANESE(2+)2vgiBF287
PGA2-PHOSPHOGLYCOLIC ACID2vggCF287 A336
FBPFRUCTOSE 1,6-BISPHOSPHATE2vgiBT477 R479 R532
FBPFRUCTOSE 1,6-BISPHOSPHATE2vgiCT477 R479 R532
FBPFRUCTOSE 1,6-BISPHOSPHATE2vgbAT477 R532
FBPFRUCTOSE 1,6-BISPHOSPHATE2vgbBT477 R532
FBPFRUCTOSE 1,6-BISPHOSPHATE2vgbCT477 R532
FBPFRUCTOSE 1,6-BISPHOSPHATE2vgbDT477 R532
FBPFRUCTOSE 1,6-BISPHOSPHATE2vgfAT477 R532
FBPFRUCTOSE 1,6-BISPHOSPHATE2vgfBT477 R532
FBPFRUCTOSE 1,6-BISPHOSPHATE2vgfCT477 R532
FBPFRUCTOSE 1,6-BISPHOSPHATE2vgfDT477 R532
FBPFRUCTOSE 1,6-BISPHOSPHATE2vggAT477 R532
FBPFRUCTOSE 1,6-BISPHOSPHATE2vggBT477 R532
FBPFRUCTOSE 1,6-BISPHOSPHATE2vggCT477 R532
FBPFRUCTOSE 1,6-BISPHOSPHATE2vggDT477 R532
FBPFRUCTOSE 1,6-BISPHOSPHATE2vgiAT477 R532
FBPFRUCTOSE 1,6-BISPHOSPHATE2vgiDT477 R532


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Conservation information for LBS of PKLR
Multiple alignments for P30613 in multiple species
LBSAA sequence# speciesSpecies
A336DGIMVARGDLG3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
A336DGVMIARGDLG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D156VAIALDTKGPE3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
D156LAIALDTKGPE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D339MVARGDLGIEI3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
D339MIARGDLGIEI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E129HEYHAESIANV1Homo sapiens
E129YEFHQSVIENA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E129HEYHAESIANI1Rattus norvegicus
E129HEYHAQSIANI1Canis lupus familiaris
E315IISKIENHEGV3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
E315IISKIENQQGL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F287IVFASFVRKAS2Homo sapiens, Canis lupus familiaris
F287IVFASFIRTSE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F287IIFASFVRKAS1Rattus norvegicus
G338IMVARGDLGIE3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
G338VMIARGDLGIE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G557VIVVTGWRPGS3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
G557VVSIQGFKGGV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G561TGWRPGSGYTN3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
G561QGFKGGVGHSN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G563WRPGSGYTNIM3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
G563FKGGVGHSNTL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K313IKIISKIENHE3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
K313IKIISKIENQQ1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L474AAIIVLTKTGR2Rattus norvegicus, Canis lupus familiaris
L474AAIIVLTTTGR1Homo sapiens
L474KAIVVLSTTGN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
M334VSDGIMVARGD3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
M334VTDGVMIARGD1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
M403GADCIMLSGET3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
M403GADCVMLSGET1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N133AESIANVREAV1Homo sapiens
N133QSVIENAVKSE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N133AESIANIREAT1Rattus norvegicus
N133AQSIANIREAV1Canis lupus familiaris
P560VTGWRPGSGYT3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
P560IQGFKGGVGHS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R116GMNIARLNFSH3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
R116GLNIIRLNFSH1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R337GIMVARGDLGI3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
R337GVMIARGDLGI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R479LTKTGRSAQLL2Rattus norvegicus, Canis lupus familiaris
R479LTTTGRSAQLL1Homo sapiens
R479LSTTGNTARLL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R532DDVDRRVQFGI3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
R532EDVHRRLKFGV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R559VVTGWRPGSGY3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
R559SIQGFKGGVGH1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R99IGPASRSVERL1Homo sapiens
R99IGPKTNSCEAI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R99IGPASRSVDRL1Rattus norvegicus
R99IGPASHSVERL1Canis lupus familiaris
S286DIVFASFVRKA2Homo sapiens, Canis lupus familiaris
S286HIVFASFIRTS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S286DIIFASFVRKA1Rattus norvegicus
S480TKTGRSAQLLS2Rattus norvegicus, Canis lupus familiaris
S480TTTGRSAQLLS1Homo sapiens
S480STTGNTARLLS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S562GWRPGSGYTNI3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
S562GFKGGVGHSNT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T371PVVCATQMLES3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
T371PVICATQMLDS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T475AIIVLTKTGRS2Rattus norvegicus, Canis lupus familiaris
T475AIIVLTTTGRS1Homo sapiens
T475AIVVLSTTGNT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T476IIVLTKTGRSA2Rattus norvegicus, Canis lupus familiaris
T476IIVLTTTGRSA1Homo sapiens
T476IVVLSTTGNTA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T477IVLTKTGRSAQ2Rattus norvegicus, Canis lupus familiaris
T477IVLTTTGRSAQ1Homo sapiens
T477VVLSTTGNTAR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T565PGSGYTNIMRV3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
T565GGVGHSNTLRI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
W525PPEAIWADDVD3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
W525KRLDDWGEDVH1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y564RPGSGYTNIMR3Homo sapiens, Rattus norvegicus, Canis lupus familiaris
Y564KGGVGHSNTLR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)


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