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 MDH2
Gene summary
Basic gene Info.Gene symbolMDH2
Gene namemalate dehydrogenase 2, NAD (mitochondrial)
SynonymsM-MDH|MDH|MGC:3559|MOR1
CytomapUCSC genome browser: 7cen-q22
Type of geneprotein-coding
RefGenesNM_001282403.1,
NM_001282404.1,NM_005918.3,NR_104165.1,
Descriptionmalate dehydrogenase, mitochondrial
Modification date20141207
dbXrefs MIM : 154100
HGNC : HGNC
Ensembl : ENSG00000146701
HPRD : 01099
Vega : OTTHUMG00000023827
ProteinUniProt: P40926
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MDH2
BioGPS: 4191
PathwayNCI Pathway Interaction Database: MDH2
KEGG: MDH2
REACTOME: MDH2
Pathway Commons: MDH2
ContextiHOP: MDH2
ligand binding site mutation search in PubMed: MDH2
UCL Cancer Institute: MDH2
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
GO:0006108malate metabolic process16740313
GO:0006475internal protein amino acid acetylation20167786


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Ligand binding site mutations for MDH2

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
V169V169MBRCA1
D57D57HCOAD1
R110R110WCOAD1
S33G31VLUAD1
R104K105NOV1
P103P103SSKCM1
G34G34EUCEC1
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 MDH2
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
G34G34E0.54310655
S33G31V0.32437551
R104K105N-1.1640437
D57D57H-0.90706909
R110R110W-0.66594213
P103P103S-0.5024405
V169V169M-0.40737006
(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 MDH2 from PDB

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Differential gene expression and gene-gene network for MDH2
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 MDH2 and the right PPI network was created from samples without mutations in the LBS of MDH2. 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 MDH2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0007097Carcinoma1Biomarker
umls:C0024667Mammary Neoplasms, Animal1Biomarker
umls:C0024668Mammary Neoplasms, Experimental1Biomarker

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

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Pharmacological information for MDH2
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
NutraceuticalDB00157NADHSmall molecule
Nutraceutical|vet_approvedDB04272Citric AcidSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of MDH2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
CITCITRIC ACID4wleAR104 R110
CITCITRIC ACID4wleBR104 R110
CITCITRIC ACID4wleCR104 R110
CITCITRIC ACID4wleDR104 R110
LMR(S)-MALIC ACID4wlfAR104 R110
LMR(S)-MALIC ACID4wlfBR104 R110
LMR(S)-MALIC ACID4wlfCR104 R110
LMR(S)-MALIC ACID4wlfDR104 R110
OAAOXALOACETATE ION4wloAR104 R110
OAAOXALOACETATE ION4wloBR104 R110
OAAOXALOACETATE ION4wloCR104 R110
OAAOXALOACETATE ION4wloDR104 R110
LMR(S)-MALIC ACID4wluAR104 R110
LMR(S)-MALIC ACID4wluBR104 R110
LMR(S)-MALIC ACID4wluCR104 R110
LMR(S)-MALIC ACID4wluDR104 R110
NAINADH4wloCS33 G34 D57 P103
NAINADH4wloAS33 G34 D57 P103 V169
NAINADH4wloBS33 G34 D57 P103 V169
NAINADH4wloDS33 G34 D57 P103 V169
NADNAD ZWITTERION4wluAS33 G34 D57 P103 V169
NADNAD ZWITTERION4wluBS33 G34 D57 P103 V169
NADNAD ZWITTERION4wluCS33 G34 D57 P103 V169
NADNAD ZWITTERION4wluDS33 G34 D57 P103 V169
NADNAD ZWITTERION4wlvAS33 G34 D57 P103 V169
NADNAD ZWITTERION4wlvBS33 G34 D57 P103 V169
NADNAD ZWITTERION4wlvCS33 G34 D57 P103 V169
NADNAD ZWITTERION4wlvDS33 G34 D57 P103 V169


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Conservation information for LBS of MDH2
Multiple alignments for P40926 in multiple species
LBSAA sequence# speciesSpecies
A100VVVIPAGVPRK3Homo sapiens, Mus musculus, Rattus norvegicus
A100LVIIPAGVPRK2Arabidopsis thaliana, Arabidopsis thaliana
A100VVIIPAGVPRK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A100MVLIPAGVPRK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A100VIVIPAGVPRK1Caenorhabditis elegans
A141MICVIANPVNS1Homo sapiens
A141KYLVVTNPVNS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A141AILVISNPVNS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A141LIAIITNPVNS1Caenorhabditis elegans
A141MVCIIANPVNS1Mus musculus
A141MICIISNPVNS1Rattus norvegicus
A141LINMISNPVNS1Arabidopsis thaliana
A141LVNMISNPVNS1Arabidopsis thaliana
A190KGLDPARVNVP3Homo sapiens, Mus musculus, Rattus norvegicus
A190TNGKAELLHIP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A190ENTDPTQERVN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A190KGHDASKTVVP1Caenorhabditis elegans
A190ANVPVAEVNVP1Arabidopsis thaliana
A190SDVNVAEVNVP1Arabidopsis thaliana
A247AGAGSATLSMA5Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Caenorhabditis elegans, Mus musculus, Rattus norvegicus
A247AGKGSATLSMA2Arabidopsis thaliana, Arabidopsis thaliana
A247NGAGSATLSMA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D57RLTLYDIAHTP3Homo sapiens, Mus musculus, Rattus norvegicus
D57SLSLYDIANTP2Arabidopsis thaliana, Arabidopsis thaliana
D57ELALFDIRGAP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D57DLRLYDLKGAK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D57HLALYDVVNTP1Caenorhabditis elegans
G101VVIPAGVPRKP3Homo sapiens, Mus musculus, Rattus norvegicus
G101VIIPAGVPRKP3Schizosaccharomyces pombe (strain 972 / ATCC 24843), Arabidopsis thaliana, Arabidopsis thaliana
G101VLIPAGVPRKP1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G101IVIPAGVPRKP1Caenorhabditis elegans
G234RIQEAGTEVVK3Homo sapiens, Mus musculus, Rattus norvegicus
G234RIQFGGDEVVK2Schizosaccharomyces pombe (strain 972 / ATCC 24843), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G234RTQDGGTEVVE2Arabidopsis thaliana, Arabidopsis thaliana
G234RIQDAGTEVVN1Caenorhabditis elegans
G34VLGASGGIGQP3Homo sapiens, Mus musculus, Rattus norvegicus
G34VLGAGGGIGQP2Schizosaccharomyces pombe (strain 972 / ATCC 24843), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G34ILGAAGGIGQP2Arabidopsis thaliana, Arabidopsis thaliana
G34LLGAAGGIGQP1Caenorhabditis elegans
G35LGASGGIGQPL3Homo sapiens, Mus musculus, Rattus norvegicus
G35LGAAGGIGQPL3Caenorhabditis elegans, Arabidopsis thaliana, Arabidopsis thaliana
G35LGAGGGIGQPL2Schizosaccharomyces pombe (strain 972 / ATCC 24843), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H200PVIGGHAGKTI3Homo sapiens, Mus musculus, Rattus norvegicus
H200PVVGGHAGITI2Caenorhabditis elegans, Arabidopsis thaliana
H200PVVGGHSGATI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H200NVIGGHSGITI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H200PVIGGHAGVTI1Arabidopsis thaliana
I120NTNATIVATLT3Homo sapiens, Mus musculus, Rattus norvegicus
I120ATNASIVRDLA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I120AINASIVRDLA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I120NTNAGIVRDLA1Caenorhabditis elegans
I120NINAGIVKNLC1Arabidopsis thaliana
I120NINAGIVKNLS1Arabidopsis thaliana
I140AMICVIANPVN1Homo sapiens
I140AKYLVVTNPVN1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I140AAILVISNPVN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I140ALIAIITNPVN1Caenorhabditis elegans
I140AMVCIIANPVN1Mus musculus
I140AMICIISNPVN1Rattus norvegicus
I140ALINMISNPVN1Arabidopsis thaliana
I140ALVNMISNPVN1Arabidopsis thaliana
I36GASGGIGQPLS3Homo sapiens, Mus musculus, Rattus norvegicus
I36GAGGGIGQPLS2Schizosaccharomyces pombe (strain 972 / ATCC 24843), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I36GAAGGIGQPLG1Caenorhabditis elegans
I36GAAGGIGQPLA1Arabidopsis thaliana
I36GAAGGIGQPLS1Arabidopsis thaliana
I58LTLYDIAHTPG3Homo sapiens, Mus musculus, Rattus norvegicus
I58LSLYDIANTPG2Arabidopsis thaliana, Arabidopsis thaliana
I58LALFDIRGAPG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I58LRLYDLKGAKG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I58LALYDVVNTPG1Caenorhabditis elegans
L113MTRDDLFNTNA4Homo sapiens, Caenorhabditis elegans, Mus musculus, Rattus norvegicus
L113MTRDDLFNINA2Arabidopsis thaliana, Arabidopsis thaliana
L113MTRDDLFATNA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L113MTRDDLFAINA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L124TIVATLTAACA3Homo sapiens, Mus musculus, Rattus norvegicus
L124SIVRDLAFAAG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L124SIVRDLAAATA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L124GIVRDLAAVIA1Caenorhabditis elegans
L124GIVKNLCTAIA1Arabidopsis thaliana
L124GIVKNLSIAIA1Arabidopsis thaliana
L172FGVTTLDIVRA3Homo sapiens, Mus musculus, Rattus norvegicus
L172FGVTTLDVVRA2Arabidopsis thaliana, Arabidopsis thaliana
L172FGVTTLDSVRA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L172FGVTTLDSIRA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L172FGVTTLDVVRS1Caenorhabditis elegans
M251SATLSMAYAGA6Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Arabidopsis thaliana
M251SATLSMAHAGA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
M251SATLSMALAGA1Caenorhabditis elegans
N117DLFNTNATIVA3Homo sapiens, Mus musculus, Rattus norvegicus
N117DLFNINAGIVK2Arabidopsis thaliana, Arabidopsis thaliana
N117DLFATNASIVR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N117DLFAINASIVR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N117DLFNTNAGIVR1Caenorhabditis elegans
N142ICVIANPVNST1Homo sapiens
N142YLVVTNPVNST1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N142ILVISNPVNST1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N142IAIITNPVNST1Caenorhabditis elegans
N142VCIIANPVNST1Mus musculus
N142ICIISNPVNST1Rattus norvegicus
N142INMISNPVNST1Arabidopsis thaliana
N142VNMISNPVNST1Arabidopsis thaliana
N178DIVRANTFVAE3Homo sapiens, Mus musculus, Rattus norvegicus
N178DVVRARTFYAG2Arabidopsis thaliana, Arabidopsis thaliana
N178DSVRASRFTSQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N178DSIRAARFISE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N178DVVRSQAFVSE1Caenorhabditis elegans
N193DPARVNVPVIG3Homo sapiens, Mus musculus, Rattus norvegicus
N193KAELLHIPVVG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N193DPTQERVNVIG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N193DASKTVVPVVG1Caenorhabditis elegans
N193PVAEVNVPVIG1Arabidopsis thaliana
N193NVAEVNVPVVG1Arabidopsis thaliana
P103IPAGVPRKPGM8Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Caenorhabditis elegans, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Arabidopsis thaliana
P189LKGLDPARVNV3Homo sapiens, Mus musculus, Rattus norvegicus
P189VTNGKAELLHI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P189VENTDPTQERV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
P189LKGHDASKTVV1Caenorhabditis elegans
P189KANVPVAEVNV1Arabidopsis thaliana
P189KSDVNVAEVNV1Arabidopsis thaliana
P99DVVVIPAGVPR3Homo sapiens, Mus musculus, Rattus norvegicus
P99DLVIIPAGVPR2Arabidopsis thaliana, Arabidopsis thaliana
P99DVVIIPAGVPR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P99DMVLIPAGVPR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
P99DVIVIPAGVPR1Caenorhabditis elegans
R104PAGVPRKPGMT8Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Caenorhabditis elegans, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Arabidopsis thaliana
R110KPGMTRDDLFN6Homo sapiens, Caenorhabditis elegans, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, Arabidopsis thaliana
R110KPGMTRDDLFA2Schizosaccharomyces pombe (strain 972 / ATCC 24843), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R176TLDIVRANTFV3Homo sapiens, Mus musculus, Rattus norvegicus
R176TLDVVRARTFY2Arabidopsis thaliana, Arabidopsis thaliana
R176TLDSVRASRFT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R176TLDSIRAARFI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R176TLDVVRSQAFV1Caenorhabditis elegans
R257AYAGARFVFSL3Homo sapiens, Mus musculus, Rattus norvegicus
R257AYAGALFADAC2Arabidopsis thaliana, Arabidopsis thaliana
R257AYAGARMASSV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R257AHAGAKFANAV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R257ALAGARFANAL1Caenorhabditis elegans
S246KAGAGSATLSM5Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Caenorhabditis elegans, Mus musculus, Rattus norvegicus
S246KAGKGSATLSM2Arabidopsis thaliana, Arabidopsis thaliana
S246KNGAGSATLSM1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S261ARFVFSLVDAM3Homo sapiens, Mus musculus, Rattus norvegicus
S261ALFADACLKGL2Arabidopsis thaliana, Arabidopsis thaliana
S261ARMASSVLRAL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S261AKFANAVLSGF1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S261ARFANALVRGI1Caenorhabditis elegans
S33AVLGASGGIGQ3Homo sapiens, Mus musculus, Rattus norvegicus
S33AVLGAGGGIGQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S33TVLGAGGGIGQ1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S33ALLGAAGGIGQ1Caenorhabditis elegans
S33AILGAAGGIGQ1Arabidopsis thaliana
S33VILGAAGGIGQ1Arabidopsis thaliana
T248GAGSATLSMAY4Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Mus musculus, Rattus norvegicus
T248GKGSATLSMAY2Arabidopsis thaliana, Arabidopsis thaliana
T248GAGSATLSMAH1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T248GAGSATLSMAL1Caenorhabditis elegans
V102VIPAGVPRKPG4Homo sapiens, Caenorhabditis elegans, Mus musculus, Rattus norvegicus
V102IIPAGVPRKPG3Schizosaccharomyces pombe (strain 972 / ATCC 24843), Arabidopsis thaliana, Arabidopsis thaliana
V102LIPAGVPRKPG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V144MISNPVNSTVP2Arabidopsis thaliana, Arabidopsis thaliana
V144VIANPVNSTIP1Homo sapiens
V144VVTNPVNSTVP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V144VISNPVNSTVP1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V144IITNPVNSTVP1Caenorhabditis elegans
V144IIANPVNSTIP1Mus musculus
V144IISNPVNSTIP1Rattus norvegicus
V169NKIFGVTTLDI3Homo sapiens, Mus musculus, Rattus norvegicus
V169KKLFGVTTLDV2Arabidopsis thaliana, Arabidopsis thaliana
V169KHLFGVTTLDS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V169KKLFGVTTLDS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V169KRVFGVTTLDV1Caenorhabditis elegans
V192LDPARVNVPVI3Homo sapiens, Mus musculus, Rattus norvegicus
V192GKAELLHIPVV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V192TDPTQERVNVI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V192HDASKTVVPVV1Caenorhabditis elegans
V192VPVAEVNVPVI1Arabidopsis thaliana
V192VNVAEVNVPVV1Arabidopsis thaliana
Y56SRLTLYDIAHT3Homo sapiens, Mus musculus, Rattus norvegicus
Y56SSLSLYDIANT2Arabidopsis thaliana, Arabidopsis thaliana
Y56SELALFDIRGA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y56TDLRLYDLKGA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y56AHLALYDVVNT1Caenorhabditis elegans


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