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 MTHFD1
Gene summary
Basic gene Info.Gene symbolMTHFD1
Gene namemethylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase
CytomapUCSC genome browser: 14q24
Type of geneprotein-coding
Description5,10-methylenetetrahydrofolate dehydrogenase, 5,10-methylenetetrahydrofolate cyclohydrolase, 10-formyltetrahydrofolate synthetaseC-1-tetrahydrofolate synthase, cytoplasmicC1-THF synthasecytoplasmic C-1-tetrahydrofolate synthase
Modification date20141207
dbXrefs MIM : 172460
Ensembl : ENSG00000100714
HPRD : 01403
Vega : OTTHUMG00000141309
ProteinUniProt: P11586
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MTHFD1
BioGPS: 4522
PathwayNCI Pathway Interaction Database: MTHFD1
Pathway Commons: MTHFD1
ContextiHOP: MTHFD1
ligand binding site mutation search in PubMed: MTHFD1
UCL Cancer Institute: MTHFD1
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

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

Ligand binding site mutations for MTHFD1

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
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.

Protein structure related information for MTHFD1
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
(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 MTHFD1 from PDB

Differential gene expression and gene-gene network for MTHFD1
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 MTHFD1 and the right PPI network was created from samples without mutations in the LBS of MTHFD1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for MTHFD1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0027794Neural Tube Defects5Biomarker, GeneticVariation
umls:C0000832Abruptio Placentae2Biomarker, GeneticVariation

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

Pharmacological information for MTHFD1
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|nutraceuticalDB00116Tetrahydrofolic acidSmall molecule
NutraceuticalDB00157NADHSmall molecule
ExperimentalDB02358LY374571Small molecule
ExperimentalDB034612'-Monophosphoadenosine 5'-DiphosphoriboseSmall molecule
ExperimentalDB04322LY249543Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of MTHFD1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
L34LY3458991dibAY52 D125
L24LY2495431diaAY52 P272

Conservation information for LBS of MTHFD1
Multiple alignments for P11586 in multiple species
LBSAA sequence# speciesSpecies
A215DILVVATGQPE3Homo sapiens, Mus musculus, Rattus norvegicus
A215DIVVVAIGQPE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A215DILVVGIGVAE1Drosophila melanogaster
A215DIVVAAIGIPH1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A215-----------1Arabidopsis thaliana
C236AVVIDCGINYV2Mus musculus, Rattus norvegicus
C236AIVIDCGINYV1Homo sapiens
C236TVVIDVGTNYV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
C236AVVIDCGINVK1Drosophila melanogaster
C236VVAIDVGINSI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C236-----------1Arabidopsis thaliana
D125PEKDVDGLTSI2Homo sapiens, Rattus norvegicus
D125AEKDVDGFGPT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D125PEKDVDGLHTV1Drosophila melanogaster
D125PEKDVDGFCET1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D125-----------1Arabidopsis thaliana
D125PEKDVDGLTSV1Mus musculus
G172HAVVVGRSKIV3Homo sapiens, Mus musculus, Rattus norvegicus
G172RSVVIGRSDIV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G172RAVVLGRSKIV1Drosophila melanogaster
G172HAVVIGRSNIV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G172-----------1Arabidopsis thaliana
G217LVVATGQPEMV3Homo sapiens, Mus musculus, Rattus norvegicus
G217VVVAIGQPEFV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G217LVVGIGVAEMV1Drosophila melanogaster
G217VVAAIGIPHFV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G217-----------1Arabidopsis thaliana
G237VVIDCGINYVP2Mus musculus, Rattus norvegicus
G237IVIDCGINYVP1Homo sapiens
G237VVIDVGTNYVA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G237VVIDCGINVKP1Drosophila melanogaster
G237VAIDVGINSIP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G237-----------1Arabidopsis thaliana
G273ITPVPGGVGPM4Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Mus musculus, Rattus norvegicus
G273LTPVPGGVGPM1Drosophila melanogaster
G273ITPVPGSVGPM1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G273-----------1Arabidopsis thaliana
G274TPVPGGVGPMT5Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Drosophila melanogaster, Mus musculus, Rattus norvegicus
G274TPVPGSVGPMT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G274-----------1Arabidopsis thaliana
G276VPGGVGPMTVA5Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Drosophila melanogaster, Mus musculus, Rattus norvegicus
G276VPGSVGPMTVA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G276-----------1Arabidopsis thaliana
H196TVTTCHSKTAH1Homo sapiens
H196TVTITHSKTRD1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H196TVTVCHSKTRN1Drosophila melanogaster
H196TVTLCHSKTES1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H196-----------1Arabidopsis thaliana
H196TVTTCHSKTAN1Mus musculus
H196TVTTCHSKTAD1Rattus norvegicus
I238VIDCGINYVPD3Homo sapiens, Mus musculus, Rattus norvegicus
I238VIDVGTNYVAD1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I238VIDCGINVKPD1Drosophila melanogaster
I238AIDVGINSIPD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I238-----------1Arabidopsis thaliana
K56LYINVKLKAAE2Homo sapiens, Mus musculus
K56TYVRMKRKAAE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K56VYIRMKIKAAT1Drosophila melanogaster
K56VYVRMKTRAAN1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K56-----------1Arabidopsis thaliana
K56LYINVKLKAAQ1Rattus norvegicus
L101GIIVQLPLPAH2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L101GFIVQLPLDSE2Mus musculus, Rattus norvegicus
L101GFLVQLPLDSE1Homo sapiens
L101GIIVQMPLDCD1Drosophila melanogaster
L101-----------1Arabidopsis thaliana
L202SKTAHLDEEVN1Homo sapiens
L202SKTRDIASYLH1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L202SKTRNLEEITR1Drosophila melanogaster
L202SKTESIADIVR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L202-----------1Arabidopsis thaliana
L202SKTANLDKEVN1Mus musculus
L202SKTADLDKEVN1Rattus norvegicus
L98TVHGFLVQLPL1Homo sapiens
L98HTHGIIVQLPL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L98RVHGIIVQMPL1Drosophila melanogaster
L98TVHGIIVQLPL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L98-----------1Arabidopsis thaliana
L98SVHGFIVQLPL1Mus musculus
L98TVHGFIVQLPL1Rattus norvegicus
M221TGQPEMVKGEW3Homo sapiens, Mus musculus, Rattus norvegicus
M221IGQPEFVKGEW1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
M221IGVAEMVKGSW1Drosophila melanogaster
M221IGIPHFVKADW1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
M221-----------1Arabidopsis thaliana
P272FITPVPGGVGP3Homo sapiens, Mus musculus, Rattus norvegicus
P272LITPVPGGVGP1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
P272HLTPVPGGVGP1Drosophila melanogaster
P272AITPVPGSVGP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P272-----------1Arabidopsis thaliana
P277PGGVGPMTVAM5Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Drosophila melanogaster, Mus musculus, Rattus norvegicus
P277PGSVGPMTVAM1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P277-----------1Arabidopsis thaliana
Q100HGIIVQLPLPA2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q100HGFIVQLPLDS2Mus musculus, Rattus norvegicus
Q100HGFLVQLPLDS1Homo sapiens
Q100HGIIVQMPLDC1Drosophila melanogaster
Q100-----------1Arabidopsis thaliana
Q218VVATGQPEMVK3Homo sapiens, Mus musculus, Rattus norvegicus
Q218VVAIGQPEFVK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q218VVGIGVAEMVK1Drosophila melanogaster
Q218VAAIGIPHFVK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q218-----------1Arabidopsis thaliana
R173AVVVGRSKIVG3Homo sapiens, Mus musculus, Rattus norvegicus
R173SVVIGRSDIVG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R173AVVLGRSKIVG1Drosophila melanogaster
R173AVVIGRSNIVG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R173-----------1Arabidopsis thaliana
S174VVVGRSKIVGA3Homo sapiens, Mus musculus, Rattus norvegicus
S174VVIGRSDIVGS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S174VVLGRSKIVGT1Drosophila melanogaster
S174VVIGRSNIVGR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S174-----------1Arabidopsis thaliana
S197VTTCHSKTAHL1Homo sapiens
S197VTITHSKTRDI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S197VTVCHSKTRNL1Drosophila melanogaster
S197VTLCHSKTESI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S197-----------1Arabidopsis thaliana
S197VTTCHSKTANL1Mus musculus
S197VTTCHSKTADL1Rattus norvegicus
T148CFIPCTPKGCL3Homo sapiens, Mus musculus, Rattus norvegicus
T148FFLPCTPKGII1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T148-FLPCTPWGCL1Drosophila melanogaster
T148LFTACTPKGIM1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T148-----------1Arabidopsis thaliana
T216ILVVATGQPEM3Homo sapiens, Mus musculus, Rattus norvegicus
T216IVVVAIGQPEF1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T216ILVVGIGVAEM1Drosophila melanogaster
T216IVVAAIGIPHF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T216-----------1Arabidopsis thaliana
T279GVGPMTVAMLM5Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Drosophila melanogaster, Mus musculus, Rattus norvegicus
T279SVGPMTVAMLL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T279-----------1Arabidopsis thaliana
V171RHAVVVGRSKI3Homo sapiens, Mus musculus, Rattus norvegicus
V171SRSVVIGRSDI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V171ARAVVLGRSKI1Drosophila melanogaster
V171KHAVVIGRSNI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V171-----------1Arabidopsis thaliana
V177GRSKIVGAPMH3Homo sapiens, Mus musculus, Rattus norvegicus
V177GRSDIVGSPVA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V177GRSKIVGTPAA1Drosophila melanogaster
V177GRSNIVGRPMS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V177-----------1Arabidopsis thaliana
V275PVPGGVGPMTV5Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Drosophila melanogaster, Mus musculus, Rattus norvegicus
V275PVPGSVGPMTV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V275-----------1Arabidopsis thaliana
V280VGPMTVAMLMQ4Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Mus musculus, Rattus norvegicus
V280VGPMTVAMLMK1Drosophila melanogaster
V280VGPMTVAMLLQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V280-----------1Arabidopsis thaliana
V55NLYINVKLKAA3Homo sapiens, Mus musculus, Rattus norvegicus
V55ATYVRMKRKAA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V55NVYIRMKIKAA1Drosophila melanogaster
V55NVYVRMKTRAA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V55-----------1Arabidopsis thaliana
V99VHGFIVQLPLD2Mus musculus, Rattus norvegicus
V99VHGFLVQLPLD1Homo sapiens
V99THGIIVQLPLP1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V99VHGIIVQMPLD1Drosophila melanogaster
V99VHGIIVQLPLP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V99-----------1Arabidopsis thaliana
Y52DDSNLYINVKL3Homo sapiens, Mus musculus, Rattus norvegicus
Y52PDSATYVRMKR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y52EDSNVYIRMKI1Drosophila melanogaster
Y52EDSNVYVRMKT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y52-----------1Arabidopsis thaliana

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