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 SMYD2
Gene summary
Basic gene Info.Gene symbolSMYD2
Gene nameSET and MYND domain containing 2
SynonymsHSKM-B|KMT3C|ZMYND14
CytomapUCSC genome browser: 1q32.3
Type of geneprotein-coding
RefGenesNM_020197.2,
DescriptionN-lysine methyltransferase SMYD2SET and MYND domain-containing protein 2histone methyltransferase SMYD2lysine N-methyltransferase 3Czinc finger, MYND domain containing 14
Modification date20141222
dbXrefs MIM : 610663
HGNC : HGNC
Ensembl : ENSG00000143499
HPRD : 15406
Vega : OTTHUMG00000037066
ProteinUniProt: Q9NRG4
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SMYD2
BioGPS: 56950
PathwayNCI Pathway Interaction Database: SMYD2
KEGG: SMYD2
REACTOME: SMYD2
Pathway Commons: SMYD2
ContextiHOP: SMYD2
ligand binding site mutation search in PubMed: SMYD2
UCL Cancer Institute: SMYD2
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0018026peptidyl-lysine monomethylation17108971


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Ligand binding site mutations for SMYD2
Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)
 : non-synonymous mutation on LBS, Circle size denotes number of samples.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
L317E319KBLCA1
E187E187KBRCA1
R306R306WCOAD1
C90E89AKIRC1
C65,R67G66VLUSC1
T220G219VLUSC1
C209C209YSKCM1
L204L204FUCEC1
C68C68YUCEC1
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 SMYD2
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
T220G219V0.2502065
L204L204F-1.4349258
C90E89A-1.1774579
E187E187K-1.1508676
L317E319K-1.1180155
C209C209Y-0.76735302
R306R306W-0.604572
C65G66V-0.57495719
R67G66V-0.57495719
C68C68Y-0.54331353
(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 SMYD2 from PDB

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Differential gene expression and gene-gene network for SMYD2
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 SMYD2 and the right PPI network was created from samples without mutations in the LBS of SMYD2. 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 SMYD2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

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Pharmacological information for SMYD2
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.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of SMYD2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ZNZINC(2+)3ribAC209
ZNZINC(2+)3ribBC209
ZNZINC(2+)3s7bAC209
ZNZINC(2+)3s7dAC209
ZNZINC(2+)3s7fAC209
ZNZINC(2+)3s7jAC209
ZNZINC(2+)3tg4AC209
ZNZINC(2+)3tg5AC209
ZNZINC(2+)4o6fAC209
ZNZINC(2+)4wuyAC209
ZNZINC(2+)4yndAC209
ZNZINC(2+)3ribAC65 C68 C90
ZNZINC(2+)3ribBC65 C68 C90
ZNZINC(2+)3s7bAC65 C68 C90
ZNZINC(2+)3s7dAC65 C68 C90
ZNZINC(2+)3s7fAC65 C68 C90
ZNZINC(2+)3s7jAC65 C68 C90
ZNZINC(2+)3tg4AC65 C68 C90
ZNZINC(2+)3tg5AC65 C68 C90
ZNZINC(2+)4o6fAC65 C68 C90
ZNZINC(2+)4wuyAC65 C68 C90
ZNZINC(2+)4yndAC65 C68 C90
IIIPeptide ligand (LEU,LYS,SER,LYS,LYS)3s7dAE187
IIIPeptide ligand (LEU,LYS,SER,LYS,LYS,GLY)3s7fAE187 R306
IIIPeptide ligand (HIS,LEU,LYS,SER,LYS,LYS,GLY,GLN)3tg5AE187 R306
IIIPeptide ligand (GLY,ARG,MET,LEU,LYS,HIS,LYS,ARG,GLN,ARG)4o6fAE187 R306
SAHS-ADENOSYL-L-HOMOCYSTEINE3ribAL204
SAMS-ADENOSYL-L-METHIONINE3s7bAL204
SAHS-ADENOSYL-L-HOMOCYSTEINE3s7dAL204
SAMS-ADENOSYL-L-METHIONINE3s7fAL204
SAMS-ADENOSYL-L-METHIONINE3s7jAL204
SAMS-ADENOSYL-L-METHIONINE3tg4AL204
SAHS-ADENOSYL-L-HOMOCYSTEINE3tg5AL204
SAHS-ADENOSYL-L-HOMOCYSTEINE4wuyAL204
SAMS-ADENOSYL-L-METHIONINE4yndAL204
BU3(R,R)-BUTANE-2,3-DIOL3s7bAL317
BU3(R,R)-BUTANE-2,3-DIOL3s7bAR67
BU3(R,R)-BUTANE-2,3-DIOL3s7bAT220


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Conservation information for LBS of SMYD2
Multiple alignments for Q9NRG4 in multiple species
LBSAA sequence# speciesSpecies
A177LVVLFAQVNCN4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
A177LTELIAQVNCN1Danio rerio
A203IFPDVALMNHS4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
A203LFPDVALMNHS1Danio rerio
C181FAQVNCNGFTI4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
C181IAQVNCNGFTI1Danio rerio
C209LMNHSCCPNVI4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
C209LMNHSCSPNVI1Danio rerio
C262SYFFTCECQEC2Homo sapiens, Bos taurus
C262SYFFTCECREC2Mus musculus, Rattus norvegicus
C262SYFFNCDCKEC1Danio rerio
C264FFTCECQECTT2Homo sapiens, Bos taurus
C264FFTCECRECTT2Mus musculus, Rattus norvegicus
C264FFNCDCKECTS1Danio rerio
C267CECQECTTKDK2Homo sapiens, Bos taurus
C267CECRECTTKDK2Mus musculus, Rattus norvegicus
C267CDCKECTSKSK1Danio rerio
C55HHCECCFARKE2Mus musculus, Rattus norvegicus
C55NHCEYCFTRKE1Homo sapiens
C55GRCECCFTRKE1Danio rerio
C55NHCEFCFARKE1Bos taurus
C65EGLSKCGRCKQ4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
C65EGLSKCGKCKQ1Danio rerio
C68SKCGRCKQAFY4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
C68SKCGKCKQAYY1Danio rerio
C90MHKLECSPMVV2Homo sapiens, Bos taurus
C90LHKLECSSMVV2Mus musculus, Rattus norvegicus
C90MHKLECSAMCA1Danio rerio
D242FTSYIDLLYPT4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
D242FNSYIDLLYPT1Danio rerio
E104NWNPSETVRLT4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
E104NWCPSETVRLV1Danio rerio
E135AVKEFESHLDK2Homo sapiens, Bos taurus
E135AVREFESHLDK2Mus musculus, Rattus norvegicus
E135TLRELEAHLDK1Danio rerio
E187NGFTIEDEELS5Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus, Bos taurus
F184VNCNGFTIEDE5Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus, Bos taurus
F259LRDSYFFTCEC4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
F259LKDSYFFNCDC1Danio rerio
F260RDSYFFTCECQ2Homo sapiens, Bos taurus
F260RDSYFFTCECR2Mus musculus, Rattus norvegicus
F260KDSYFFNCDCK1Danio rerio
G16RFCSPGKGRGL2Homo sapiens, Bos taurus
G16RFCSAGKGRGL2Mus musculus, Rattus norvegicus
G16RFLSPGKGRGL1Danio rerio
G18CSPGKGRGLRA2Homo sapiens, Bos taurus
G18CSAGKGRGLRA2Mus musculus, Rattus norvegicus
G18LSPGKGRGLKA1Danio rerio
G183QVNCNGFTIED5Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus, Bos taurus
G394GRLYMGLENKA3Mus musculus, Rattus norvegicus, Bos taurus
G394GRLYMGLEHKA1Homo sapiens
G394GRLYLGLEKRT1Danio rerio
H137KEFESHLDKLD2Homo sapiens, Bos taurus
H137REFESHLDKLD2Mus musculus, Rattus norvegicus
H137RELEAHLDKLD1Danio rerio
H193DEELSHLGSAI4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
H193DEELSHLGSAL1Danio rerio
H207VALMNHSCCPN4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
H207VALMNHSCSPN1Danio rerio
H341NVYMLHMMYQA5Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus, Bos taurus
H86EDWPMHKLECS2Homo sapiens, Bos taurus
H86EDWPLHKLECS2Mus musculus, Rattus norvegicus
H86GDWPMHKLECS1Danio rerio
I149EKKDLIQSDIA3Homo sapiens, Mus musculus, Rattus norvegicus
I149EKNEMNDTDIA1Danio rerio
I149EKRDLIQSDIA1Bos taurus
I214CCPNVIVTYKG4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
I214CSPNVIVTYKG1Danio rerio
I241VFTSYIDLLYP4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
I241IFNSYIDLLYP1Danio rerio
K145KLDNEKKDLIQ3Homo sapiens, Mus musculus, Rattus norvegicus
K145KLDNEKNEMND1Danio rerio
K145KLDNEKRDLIQ1Bos taurus
K17FCSPGKGRGLR2Homo sapiens, Bos taurus
K17FCSAGKGRGLR2Mus musculus, Rattus norvegicus
K17FLSPGKGRGLK1Danio rerio
L141SHLDKLDNEKK3Homo sapiens, Mus musculus, Rattus norvegicus
L141AHLDKLDNEKN1Danio rerio
L141SHLDKLDNEKR1Bos taurus
L191IEDEELSHLGS5Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus, Bos taurus
L204FPDVALMNHSC5Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus, Bos taurus
L244SYIDLLYPTED5Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus, Bos taurus
L317KSPSELLEICE4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
L317KTPSELLEICE1Danio rerio
L379YPLYSLNVASM2Homo sapiens, Bos taurus
L379YPVYSLNVASM2Mus musculus, Rattus norvegicus
L379YPPYSLNVASM1Danio rerio
M205PDVALMNHSCC4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
M205PDVALMNHSCS1Danio rerio
N180LFAQVNCNGFT4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
N180LIAQVNCNGFT1Danio rerio
N182AQVNCNGFTIE5Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus, Bos taurus
N206DVALMNHSCCP4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
N206DVALMNHSCSP1Danio rerio
N380PLYSLNVASMW2Homo sapiens, Bos taurus
N380PVYSLNVASMW2Mus musculus, Rattus norvegicus
N380PPYSLNVASMY1Danio rerio
P314KHYKSPSELLE4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
P314KHYKTPSELLE1Danio rerio
Q345LHMMYQAMGVC5Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus, Bos taurus
R19SPGKGRGLRAL2Homo sapiens, Bos taurus
R19SAGKGRGLRAL2Mus musculus, Rattus norvegicus
R19SPGKGRGLKAI1Danio rerio
R253EDRNDRLRDSY4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
R253EDRIERLKDSY1Danio rerio
R306VIEEFRRAKHY5Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus, Bos taurus
R390WLKLGRLYMGL4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
R390YLKLGRLYLGL1Danio rerio
R67LSKCGRCKQAF4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
R67LSKCGKCKQAY1Danio rerio
S196LSHLGSAIFPD4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
S196LSHLGSALFPD1Danio rerio
S239EEVFTSYIDLL2Homo sapiens, Bos taurus
S239DEVFTSYIDLL2Mus musculus, Rattus norvegicus
S239EEIFNSYIDLL1Danio rerio
S257DRLRDSYFFTC4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
S257ERLKDSYFFNC1Danio rerio
T105WNPSETVRLTA4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
T105WCPSETVRLVA1Danio rerio
T185NCNGFTIEDEE5Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus, Bos taurus
T220VTYKGTLAEVR4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
T220VTYKGTVAEVR1Danio rerio
T238GEEVFTSYIDL2Homo sapiens, Bos taurus
T238GDEVFTSYIDL2Mus musculus, Rattus norvegicus
T238EEEIFNSYIDL1Danio rerio
T44YAYVLTVNERG2Homo sapiens, Danio rerio
T44YACVLTVGERG2Mus musculus, Rattus norvegicus
T44YAYVLTVSERG1Bos taurus
V179VLFAQVNCNGF4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
V179ELIAQVNCNGF1Danio rerio
V215CPNVIVTYKGT4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
V215SPNVIVTYKGT1Danio rerio
V349YQAMGVCLYMQ5Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus, Bos taurus
W356LYMQDWEGALK2Mus musculus, Rattus norvegicus
W356LYMQDWEGALQ1Homo sapiens
W356LYMQDWDGAMK1Danio rerio
W356LYMQDWEGALR1Bos taurus
W83CQKEDWPLHKL2Mus musculus, Rattus norvegicus
W83CQKEDWPMHKL1Homo sapiens
W83CQRGDWPMHKL1Danio rerio
W83CQREDWPMHKL1Bos taurus
Y240EVFTSYIDLLY4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
Y240EIFNSYIDLLY1Danio rerio
Y245YIDLLYPTEDR5Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus, Bos taurus
Y258RLRDSYFFTCE4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
Y258RLKDSYFFNCD1Danio rerio
Y344MLHMMYQAMGV5Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus, Bos taurus
Y352MGVCLYMQDWE4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
Y352MGVCLYMQDWD1Danio rerio
Y370KIIKPYSKHYP3Homo sapiens, Mus musculus, Rattus norvegicus
Y370KIIHPYSVHYP1Danio rerio
Y370KIIQPYSKHYP1Bos taurus
Y374PYSKHYPLYSL2Homo sapiens, Bos taurus
Y374PYSKHYPVYSL2Mus musculus, Rattus norvegicus
Y374PYSVHYPPYSL1Danio rerio
Y41CPAYAYVLTVN2Homo sapiens, Danio rerio
Y41CPAYACVLTVG2Mus musculus, Rattus norvegicus
Y41CPAYAYVLTVS1Bos taurus
Y54GHHCECCFARK2Mus musculus, Rattus norvegicus
Y54GNHCEYCFTRK1Homo sapiens
Y54GGRCECCFTRK1Danio rerio
Y54GNHCEFCFARK1Bos taurus


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