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 SMYD3
Gene summary
Basic gene Info.Gene symbolSMYD3
Gene nameSET and MYND domain containing 3
SynonymsKMT3E|ZMYND1|ZNFN3A1|bA74P14.1
CytomapUCSC genome browser: 1q44
Type of geneprotein-coding
RefGenesNM_001167740.1,
NM_022743.2,
DescriptionSET and MYND domain-containing protein 3bA74P14.1 (novel protein)histone-lysine N-methyltransferase SMYD3zinc finger MYND domain-containing protein 1zinc finger protein, subfamily 3A (MYND domain containing), 1zinc finger, MYND domain containing 1
Modification date20141207
dbXrefs MIM : 608783
HGNC : HGNC
Ensembl : ENSG00000185420
HPRD : 12297
Vega : OTTHUMG00000040508
ProteinUniProt: Q9H7B4
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SMYD3
BioGPS: 64754
PathwayNCI Pathway Interaction Database: SMYD3
KEGG: SMYD3
REACTOME: SMYD3
Pathway Commons: SMYD3
ContextiHOP: SMYD3
ligand binding site mutation search in PubMed: SMYD3
UCL Cancer Institute: SMYD3
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 SMYD3
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
C49D50NBRCA1
H206S207IBRCA1
E294K292NGBM1
H83,C87R85LLUAD1
M190M190LLUAD1
V368H366RLUAD1
S182S182FSKCM1
E294I293SUCEC1
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 SMYD3
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
E294I293S-1.1521773
C49D50N-0.76784219
E294K292N-0.7619743
M190M190L-0.57505712
S182S182F-0.50538855
H206S207I-0.44917875
H83R85L-0.34321898
C87R85L-0.34321898
V368H366R-0.19833516
(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 SMYD3 from PDB

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Differential gene expression and gene-gene network for SMYD3
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 SMYD3 and the right PPI network was created from samples without mutations in the LBS of SMYD3. 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 SMYD3
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0236733Amphetamine-Related Disorders1Biomarker

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

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Pharmacological information for SMYD3
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 SMYD3 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ZNZINC(2+)3mekAC49
ZNZINC(2+)3oxfAC49
ZNZINC(2+)3oxfBC49
ZNZINC(2+)3oxgAC49
ZNZINC(2+)3oxlAC49
ZNZINC(2+)3pdnAC49
ZNZINC(2+)3qwpAC49
ZNZINC(2+)3ru0AC49
ZNZINC(2+)3ru0BC49
ZNZINC(2+)5cclAC49
ZNZINC(2+)5ccmAC49
SAMS-ADENOSYL-L-METHIONINE3mekAH206
SAHS-ADENOSYL-L-HOMOCYSTEINE3oxfAH206
SAHS-ADENOSYL-L-HOMOCYSTEINE3oxfBH206
SAHS-ADENOSYL-L-HOMOCYSTEINE3oxgAH206
SAHS-ADENOSYL-L-HOMOCYSTEINE3oxlAH206
SFGSINEFUNGIN3pdnAH206
SAMS-ADENOSYL-L-METHIONINE3qwpAH206
SFGSINEFUNGIN3ru0AH206
SFGSINEFUNGIN3ru0BH206
SAMS-ADENOSYL-L-METHIONINE5cclAH206
SAMS-ADENOSYL-L-METHIONINE5ccmAH206
ZNZINC(2+)3mekAH83 C87
ZNZINC(2+)3oxfAH83 C87
ZNZINC(2+)3oxfBH83 C87
ZNZINC(2+)3oxgAH83 C87
ZNZINC(2+)3oxlAH83 C87
ZNZINC(2+)3pdnAH83 C87
ZNZINC(2+)3qwpAH83 C87
ZNZINC(2+)3ru0AH83 C87
ZNZINC(2+)3ru0BH83 C87
ZNZINC(2+)5cclAH83 C87
ZNZINC(2+)5ccmAH83 C87
4ZW2-OXIDANYLIDENE-N-PIPERIDIN-4-YL-1,3-DIHYDROINDOLE-5- CARBOXAMIDE5cclAS182
4ZX6-CHLORANYL-2-OXIDANYLIDENE-N-[(1S,5R)-8-[4- [(PHENYLMETHYL)AMINO]PIPERIDIN-1-YL]SULFONYL-8- AZABICYCLO[3.2.1]OCTAN-3-YL]-1,3-DIHYDROINDOLE-5- CARBOXAMIDE5ccmAS182 M190 E294 V368


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Conservation information for LBS of SMYD3
Multiple alignments for Q9H7B4 in multiple species
LBSAA sequence# speciesSpecies
C180FAKVICNSFTI2Homo sapiens, Mus musculus
C180FCRLAVNAMNL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C180FSKFSCNAHSI1Arabidopsis thaliana
C186NSFTICNAEMQ2Homo sapiens, Mus musculus
C186NAMNLVTSSFD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C186NAHSICDSELR1Arabidopsis thaliana
C238EELTICYLDML2Homo sapiens, Mus musculus
C238EQLFISYIDIR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C238SEITISYIETA1Arabidopsis thaliana
C333K-VLDCAMDAC2Homo sapiens, Mus musculus
C333KSSADEFLDAL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C333R-TREKLLKML1Arabidopsis thaliana
C49SRGVVCDRCLL2Homo sapiens, Mus musculus
C49NLTRTCSTCTE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C49SSESRCDGCFK1Arabidopsis thaliana
C52VVCDRCLLGKE2Homo sapiens, Mus musculus
C52RTCSTCTEEKV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C52SRCDGCFKTN-1Arabidopsis thaliana
C62EKLMRCSQCRV1Homo sapiens
C62VKTQRCAACKI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C62-NLKKCSACQV1Arabidopsis thaliana
C62EKLMRCSQCRI1Mus musculus
C65MRCSQCRVAKY1Homo sapiens
C65QRCAACKIIHY1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C65KKCSACQVVWY1Arabidopsis thaliana
C65MRCSQCRIAKY1Mus musculus
C71RVAKYCSAKCQ1Homo sapiens
C71KIIHYCSKGCQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C71QVVWYCGSSCQ1Arabidopsis thaliana
C71RIAKYCSAKCQ1Mus musculus
C75YCSAKCQKKAW2Homo sapiens, Mus musculus
C75YCSKGCQKADW1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C75YCGSSCQKSEW1Arabidopsis thaliana
C87DHKRECKC---1Homo sapiens
C87FHKLECKA---1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C87LHRDECKALTR1Arabidopsis thaliana
C87DHRRECSC---1Mus musculus
D241TICYLDMLMTS2Homo sapiens, Mus musculus
D241FISYIDIRLPK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D241TISYIETAGST1Arabidopsis thaliana
D332LK-VLDCAMDA2Homo sapiens, Mus musculus
D332LKSSADEFLDA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D332MR-TREKLLKM1Arabidopsis thaliana
E130FYD-LESNINK1Homo sapiens
E130IIEPMEGHQNE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E130LVEALVSHMSE1Arabidopsis thaliana
E130FYD-LESNISK1Mus musculus
E192NAEMQEVGVGL2Homo sapiens, Mus musculus
E192TSSFDSLGMCL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E192DSELRPQGIGL1Arabidopsis thaliana
E294SLKKIEELKAH2Homo sapiens, Mus musculus
E294LMKNLAMARDL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E294LLRSKEEVKKL1Arabidopsis thaliana
F183VICNSFTICNA2Homo sapiens, Mus musculus
F183LAVNAMNLVTS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F183FSCNAHSICDS1Arabidopsis thaliana
F259RDQYCFECDCF1Homo sapiens
F259LKKYFFSCYCP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F259KEQYLFHCQCA1Arabidopsis thaliana
F259RDQYCFECDCI1Mus musculus
G15-TAKRGNGLRA1Homo sapiens
G15-LPEFGKGTVA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G15NLPQKGRSLFT1Arabidopsis thaliana
G15-TANRGNGLRA1Mus musculus
G17AKRGNGLRAVT1Homo sapiens
G17PEFGKGTVATD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G17PQKGRSLFTAR1Arabidopsis thaliana
G17ANRGNGLRAVA1Mus musculus
G232RDIEVGEELTI1Homo sapiens
G232RDIKKDEQLFI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G232DNISKDSEITI1Arabidopsis thaliana
G232REIEAGEELTI1Mus musculus
H206ISLLNHSCDPN1Homo sapiens
H206LCRLNHSCDPN1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H206VSIINHSCSPN1Arabidopsis thaliana
H206MSLLNHSCDPN1Mus musculus
H83KAWPDHKRECK1Homo sapiens
H83ADWPFHKLECK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H83SEWKLHRDECK1Arabidopsis thaliana
H83KAWPDHRRECS1Mus musculus
I214DPNCSIVFNGP2Homo sapiens, Mus musculus
I214DPNCQIIFDGA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I214SPNAVLVFEEQ1Arabidopsis thaliana
I237GEELTICYLDM2Homo sapiens, Mus musculus
I237DEQLFISYIDI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I237DSEITISYIET1Arabidopsis thaliana
K329----LK-VLDC2Homo sapiens, Mus musculus
K329AALYLKSSADE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K329SIPLMR-TREK1Arabidopsis thaliana
L203YPSISLLNHSC1Homo sapiens
L203DTILCRLNHSC1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L203FPLVSIINHSC1Arabidopsis thaliana
L203YPSMSLLNHSC1Mus musculus
L204PSISLLNHSCD1Homo sapiens
L204TILCRLNHSCD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L204PLVSIINHSCS1Arabidopsis thaliana
L204PSMSLLNHSCD1Mus musculus
L240LTICYLDMLMT2Homo sapiens, Mus musculus
L240LFISYIDIRLP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L240ITISYIETAGS1Arabidopsis thaliana
M190ICNAEMQEVGV2Homo sapiens, Mus musculus
M190LVTSSFDSLGM1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
M190ICDSELRPQGI1Arabidopsis thaliana
N132D-LESNINKLT1Homo sapiens
N132EPMEGHQNEFQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N132EALVSHMSEID1Arabidopsis thaliana
N132D-LESNISKLT1Mus musculus
N16TAKRGNGLRAV1Homo sapiens
N16LPEFGKGTVAT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N16LPQKGRSLFTA1Arabidopsis thaliana
N16TANRGNGLRAV1Mus musculus
N181AKVICNSFTIC2Homo sapiens, Mus musculus
N181CRLAVNAMNLV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N181SKFSCNAHSIC1Arabidopsis thaliana
N205SISLLNHSCDP1Homo sapiens
N205ILCRLNHSCDP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N205LVSIINHSCSP1Arabidopsis thaliana
N205SMSLLNHSCDP1Mus musculus
R14--TAKRGNGLR1Homo sapiens
R14--LPEFGKGTV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R14SNLPQKGRSLF1Arabidopsis thaliana
R14--TANRGNGLR1Mus musculus
R19RGNGLRAVTPL1Homo sapiens
R19FGKGTVATDNI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R19KGRSLFTARDF1Arabidopsis thaliana
R19RGNGLRAVAPL1Mus musculus
S182KVICNSFTICN2Homo sapiens, Mus musculus
S182RLAVNAMNLVT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S182KFSCNAHSICD1Arabidopsis thaliana
S202LYPSISLLNHS1Homo sapiens
S202LDTILCRLNHS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S202LFPLVSIINHS1Arabidopsis thaliana
S202LYPSMSLLNHS1Mus musculus
T184ICNSFTICNAE2Homo sapiens, Mus musculus
T184AVNAMNLVTSS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T184SCNAHSICDSE1Arabidopsis thaliana
V21NGLRAVTPLRP1Homo sapiens
V21KGTVATDNIPI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V21RSLFTARDFRP1Arabidopsis thaliana
V21NGLRAVAPLRP1Mus musculus
V231VRDIEVGEELT1Homo sapiens
V231KRDIKKDEQLF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V231MDNISKDSEIT1Arabidopsis thaliana
V231VREIEAGEELT1Mus musculus
V368PGSHPVR----2Homo sapiens, Mus musculus
V368PNDKPLEMEFP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V368PATHPLI----1Arabidopsis thaliana
Y124ESEKLYSFYD-2Homo sapiens, Mus musculus
Y124-WQKNPAIIEP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y124TTTDNYSLVEA1Arabidopsis thaliana
Y239ELTICYLDMLM2Homo sapiens, Mus musculus
Y239QLFISYIDIRL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y239EITISYIETAG1Arabidopsis thaliana
Y257QLRDQYCFECD2Homo sapiens, Mus musculus
Y257QLLKKYFFSCY1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y257SLKEQYLFHCQ1Arabidopsis thaliana


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