mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 MMP3
Gene summary
Basic gene Info.Gene symbolMMP3
Gene namematrix metallopeptidase 3 (stromelysin 1, progelatinase)
SynonymsCHDS6|MMP-3|SL-1|STMY|STMY1|STR1
CytomapUCSC genome browser: 11q22.3
Type of geneprotein-coding
RefGenesNM_002422.3,
Descriptionmatrix metalloproteinase 3 (stromelysin 1, progelatinase)matrix metalloproteinase-3proteoglycanasestromelysin-1transin-1
Modification date20141207
dbXrefs MIM : 185250
HGNC : HGNC
Ensembl : ENSG00000149968
HPRD : 01703
Vega : OTTHUMG00000048254
ProteinUniProt: P08254
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MMP3
BioGPS: 4314
PathwayNCI Pathway Interaction Database: MMP3
KEGG: MMP3
REACTOME: MMP3
Pathway Commons: MMP3
ContextiHOP: MMP3
ligand binding site mutation search in PubMed: MMP3
UCL Cancer Institute: MMP3
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:0006508proteolysis12867428
GO:0010727negative regulation of hydrogen peroxide metabolic process20969476
GO:0032461positive regulation of protein oligomerization19022250


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Ligand binding site mutations for MMP3
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
Q202Q202KBRCA1
C92C92RCOAD1
L243L243FCOAD1
P107P107LGBM1
D124D124HHNSC1
C92P90SLUAD1
E156E154KSKCM1
H218H218NSKCM1
T208T210STHCA1
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 MMP3
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
Q202Q202K-1.2854662
C92P90S-1.1552983
T208T210S-0.93132828
C92C92R-0.73860965
L243L243F-0.71094109
D124D124H-0.5772554
H218H218N-0.52906762
P107P107L-0.51220604
E156E154K-0.42652877
(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 MMP3 from PDB

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Differential gene expression and gene-gene network for MMP3
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 MMP3 and the right PPI network was created from samples without mutations in the LBS of MMP3. 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 MMP3
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1956346Coronary Artery Disease19AlteredExpression, Biomarker, GeneticVariation
umls:C1458155Breast Neoplasms8AlteredExpression, Biomarker, GeneticVariation
umls:C0004114Astrocytoma4Biomarker, GeneticVariation
umls:C0948480Coronary Restenosis3Biomarker
umls:C0020429Hyperalgesia2Biomarker
umls:C2937358Cerebral Hemorrhage1Biomarker
umls:C0027626Neoplasm Invasiveness1Biomarker
umls:C0031117Peripheral Nervous System Diseases1Biomarker

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

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Pharmacological information for MMP3
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|investigationalDB00786MarimastatSmall molecule
ExperimentalDB01877N-Hydroxy 1n(4-Methoxyphenyl)Sulfonyl-4-(Z,E-N-Methoxyimino)Pyrrolidine-2r-CarboxamideSmall molecule
ExperimentalDB019963-MethylpyridineSmall molecule
ExperimentalDB02090A Disubstituted Succinyl Caprolactam Hydroxymate Mmp3inhibitorSmall molecule
ExperimentalDB02350N-Hydroxy-4-[(4-Methoxylphenyl)Sulfonyl]-2,2-Dimethyl-Hexahydro-1,4-Thiazepine-3(S)-CarboxamideSmall molecule
ExperimentalDB02367(1n)-4-N-Butoxyphenylsulfonyl-(2r)-N-Hydroxycarboxamido-(4s)-Methanesulfonylamino-PyrrolidineSmall molecule
ExperimentalDB024493-(1h-Indol-3-Yl)-2-[4-(4-Phenyl-Piperidin-1-Yl)-Benzenesulfonylamino]-Propionic AcidSmall molecule
ExperimentalDB02697HydroxyaminovalineSmall molecule
ExperimentalDB030331-Methyloxy-4-Sulfone-BenzeneSmall molecule
ExperimentalDB033685-Methyl-5-(4-Phenoxy-Phenyl)-Pyrimidine-2,4,6-TrioneSmall molecule
ExperimentalDB041401-Benzyl-3-(4-Methoxy-Benzenesulfonyl)-6-Oxo-Hexahydro-Pyrimidine-4-Carboxylic Acid HydroxyamideSmall molecule
ExperimentalDB04232N-Hydroxy-1-(4-Methoxyphenyl)Sulfonyl-4-Benzyloxycarbonyl-Piperazine-2-CarboxamideSmall molecule
ExperimentalDB04416R-2-{[4'-Methoxy-(1,1'-Biphenyl)-4-Yl]-Sulfonyl}-Amino-6-Methoxy-Hex-4-Ynoic AcidSmall molecule
ExperimentalDB073902-[3-(5-MERCAPTO-[1,3,4]THIADIAZOL-2-YL)-UREIDO]-N-METHYL-3-PHENYL-PROPIONAMIDESmall molecule
ExperimentalDB07986[4-(4-PHENYL-PIPERIDIN-1-YL)-BENZENESULFONYLAMINO]-ACETIC ACIDSmall molecule
ExperimentalDB07987[2-(5-MERCAPTO-[1,3,4]THIADIAZOL-2-YLCARBAMOYL)-1-PHENYL-ETHYL]-CARBAMIC ACID BENZYL ESTERSmall molecule
ExperimentalDB079882-[3-(5-MERCAPTO-[1,3,4]THIADIAZOL-2YL)-UREIDO]-N-METHYL-3-PENTAFLUOROPHENYL-PROPIONAMIDESmall molecule
ExperimentalDB08029N~2~-(biphenyl-4-ylsulfonyl)-N-hydroxy-N~2~-(2-hydroxyethyl)glycinamideSmall molecule
ExperimentalDB080303-[(4'-cyanobiphenyl-4-yl)oxy]-N-hydroxypropanamideSmall molecule
ExperimentalDB08271N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACIDSmall molecule
ExperimentalDB08507N-[[2-METHYL-4-HYDROXYCARBAMOYL]BUT-4-YL-N]-BENZYL-P-[PHENYL]-P-[METHYL]PHOSPHINAMIDSmall molecule
ExperimentalDB086432-(2-{2-[(BIPHENYL-4-YLMETHYL)-AMINO]-3-MERCAPTO-PENTANOYLAMINO}-ACETYLAMINO)-3-METHYL-BUTYRIC ACID METHYL ESTERSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of MMP3 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
TR12-(2-{2-[(BIPHENYL-4-YLMETHYL)-AMINO]-3-MERCAPTO-PENTANOYLAMINO}-ACETYLAMINO)-3-METHYL-BUTYRIC ACIDMETHYL ESTER1c8tAQ202
TR12-(2-{2-[(BIPHENYL-4-YLMETHYL)-AMINO]-3-MERCAPTO-PENTANOYLAMINO}-ACETYLAMINO)-3-METHYL-BUTYRIC ACIDMETHYL ESTER1c8tBQ202


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Conservation information for LBS of MMP3
Multiple alignments for P08254 in multiple species
LBSAA sequence# speciesSpecies
A157LYEGEADIMIS1Homo sapiens
A157ISEGEADIMIS1Mus musculus
A157TDEGEADIKIS1Canis lupus familiaris
A182PGNVLAHAYAP1Homo sapiens
A182PGTVLAHAYAP1Mus musculus
A182PGNVLGHAYPP1Canis lupus familiaris
A184NVLAHAYAPGP1Homo sapiens
A184TVLAHAYAPGP1Mus musculus
A184NVLGHAYPPGP1Canis lupus familiaris
A186LAHAYAPGPGI2Homo sapiens, Mus musculus
A186LGHAYPPGPGI1Canis lupus familiaris
A234SANTEALMYPL1Homo sapiens
A234SAKAEALMYPV1Mus musculus
A234SADPSALMYPV1Canis lupus familiaris
C92MRKPRCGVPDV1Homo sapiens
C92MHKPRCGVPDV1Mus musculus
C92MRRPRCGVPDV1Canis lupus familiaris
D124VNYTPDLPKDA1Homo sapiens
D124VNYTPDLPRQS1Mus musculus
D124MNYTPDLPRDA1Canis lupus familiaris
D158YEGEADIMISF1Homo sapiens
D158SEGEADIMISF1Mus musculus
D158DEGEADIKISF1Canis lupus familiaris
D170VREHGDFYPFD1Homo sapiens
D170VGEHGDFVPFD1Mus musculus
D170VRDHGDFNPFD1Canis lupus familiaris
D175DFYPFDGPGNV1Homo sapiens
D175DFVPFDGPGTV1Mus musculus
D175DFNPFDGPGNV1Canis lupus familiaris
D194PGINGDAHFDD2Homo sapiens, Mus musculus
D194PGIYGDAHFDD1Canis lupus familiaris
D198GDAHFDDDEQW2Homo sapiens, Canis lupus familiaris
D198GDAHFDDDERW1Mus musculus
D199DAHFDDDEQWT2Homo sapiens, Canis lupus familiaris
D199DAHFDDDERWT1Mus musculus
D200AHFDDDEQWTK1Homo sapiens
D200AHFDDDERWTE1Mus musculus
D200AHFDDDEQWTS1Canis lupus familiaris
E156RLYEGEADIMI1Homo sapiens
E156RISEGEADIMI1Mus musculus
E156RTDEGEADIKI1Canis lupus familiaris
E201HFDDDEQWTKD1Homo sapiens
E201HFDDDERWTED1Mus musculus
E201HFDDDEQWTSD1Canis lupus familiaris
E219LVAAHELGHSL2Mus musculus, Canis lupus familiaris
E219LVAAHEIGHSL1Homo sapiens
E233HSANTEALMYP1Homo sapiens
E233HSAKAEALMYP1Mus musculus
E233HSADPSALMYP1Canis lupus familiaris
F103GHFRTFPGIPK1Homo sapiens
F103GGFSTFPGSPK1Mus musculus
F103GDFTTFPGMPK1Canis lupus familiaris
F174GDFYPFDGPGN1Homo sapiens
F174GDFVPFDGPGT1Mus musculus
F174GDFNPFDGPGN1Canis lupus familiaris
F227HSLGLFHSANT1Homo sapiens
F227HSLGLYHSAKA1Mus musculus
F227HSLGLFHSADP1Canis lupus familiaris
F249TDLTRFRLSQD1Homo sapiens
F249TDLSRFHLSQD1Mus musculus
F249ADLARFHLSQD1Canis lupus familiaris
G176FYPFDGPGNVL1Homo sapiens
G176FVPFDGPGTVL1Mus musculus
G176FNPFDGPGNVL1Canis lupus familiaris
G178PFDGPGNVLAH1Homo sapiens
G178PFDGPGTVLAH1Mus musculus
G178PFDGPGNVLGH1Canis lupus familiaris
G190YAPGPGINGDA2Homo sapiens, Mus musculus
G190YPPGPGIYGDA1Canis lupus familiaris
G193GPGINGDAHFD2Homo sapiens, Mus musculus
G193GPGIYGDAHFD1Canis lupus familiaris
H168FAVREHGDFYP1Homo sapiens
H168FAVGEHGDFVP1Mus musculus
H168FAVRDHGDFNP1Canis lupus familiaris
H183GNVLAHAYAPG1Homo sapiens
H183GTVLAHAYAPG1Mus musculus
H183GNVLGHAYPPG1Canis lupus familiaris
H196INGDAHFDDDE2Homo sapiens, Mus musculus
H196IYGDAHFDDDE1Canis lupus familiaris
H218FLVAAHELGHS2Mus musculus, Canis lupus familiaris
H218FLVAAHEIGHS1Homo sapiens
H222AHEIGHSLGLF1Homo sapiens
H222AHELGHSLGLY1Mus musculus
H222AHELGHSLGLF1Canis lupus familiaris
H228SLGLFHSANTE1Homo sapiens
H228SLGLYHSAKAE1Mus musculus
H228SLGLFHSADPS1Canis lupus familiaris
H241MYPLYHSLTDL1Homo sapiens
H241MYPVYKSSTDL1Mus musculus
H241MYPVYNVLADL1Canis lupus familiaris
I191APGPGINGDAH2Homo sapiens, Mus musculus
I191PPGPGIYGDAH1Canis lupus familiaris
L181GPGNVLAHAYA1Homo sapiens
L181GPGTVLAHAYA1Mus musculus
L181GPGNVLGHAYP1Canis lupus familiaris
L214GTNLFLVAAHE3Homo sapiens, Mus musculus, Canis lupus familiaris
L235ANTEALMYPLY1Homo sapiens
L235AKAEALMYPVY1Mus musculus
L235ADPSALMYPVY1Canis lupus familiaris
L239ALMYPLYHSLT1Homo sapiens
L239ALMYPVYKSST1Mus musculus
L239ALMYPVYNVLA1Canis lupus familiaris
L243PLYHSLTDLTR1Homo sapiens
L243PVYKSSTDLSR1Mus musculus
L243PVYNVLADLAR1Canis lupus familiaris
M236NTEALMYPLYH1Homo sapiens
M236KAEALMYPVYK1Mus musculus
M236DPSALMYPVYN1Canis lupus familiaris
N179FDGPGNVLAHA1Homo sapiens
N179FDGPGTVLAHA1Mus musculus
N179FDGPGNVLGHA1Canis lupus familiaris
N192PGPGINGDAHF2Homo sapiens, Mus musculus
N192PGPGIYGDAHF1Canis lupus familiaris
P107TFPGIPKWRKT1Homo sapiens
P107TFPGSPKWRKS1Mus musculus
P107TFPGMPKWRKT1Canis lupus familiaris
P173HGDFYPFDGPG1Homo sapiens
P173HGDFVPFDGPG1Mus musculus
P173HGDFNPFDGPG1Canis lupus familiaris
P177YPFDGPGNVLA1Homo sapiens
P177VPFDGPGTVLA1Mus musculus
P177NPFDGPGNVLG1Canis lupus familiaris
P238EALMYPLYHSL1Homo sapiens
P238EALMYPVYKSS1Mus musculus
P238SALMYPVYNVL1Canis lupus familiaris
Q202FDDDEQWTKDT1Homo sapiens
Q202FDDDERWTEDV1Mus musculus
Q202FDDDEQWTSDT1Canis lupus familiaris
T122RIVNYTPDLPK1Homo sapiens
T122RIVNYTPDLPR1Mus musculus
T122RIMNYTPDLPR1Canis lupus familiaris
T208WTKDTTGTNLF1Homo sapiens
T208WTEDVTGTNLF1Mus musculus
T208WTSDTSGTNLF1Canis lupus familiaris
T232FHSANTEALMY1Homo sapiens
T232YHSAKAEALMY1Mus musculus
T232FHSADPSALMY1Canis lupus familiaris
V180DGPGNVLAHAY1Homo sapiens
V180DGPGTVLAHAY1Mus musculus
V180DGPGNVLGHAY1Canis lupus familiaris
V215TNLFLVAAHEL2Mus musculus, Canis lupus familiaris
V215TNLFLVAAHEI1Homo sapiens
W203DDDEQWTKDTT1Homo sapiens
W203DDDERWTEDVT1Mus musculus
W203DDDEQWTSDTS1Canis lupus familiaris
Y172EHGDFYPFDGP1Homo sapiens
Y172EHGDFVPFDGP1Mus musculus
Y172DHGDFNPFDGP1Canis lupus familiaris
Y185VLAHAYAPGPG2Homo sapiens, Mus musculus
Y185VLGHAYPPGPG1Canis lupus familiaris
Y237TEALMYPLYHS1Homo sapiens
Y237AEALMYPVYKS1Mus musculus
Y237PSALMYPVYNV1Canis lupus familiaris
Y240LMYPLYHSLTD1Homo sapiens
Y240LMYPVYKSSTD1Mus musculus
Y240LMYPVYNVLAD1Canis lupus familiaris


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