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 MLYCD

Gene summary

Basic gene Info.	Gene symbol	MLYCD
	Gene name	malonyl-CoA decarboxylase
	Synonyms	MCD
	Cytomap	UCSC genome browser: 16q24
	Type of gene	protein-coding
	RefGenes	NM_012213.2,
	Description	malonyl coenzyme A decarboxylasemalonyl-CoA decarboxylase, mitochondrial
	Modification date	20141207
dbXrefs	MIM : 606761
	HGNC : HGNC
	HPRD : 05999
Protein	UniProt: O95822 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MLYCD
	BioGPS: 23417
Pathway	NCI Pathway Interaction Database: MLYCD
	KEGG: MLYCD
	REACTOME: MLYCD
	Pathway Commons: MLYCD
Context	iHOP: MLYCD
	ligand binding site mutation search in PubMed: MLYCD
	UCL Cancer Institute: MLYCD
Assigned class in mutLBSgeneDB	B: This gene belongs to targetable_mutLBSgenes.

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

GO ID	GO Term	PubMed ID
GO:0006085	acetyl-CoA biosynthetic process	10417274
GO:0006633	fatty acid biosynthetic process	15003260
GO:2001294	malonyl-CoA catabolic process	10417274

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Ligand binding site mutations for MLYCD

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
L293	T294A	STAD	1

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 MLYCD

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.

LBS	AAchange of nsSNV	Relative stability change
L293	T294A	-0.88418873

(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 MLYCD from PDB

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Differential gene expression and gene-gene network for MLYCD

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 MLYCD and the right PPI network was created from samples without mutations in the LBS of MLYCD. 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 MLYCD

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0342793	Malonic aciduria	6	Biomarker, GeneticVariation

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for MLYCD

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 status

DrugBank ID

Name

Type

Drug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of MLYCD go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
0OR		N~3~-[(2R)-2-HYDROXY-4-{[(S)-HYDROXY(PHOSPHONOOXY) PHOSPHORYL]OXY}-3,3-DIMETHYLBUTANOYL]-BETA-ALANINAMIDE	4f0x	B	L293
0OR		N~3~-[(2R)-2-HYDROXY-4-{[(S)-HYDROXY(PHOSPHONOOXY) PHOSPHORYL]OXY}-3,3-DIMETHYLBUTANOYL]-BETA-ALANINAMIDE	4f0x	D	L293
0OR		N~3~-[(2R)-2-HYDROXY-4-{[(S)-HYDROXY(PHOSPHONOOXY) PHOSPHORYL]OXY}-3,3-DIMETHYLBUTANOYL]-BETA-ALANINAMIDE	4f0x	E	L293
0OR		N~3~-[(2R)-2-HYDROXY-4-{[(S)-HYDROXY(PHOSPHONOOXY) PHOSPHORYL]OXY}-3,3-DIMETHYLBUTANOYL]-BETA-ALANINAMIDE	4f0x	G	L293

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Conservation information for LBS of MLYCD

Multiple alignments for O95822 in multiple species

LBS	AA sequence	# species	Species
E302	GLQGVELGTFL	3	Homo sapiens, Mus musculus, Rattus norvegicus
F422	NPVANFHLQNG	3	Homo sapiens, Mus musculus, Rattus norvegicus
G300	QQGLQGVELGT	3	Homo sapiens, Mus musculus, Rattus norvegicus
G304	QGVELGTFLIK	3	Homo sapiens, Mus musculus, Rattus norvegicus
H423	PVANFHLQNGA	3	Homo sapiens, Mus musculus, Rattus norvegicus
I291	AIFYSISLTQQ	2	Homo sapiens, Mus musculus
I291	AVFYSISLTQQ	1	Rattus norvegicus
L293	FYSISLTQQGL	3	Homo sapiens, Mus musculus, Rattus norvegicus
L303	LQGVELGTFLI	3	Homo sapiens, Mus musculus, Rattus norvegicus
P330	FSSLSPIPGFT	3	Homo sapiens, Mus musculus, Rattus norvegicus
S292	IFYSISLTQQG	2	Homo sapiens, Mus musculus
S292	VFYSISLTQQG	1	Rattus norvegicus
S329	AFSSLSPIPGF	2	Mus musculus, Rattus norvegicus
S329	VFSSLSPIPGF	1	Homo sapiens
T305	GVELGTFLIKR	3	Homo sapiens, Mus musculus, Rattus norvegicus
V301	QGLQGVELGTF	3	Homo sapiens, Mus musculus, Rattus norvegicus
V419	YALNPVANFHL	3	Homo sapiens, Mus musculus, Rattus norvegicus