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 PDXK
Gene summary
Basic gene Info.Gene symbolPDXK
Gene namepyridoxal (pyridoxine, vitamin B6) kinase
CytomapUCSC genome browser: 21q22.3
Type of geneprotein-coding
Descriptionepididymis secretory sperm binding protein Li 1apyridoxal kinasepyridoxamine kinasepyridoxine kinasevitamin B6 kinase
Modification date20141207
dbXrefs MIM : 179020
Ensembl : ENSG00000160209
HPRD : 01526
Vega : OTTHUMG00000086870
ProteinUniProt: O00764
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDXK
BioGPS: 8566
PathwayNCI Pathway Interaction Database: PDXK
Pathway Commons: PDXK
ContextiHOP: PDXK
ligand binding site mutation search in PubMed: PDXK
UCL Cancer Institute: PDXK
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0008283cell proliferation10930737
GO:0042823pyridoxal phosphate biosynthetic process10987144

Ligand binding site mutations for PDXK
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
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 PDXK
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 PDXK from PDB

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


Phenotype information for PDXK
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0038220Status Epilepticus1Biomarker

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

Pharmacological information for PDXK
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|nutraceuticalDB00147PyridoxalSmall molecule
Approved|nutraceutical|vet_approvedDB00165PyridoxineSmall molecule
ExperimentalDB03909Adenosine-5'-[Beta, Gamma-Methylene]TriphosphateSmall molecule
ExperimentalDB04770O6-(R)-ROSCOVITINE, R-2-(6-BENZYLOXY-9-ISOPROPYL-9H-PURIN-2-YLAMINO)-BUTAN-1-OLSmall molecule
ExperimentalDB04776(2R)-2-({6-[benzyl(methyl)amino]-9-isopropyl-9H-purin-2-yl}amino)butan-1-olSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of PDXK go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ANPAMP-PNP2ajpBD113 A228 F230
ANPAMP-PNP2ajpAD113 A228 F230 L267
ATPATP2yxuBD113 A228 L263 L267
ATPATP3fhxBD113 A228 L263 L267
ATPATP3fhyAD113 A228 L263 L267
ATPATP3keuBD113 A228 L263 L267
ATPATP4en4BD113 A228 L263 L267
ATPATP2yxuAD113 A228 L267
ATPATP3fhxAD113 A228 L267
ATPATP3keuAD113 A228 L267
ATPATP4en4AD113 A228 L267
ATPATP3fhyBD113 L263 L267

Conservation information for LBS of PDXK
Multiple alignments for O00764 in multiple species
LBSAA sequence# speciesSpecies
A228IRKVDAVFVGT1Homo sapiens
A228IHKIPAYFTGT1Arabidopsis thaliana
A228MHKVDAVFVGT1Bos taurus
A228MRKVEAVFVGT1Mus musculus
A228MRKVDPVFVGT1Rattus norvegicus
C5-MEEECRVLSI2Homo sapiens, Bos taurus
C5-MEGECRVLSI2Mus musculus, Rattus norvegicus
C5LPSDTGRVLSI1Arabidopsis thaliana
D113LVYVCDPVMGD3Bos taurus, Mus musculus, Rattus norvegicus
D113LVYVCDPVLGD1Homo sapiens
D113LTYVCDPVMGD1Arabidopsis thaliana
D118DPVMGDKWNGE2Mus musculus, Rattus norvegicus
D118DPVLGDKWDGE1Homo sapiens
D118DPVMGD----E1Arabidopsis thaliana
D118DPVMGDQRDGE1Bos taurus
D145VVPVADIITPN2Bos taurus, Mus musculus
D145VVPLADIITPN1Homo sapiens
D145VVPLASMLTPN1Arabidopsis thaliana
D145VVPMADIITPN1Rattus norvegicus
D181HSMGPDTVVIT2Homo sapiens, Bos taurus
D181HAAGPSKVVIT1Arabidopsis thaliana
D181HCMGPDTVVIT1Mus musculus
D181HRMGPDTVVIT1Rattus norvegicus
D235FVGTGDLFAAM4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
D235FTGTGDLMTAL1Arabidopsis thaliana
D78NMNKYDYVLTG1Homo sapiens
D78DLLFYTHVLTG1Arabidopsis thaliana
D78DVNKYDYVLTG1Mus musculus
D78NVNKYDYVLTG1Rattus norvegicus
D96LAMVVDIVQEL2Homo sapiens, Bos taurus
D96LDTILEVINKL1Arabidopsis thaliana
D96LAMVVDIVREL1Mus musculus
D96LGMVVDIVQEL1Rattus norvegicus
E100VDIVQELKQQN3Homo sapiens, Bos taurus, Rattus norvegicus
E100LEVINKLRSVN1Arabidopsis thaliana
E100VDIVRELKQQN1Mus musculus
E153TPNQFEAELLS3Homo sapiens, Mus musculus, Rattus norvegicus
E153TPNQFEAEKLT1Arabidopsis thaliana
E153TPNQFEAELLT1Bos taurus
E4--MEEECRVLS2Homo sapiens, Bos taurus
E4--MEGECRVLS2Mus musculus, Rattus norvegicus
E4ALPSDTGRVLS1Arabidopsis thaliana
E61VLNSDELQELY2Homo sapiens, Bos taurus
E61VLNGQQLCDLI1Arabidopsis thaliana
E61VLKSQELHELY1Mus musculus
E61VLTSQELHALY1Rattus norvegicus
F230KVDAVFVGTGD2Homo sapiens, Bos taurus
F230KIPAYFTGTGD1Arabidopsis thaliana
F230KVEAVFVGTGD1Mus musculus
F230KVDPVFVGTGD1Rattus norvegicus
F237GTGDLFAAMLL4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F237GTGDLMTALLL1Arabidopsis thaliana
F33LQVLGFEVDAV3Bos taurus, Mus musculus, Rattus norvegicus
F33LQVLGFEIDAV1Homo sapiens
F33LQLLGYDVDPI1Arabidopsis thaliana
F43VNSVQFSNHTG4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F43INSVQFSNHTG1Arabidopsis thaliana
G179MLHSMGPDTVV2Homo sapiens, Bos taurus
G179ILHAAGPSKVV1Arabidopsis thaliana
G179MLHCMGPDTVV1Mus musculus
G179VLHRMGPDTVV1Rattus norvegicus
G20VRGYVGNRAAM2Mus musculus, Rattus norvegicus
G20IRGYVGNRAAT1Homo sapiens
G20VQGYVGNKSAV1Arabidopsis thaliana
G232DAVFVGTGDLF2Homo sapiens, Bos taurus
G232PAYFTGTGDLM1Arabidopsis thaliana
G232EAVFVGTGDLF1Mus musculus
G232DPVFVGTGDLF1Rattus norvegicus
G234VFVGTGDLFAA4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
G234YFTGTGDLMTA1Arabidopsis thaliana
G32PLQVLGFEVDA3Bos taurus, Mus musculus, Rattus norvegicus
G32PLQVLGFEIDA1Homo sapiens
G32PLQLLGYDVDP1Arabidopsis thaliana
H246LLAWTHKHPNN2Homo sapiens, Bos taurus
H246LLAWTHKHPDN2Mus musculus, Rattus norvegicus
H246LLGWSNKYPDN1Arabidopsis thaliana
H46VQFSNHTGYAH3Homo sapiens, Mus musculus, Rattus norvegicus
H46VQFSNHTGYPT1Arabidopsis thaliana
K225RMDIRKVDAVF1Homo sapiens
K225KILIHKIPAYF1Arabidopsis thaliana
K225RMEMHKVDAVF1Bos taurus
K225RMEMRKVEAVF1Mus musculus
K225RMEMRKVDPVF1Rattus norvegicus
K247LAWTHKHPNNL2Homo sapiens, Bos taurus
K247LAWTHKHPDNL2Mus musculus, Rattus norvegicus
K247LGWSNKYPDNL1Arabidopsis thaliana
L199QGSNYLIVLGS1Homo sapiens
L199--GGILLLIGS1Arabidopsis thaliana
L199RGSDYLMALGS1Bos taurus
L199QGSDYLIALGS1Mus musculus
L199KGSDYLMALGS1Rattus norvegicus
L263KTVSAMQHVLQ2Mus musculus, Rattus norvegicus
L263KTVSTLHHVLQ1Homo sapiens
L263LAVSTLQALLR1Arabidopsis thaliana
L263KTVSAMHHVLQ1Bos taurus
L267AMQHVLQRTIR2Mus musculus, Rattus norvegicus
L267TLHHVLQRTIQ1Homo sapiens
L267TLQALLRRTLD1Arabidopsis thaliana
L267AMHHVLQRTIK1Bos taurus
L31FPLQVLGFEVD3Bos taurus, Mus musculus, Rattus norvegicus
L31FPLQVLGFEID1Homo sapiens
L31FPLQLLGYDVD1Arabidopsis thaliana
M93KSFLAMVVDIV3Homo sapiens, Bos taurus, Mus musculus
M93VSFLDTILEVI1Arabidopsis thaliana
M93KSFLGMVVDIV1Rattus norvegicus
N150DIITPNQFEAE4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
N150SMLTPNQFEAE1Arabidopsis thaliana
P149ADIITPNQFEA4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
P149ASMLTPNQFEA1Arabidopsis thaliana
Q63NSDELQELYEG1Homo sapiens
Q63NGQQLCDLIEG1Arabidopsis thaliana
Q63KSQELHELYEG1Mus musculus
Q63TSQELHALYEG1Rattus norvegicus
R224IRMDIRKVDAV1Homo sapiens
R224FKILIHKIPAY1Arabidopsis thaliana
R224IRMEMHKVDAV1Bos taurus
R224IRMEMRKVEAV1Mus musculus
R224IRMEMRKVDPV1Rattus norvegicus
R70LYEGLRLNNMN1Homo sapiens
R70LIEGLEANDLL1Arabidopsis thaliana
R70LYEGLKVNDVN1Mus musculus
R70LYEGLKANNVN1Rattus norvegicus
S12VLSIQSHVVRG3Bos taurus, Mus musculus, Rattus norvegicus
S12VLSIQSHVIRG1Homo sapiens
S12VLSIQSHTVQG1Arabidopsis thaliana
S187TVVITSSDLPS3Homo sapiens, Mus musculus, Rattus norvegicus
S187KVVITSITI--1Arabidopsis thaliana
S187TVVITSSDLLS1Bos taurus
T148VADIITPNQFE2Bos taurus, Mus musculus
T148LADIITPNQFE1Homo sapiens
T148LASMLTPNQFE1Arabidopsis thaliana
T148MADIITPNQFE1Rattus norvegicus
T186DTVVITSSDLP3Homo sapiens, Mus musculus, Rattus norvegicus
T186SKVVITSITI-1Arabidopsis thaliana
T186DTVVITSSDLL1Bos taurus
T233AVFVGTGDLFA3Homo sapiens, Bos taurus, Mus musculus
T233AYFTGTGDLMT1Arabidopsis thaliana
T233PVFVGTGDLFA1Rattus norvegicus
T47QFSNHTGYAHW3Homo sapiens, Mus musculus, Rattus norvegicus
T47QFSNHTGYPTF1Arabidopsis thaliana
V115YVCDPVMGDKW2Mus musculus, Rattus norvegicus
V115YVCDPVLGDKW1Homo sapiens
V115YVCDPVMGD--1Arabidopsis thaliana
V115YVCDPVMGDQR1Bos taurus
V19VVRGYVGNRAA3Bos taurus, Mus musculus, Rattus norvegicus
V19VIRGYVGNRAA1Homo sapiens
V19TVQGYVGNKSA1Arabidopsis thaliana
V201SDYLMALGSQR2Bos taurus, Rattus norvegicus
V201SNYLIVLGSQR1Homo sapiens
V201GGILLLIGSHQ1Arabidopsis thaliana
V201SDYLIALGSQR1Mus musculus
V226MDIRKVDAVFV1Homo sapiens
V226ILIHKIPAYFT1Arabidopsis thaliana
V226MEMHKVDAVFV1Bos taurus
V226MEMRKVEAVFV1Mus musculus
V226MEMRKVDPVFV1Rattus norvegicus
V231VDAVFVGTGDL2Homo sapiens, Bos taurus
V231IPAYFTGTGDL1Arabidopsis thaliana
V231VEAVFVGTGDL1Mus musculus
V231VDPVFVGTGDL1Rattus norvegicus
V41DAVNSVQFSNH4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
V41DPINSVQFSNH1Arabidopsis thaliana
V56HWKGQVLNSDE2Homo sapiens, Bos taurus
V56TFKGQVLNGQQ1Arabidopsis thaliana
V56HWKGQVLKSQE1Mus musculus
V56HWKGQVLTSQE1Rattus norvegicus
Y127GEGSMYVPQDL2Mus musculus, Rattus norvegicus
Y127GEGSMYVPEDL1Homo sapiens
Y127-EGKLYVPEEL1Arabidopsis thaliana
Y127GEGAMYVPDDL1Bos taurus
Y66ELQELYEGLRL1Homo sapiens
Y66QLCDLIEGLEA1Arabidopsis thaliana
Y66ELHELYEGLKV1Mus musculus
Y66ELHALYEGLKA1Rattus norvegicus
Y84YVLTGYTRDKS4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Y84HVLTGYIGSVS1Arabidopsis thaliana

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