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ESD

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Summary

ESD (esterase D, HGNC:3465) is a protein-coding gene on chromosome 13q14.2, encoding S-formylglutathione hydrolase (P10768). Serine hydrolase involved in the detoxification of formaldehyde.

This gene encodes a serine hydrolase that belongs to the esterase D family. The encoded enzyme is active toward numerous substrates including O-acetylated sialic acids, and it may be involved in the recycling of sialic acids. This gene is used as a genetic marker for retinoblastoma and Wilson’s disease.

Source: NCBI Gene 2098 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 43 total
  • Druggable target: yes
  • MANE Select transcript: NM_001984

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:3465
Approved symbolESD
Nameesterase D
Location13q14.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000139684
Ensembl biotypeprotein_coding
OMIM133280
Entrez2098

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 26 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000378697, ENST00000378720, ENST00000412582, ENST00000471867, ENST00000495654, ENST00000898788, ENST00000898789, ENST00000898790, ENST00000898791, ENST00000898792, ENST00000898793, ENST00000898794, ENST00000898795, ENST00000898796, ENST00000898797, ENST00000898798, ENST00000898799, ENST00000898800, ENST00000898801, ENST00000898802, ENST00000898803, ENST00000898804, ENST00000898805, ENST00000928760, ENST00000928761, ENST00000961015, ENST00000961016

RefSeq mRNA: 1 — MANE Select: NM_001984 NM_001984

CCDS: CCDS9404

Canonical transcript exons

ENST00000378720 — 10 exons

ExonStartEnd
ENSE000012063844677993546780033
ENSE000012064084679339746793444
ENSE000012431844679710546797161
ENSE000013742164677745646777623
ENSE000014784884677125646771496
ENSE000035058964678425246784350
ENSE000035829894678149646781615
ENSE000035830014678266746782791
ENSE000036446724678702146787109
ENSE000036572374679134646791420

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.06.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 99.6282 / max 1561.5565, expressed in 1819 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
13722295.23091819
1372234.39721621

Top tissues by expression

295 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
blood vessel layerUBERON:000479799.06gold quality
popliteal arteryUBERON:000225098.98gold quality
tibial arteryUBERON:000761098.98gold quality
descending thoracic aortaUBERON:000234598.95gold quality
hair follicleUBERON:000207398.93gold quality
germinal epithelium of ovaryUBERON:000130498.89gold quality
aortaUBERON:000094798.88gold quality
right coronary arteryUBERON:000162598.83gold quality
adrenal tissueUBERON:001830398.83gold quality
choroid plexus epitheliumUBERON:000391198.81gold quality
cranial nerve IIUBERON:000094198.80gold quality
ganglionic eminenceUBERON:000402398.78gold quality
mucosa of stomachUBERON:000119998.77gold quality
pigmented layer of retinaUBERON:000178298.77gold quality
saphenous veinUBERON:000731898.76gold quality
thoracic aortaUBERON:000151598.75gold quality
ventricular zoneUBERON:000305398.74gold quality
ascending aortaUBERON:000149698.73gold quality
cauda epididymisUBERON:000436098.70gold quality
left coronary arteryUBERON:000162698.67gold quality
superficial temporal arteryUBERON:000161498.66gold quality
coronary arteryUBERON:000162198.66gold quality
smooth muscle tissueUBERON:000113598.59gold quality
urethraUBERON:000005798.58gold quality
parietal pleuraUBERON:000240098.49gold quality
heart right ventricleUBERON:000208098.47gold quality
endocervixUBERON:000045898.46gold quality
rectumUBERON:000105298.45gold quality
body of uterusUBERON:000985398.44gold quality
cortical plateUBERON:000534398.39gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-HCAD-4yes69.77
E-MTAB-10287yes45.09
E-MTAB-10042yes14.43
E-CURD-122yes5.25
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYC

miRNA regulators (miRDB)

12 targeting ESD, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-3163100.0077.238605
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-205299.7969.372031
HSA-MIR-608399.4768.732393
HSA-MIR-892C-5P99.1670.562116
HSA-MIR-7854-3P99.0866.261117
HSA-MIR-129-1-3P98.8668.41779
HSA-MIR-129-2-3P98.8668.41779
HSA-MIR-425797.8668.051190
HSA-MIR-625-3P97.3266.55554

Literature-anchored findings (GeneRIF, showing 6)

  • The analysis involved the data on nine polymorphic codominant loci: HP, GC, TF, PI, PGM1, GLO1, C3, ACP1, and ESD. The loci were selected by significance of differences in genotype frequencies between tuberculosis patients and healthy controls (PMID:12942785)
  • Autoantibodies to EsteD and BB-CK produced in experimental autoimmune uveoretinitis -induced mice were also detected in some endogenous uveitis patients, suggesting that these proteins might be autoantigens. (PMID:18552983)
  • catalytic triad residues–Ser-153, His264, and Asp230–involved in catalysis. Mutagenesis of any of the catalytic triad residues to alanine abolished the enzyme activity. Backbone amides of Leu54 & Met150 are involved in the formation of the oxyanion hole (PMID:19126594)
  • Abhydrolase domain-containing protein 11 and Esterase D predict the development of distant metastases and the presence of aggressive lung adenocarcinomas. (PMID:21596165)
  • rs7996797 located on chr13q14.1-q14.2 near the ESD gene was the most significantly associated with hallux valgus in females in genome-wide association meta-analyses. (PMID:26337638)
  • Esterase D interacts with metallothionein 2A and inhibits the migration of A549 lung cancer cells in vitro. (PMID:36649442)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioesdENSDARG00000019496
mus_musculusEsdENSMUSG00000021996
rattus_norvegicusEsdENSRNOG00000009512
drosophila_melanogasterCG4390FBGN0038771
caenorhabditis_elegansY48G10A.1WBGENE00013018

Protein

Protein identifiers

S-formylglutathione hydrolase — P10768 (reviewed: P10768)

Alternative names: Esterase D, Methylumbelliferyl-acetate deacetylase

All UniProt accessions (5): P10768, A0A140VJJ2, H7BZT7, U3KQT1, X6RA14

UniProt curated annotations — full annotation on UniProt →

Function. Serine hydrolase involved in the detoxification of formaldehyde.

Subunit / interactions. Homodimer.

Subcellular location. Cytoplasm. Cytoplasmic vesicle.

Polymorphism. There are two major electrophoretic isotypes. The sequence of the ESD*1 variant is shown.

Similarity. Belongs to the esterase D family.

RefSeq proteins (1): NP_001975* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000801Esterase-likeFamily
IPR014186S-formylglutathione_hydrolFamily
IPR029058AB_hydrolase_foldHomologous_superfamily

Pfam: PF00756

Catalyzed reactions (Rhea), 2 shown:

  • 4-methylumbelliferyl acetate + H2O = 4-methylumbelliferone + acetate + H(+) (RHEA:12208)
  • S-formylglutathione + H2O = formate + glutathione + H(+) (RHEA:14961)

UniProt features (44 total): helix 14, strand 10, mutagenesis site 8, active site 3, modified residue 3, turn 2, sequence variant 2, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
3FCXX-RAY DIFFRACTION1.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P10768-F198.280.99

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (3): 149 (charge relay system); 226 (charge relay system); 260 (charge relay system)

Post-translational modifications (3): 2, 4, 200

Mutagenesis-validated functional residues (8):

PositionPhenotype
5483% of wild-type activity.
149loss of activity.
1491.3% of wild-type activity.
15062% increase in activity.
2264.3% of wild-type activity.
2269% of wild-type activity.
2603% of wild-type activity.
2601.3% of wild-type activity.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-156590Glutathione conjugation

MSigDB gene sets: 201 (showing top): MORF_DNMT1, REACTOME_BIOLOGICAL_OXIDATIONS, GCM_NPM1, MORF_RRM1, GOBP_ALDEHYDE_CATABOLIC_PROCESS, HSIAO_HOUSEKEEPING_GENES, DARWICHE_SKIN_TUMOR_PROMOTER_UP, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_UP, KYNG_DNA_DAMAGE_DN, KYNG_DNA_DAMAGE_BY_4NQO, DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP, MORF_HDAC2, HNF1_Q6, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND

GO Biological Process (1): formaldehyde catabolic process (GO:0046294)

GO Molecular Function (7): hydrolase activity, acting on ester bonds (GO:0016788), S-formylglutathione hydrolase activity (GO:0018738), identical protein binding (GO:0042802), methylumbelliferyl-acetate deacetylase activity (GO:0047374), carboxylic ester hydrolase activity (GO:0052689), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (5): endoplasmic reticulum lumen (GO:0005788), cytosol (GO:0005829), cytoplasmic vesicle (GO:0031410), extracellular exosome (GO:0070062), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Phase II - Conjugation of compounds1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm2
cellular anatomical structure2
small molecule catabolic process1
aldehyde catabolic process1
formaldehyde metabolic process1
cellular detoxification of aldehyde1
hydrolase activity1
thiolester hydrolase activity1
protein binding1
deacetylase activity1
carboxylic ester hydrolase activity1
hydrolase activity, acting on ester bonds1
binding1
catalytic activity1
endoplasmic reticulum1
intracellular organelle lumen1
intracellular vesicle1
extracellular vesicle1
intracellular anatomical structure1

Protein interactions and networks

STRING

1664 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ESDCES5AQ6NT32923
ESDCES2O00748868
ESDCES3Q6UWW8860
ESDADH5P11766847
ESDCES1P23141791
ESDPGM1P36871777
ESDHAGHQ16775756
ESDNDUFAB1O14561721
ESDPGDP52209720
ESDSLC30A4O14863713
ESDGLO1P78375662
ESDLPAP08519638
ESDCPP00450634
ESDTFPIP10646588
ESDACP1P24666583

IntAct

52 interactions, top by confidence:

ABTypeScore
FSD2ESDpsi-mi:“MI:0915”(physical association)0.870
ESDFSD2psi-mi:“MI:0915”(physical association)0.870
ESDESDpsi-mi:“MI:0915”(physical association)0.740
TK2psi-mi:“MI:0915”(physical association)0.400
ESDPLCG2psi-mi:“MI:0915”(physical association)0.370
ESDCRKpsi-mi:“MI:0915”(physical association)0.370
OTUB1EPM2Apsi-mi:“MI:0914”(association)0.350
KSR1FBLL1psi-mi:“MI:0914”(association)0.350
CAV1PPM1Gpsi-mi:“MI:0914”(association)0.350
CAV1ACOT7psi-mi:“MI:0914”(association)0.350
MAP3K7ACOT7psi-mi:“MI:0914”(association)0.350
RIPK4TBCApsi-mi:“MI:0914”(association)0.350
MYLKACOT7psi-mi:“MI:0914”(association)0.350
MYLK4AP3D1psi-mi:“MI:0914”(association)0.350
CDKL3psi-mi:“MI:0914”(association)0.350
PRKD2ACOT7psi-mi:“MI:0914”(association)0.350
DDA1PGK1psi-mi:“MI:0914”(association)0.350
ACTR2psi-mi:“MI:0914”(association)0.350
ESDPIKFYVEpsi-mi:“MI:0914”(association)0.350
MBNL1SAP30psi-mi:“MI:0914”(association)0.350
SAR1BUBA6psi-mi:“MI:0914”(association)0.350
FSD2MID1psi-mi:“MI:0914”(association)0.350
FSD2MYO9Apsi-mi:“MI:0914”(association)0.350
VCAM1psi-mi:“MI:0914”(association)0.350

BioGRID (93): ESD (Two-hybrid), FSD2 (Two-hybrid), ESD (Co-fractionation), ESD (Co-fractionation), ESD (Co-fractionation), ESD (Co-fractionation), ESD (Co-fractionation), ESD (Co-fractionation), ESD (Co-fractionation), ESD (Co-fractionation), ESD (Co-fractionation), ESD (Co-fractionation), ESD (Co-fractionation), ESD (Co-fractionation), ESD (Co-fractionation)

ESM2 similar proteins: A0A0H2URB1, A1A834, A1AD14, A1AXZ2, A7ZIA3, A7ZNX7, A7ZX03, A8A215, A8FRR2, B0BNE5, B1IYB5, B1J086, B1LIP0, B1LKQ1, B1X7P2, B1XEU8, B4S5S1, P10768, P23553, P29368, P33018, P36838, P40363, P44556, P46544, P51025, P63731, P63732, P76049, P94388, Q08E20, Q0T2X0, Q0TFT6, Q0TKS8, Q1R9R8, Q1RFI8, Q31YW2, Q32EQ3, Q3Z052, Q3Z551

Diamond homologs: A1A834, A1AD14, A1AXZ2, A7ZIA3, A7ZNX7, A7ZX03, A8A215, B0BNE5, B1IYB5, B1J086, B1LIP0, B1LKQ1, B1X7P2, B1XEU8, P10768, P33018, P40363, P44556, P51025, Q08E20, Q0T2X0, Q0TFT6, Q0TKS8, Q1R9R8, Q1RFI8, Q31YW2, Q32EQ3, Q3Z052, Q3Z551, Q8FFU3, Q8FKG2, Q8LAS8, Q8X5J5, Q8X635, Q9GJT2, Q9R0P3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

43 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance34
Likely benign0
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1302 predictions. Top by Δscore:

VariantEffectΔscore
13:46777447:AATAC:Adonor_loss1.0000
13:46777448:ATACT:Adonor_loss1.0000
13:46777449:TACTT:Tdonor_loss1.0000
13:46777450:ACT:Adonor_loss1.0000
13:46777451:C:CGdonor_loss1.0000
13:46777452:TT:Tdonor_loss1.0000
13:46777453:TGC:Tdonor_loss1.0000
13:46777455:CCT:Cdonor_gain1.0000
13:46777619:TAAGC:Tacceptor_gain1.0000
13:46777620:AAGC:Aacceptor_gain1.0000
13:46777621:AGC:Aacceptor_gain1.0000
13:46777621:AGCCT:Aacceptor_loss1.0000
13:46777622:GC:Gacceptor_gain1.0000
13:46777623:CCTG:Cacceptor_gain1.0000
13:46777624:C:Aacceptor_loss1.0000
13:46777624:C:CCacceptor_gain1.0000
13:46777625:T:Gacceptor_loss1.0000
13:46777626:G:Cacceptor_gain1.0000
13:46777626:G:GCacceptor_gain1.0000
13:46780030:CAGA:Cacceptor_gain1.0000
13:46780034:C:CCacceptor_gain1.0000
13:46780037:C:CTacceptor_gain1.0000
13:46780038:A:Tacceptor_gain1.0000
13:46780043:C:CTacceptor_gain1.0000
13:46781494:A:ACdonor_gain1.0000
13:46781495:C:CCdonor_gain1.0000
13:46782662:ATTAC:Adonor_loss1.0000
13:46782663:TTAC:Tdonor_loss1.0000
13:46782664:TA:Tdonor_loss1.0000
13:46782665:A:Cdonor_loss1.0000

AlphaMissense

1864 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
13:46771485:A:CH260Q0.998
13:46771485:A:TH260Q0.998
13:46781552:A:GS149P0.998
13:46771487:G:CH260D0.997
13:46777540:A:CF228L0.996
13:46777540:A:TF228L0.996
13:46777542:A:GF228L0.996
13:46777548:C:GD226H0.996
13:46782733:A:CF105L0.996
13:46782733:A:TF105L0.996
13:46782735:A:GF105L0.996
13:46784256:G:CS84R0.996
13:46784256:G:TS84R0.996
13:46784258:T:GS84R0.996
13:46777523:A:GL234S0.995
13:46777547:T:AD226V0.995
13:46777557:C:AG223W0.995
13:46781557:C:TG147D0.995
13:46784340:G:CC56W0.995
13:46777466:C:GR253P0.994
13:46781545:C:TG151E0.994
13:46781553:G:CH148Q0.994
13:46781553:G:TH148Q0.994
13:46781555:G:CH148D0.994
13:46784347:A:GL54S0.994
13:46784350:C:TG53D0.994
13:46787021:C:GG53R0.994
13:46777557:C:GG223R0.993
13:46777557:C:TG223R0.993
13:46780007:G:CC176W0.993

dbSNP variants (sampled 300 via entrez): RS1000401908 (13:46791434 G>C), RS1000408001 (13:46798723 A>C,G), RS1000455072 (13:46784546 C>T), RS1000465190 (13:46798099 G>A), RS1000526282 (13:46784187 A>G), RS1000703416 (13:46777828 C>A), RS1000752977 (13:46791774 T>C), RS1000810591 (13:46796215 C>A), RS1000926398 (13:46795821 C>T), RS1001293655 (13:46788062 T>C), RS1001342004 (13:46772969 C>G,T), RS1001560700 (13:46773454 A>C), RS1001638335 (13:46780345 A>C,G), RS1001807038 (13:46792288 A>G), RS1002022692 (13:46799364 A>G)

Disease associations

OMIM: gene MIM:133280 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

StudyTraitp-value
GCST006585_2486Blood protein levels1.000000e-07
GCST009391_713Metabolite levels9.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0010531S-adenosylhomocysteine measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2189130 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

3 potent at pChembl≥5 of 3 total, top 3 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
9.10Kd0.8nMCHEMBL4635246
6.93Kd116.5nMCHEMBL5653589
6.93ED50116.5nMCHEMBL5653589

PubChem BioAssay actives

2 with measured affinity, of 16 total; 2 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-chloro-2-(3-phenyl-2-pyridin-2-yl-3,4-dihydropyrazol-5-yl)phenol1662249: Binding affinity to human ESD expressed in HEK293T cells assessed as dissociation constantkd0.0008uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148341: Binding affinity to human ESD incubated for 45 mins by Kinobead based pull down assaykd0.1164uM

CTD chemical–gene interactions

59 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Cadmium Chlorideincreases abundance, increases expression, decreases expression4
bisphenol Adecreases expression, increases expression3
sodium arseniteincreases abundance, increases expression, decreases expression3
Valproic Acidaffects expression, increases expression3
Cadmiumdecreases expression, increases abundance, increases expression2
aristolochic acid Idecreases expression, increases expression1
bisphenol Fincreases expression1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
beta-lapachoneincreases expression1
arseniteaffects binding, increases reaction1
methylparabendecreases expression1
perfluorooctanoic acidincreases expression1
sulindac sulfideincreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
microcystin RRdecreases expression1
glycidamideincreases expression1
K 7174decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
nutlin 3affects cotreatment, increases secretion1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
5-(2,4-dihydroxy-5-isopropylphenyl)-4-(4-morpholin-4-ylmethylphenyl)isoxazole-3-carboxylic acid ethylamideincreases expression1
STA 9090increases expression1
jinfukangdecreases expression1
LDN 193189affects cotreatment, increases expression1
bisphenol AFincreases expression1
Temozolomidedecreases expression1

ChEMBL screening assays

15 unique, capped per target: 15 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL2209086BindingInhibition of ESD binding to FP-biotin in [12C][14N]-lysine, arginine and [13C6][15N2]-lysine, arginine labeled HEK293T cells at 20 uM after 1 hr by isotopic activity-based protein profiling-MudPIT assayDiscovery and optimization of sulfonyl acrylonitriles as selective, covalent inhibitors of protein phosphatase methylesterase-1. — J Med Chem

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B2WQAbcam HEK293T ESD KOTransformed cell lineFemale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
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Sources 78

This page pulls from 78 datasets indexed by BioBTree:

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