ASpdb: an integrative knowledgebase of human protein isoforms from experimental and AI-predicted structures

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	Protein Summary
	AS Summary
	Protein Functional Features
	Gene Isoform Structures and Expression Levels
	Protein Structures
	pLDDT Score Distribution
	Ramachandran Plot of Protein Structures
	Potential Active Site Information
	Protein Structure and Feature Comparision
	Protein-Protein Interaction
	Related Drugs
	Related Diseases
	Clinically Important Variants

Protein:ECE1

Protein Summary

Gene summary

Gene name: ECE1
ASpdb.0 ID: 1889
	Gene
Gene symbol	ECE1
Gene ID	1889
Gene name	endothelin converting enzyme 1
Synonyms	ECE
Cytomap	1p36.12
Type of gene	protein-coding
Description	endothelin-converting enzyme 1ECE-1
Modification date	20240407
UniProtAcc	P42892

Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Gene	ECE1	GO:0004175	endopeptidase activity	7805846\|18039931
Gene	ECE1	GO:0005768	endosome	18039931
Gene	ECE1	GO:0008270	zinc ion binding	18992253
Gene	ECE1	GO:0009897	external side of plasma membrane	9449382\|9710124
Gene	ECE1	GO:0010814	substance P catabolic process	18039931
Gene	ECE1	GO:0010815	bradykinin catabolic process	18039931
Gene	ECE1	GO:0010816	calcitonin catabolic process	18039931
Gene	ECE1	GO:0016020	membrane	7805846
Gene	ECE1	GO:0016485	protein processing	7805846
Gene	ECE1	GO:0016486	peptide hormone processing	7864876
Gene	ECE1	GO:0033093	Weibel-Palade body	9710124
Gene	ECE1	GO:0034959	endothelin maturation	7805846
Gene	ECE1	GO:0042447	hormone catabolic process	7864876
Gene	ECE1	GO:0048471	perinuclear region of cytoplasm	9710124

AS Summary

Information of the canonical protein with experimentally identified structure from PDB (2023).

UniProt Acc	File name	PDB ID	Method	Resolution	Chain	Start	End
P42892-1	P42892-1_3dwb_A.pdb	3DWB	X-ray	2.38	A	101	770

ASpdb's canonical and alternatively spliced isoform information.

accession_id

gene_name

canonical_id

alternative_id

canonical_length

alternative_length

canonical_start

canonical_end

type

originalSEQ

variationSEQ

alternative_start

alternative_end

P42892

ECE1

P42892-1

P42892-2

770

758

Substitution

MRGVWPPPVSALLSALGMSTYKRATLDEEDLVDSLSEGDAYPNG

MPLQGLGLQRNPFLQGKRGPGLTSSPPLLPPS

P42892

ECE1

P42892-1

P42892-3

770

754

Substitution

MRGVWPPPVSALLSALG

P42892

ECE1

P42892-1

P42892-4

770

767

Substitution

MRGVWPPPVSALLSALG

MEALRESVLHLALQ

Multiple sequence alignment of our canonical and alternatively spliced ECE1

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of ECE1

UniProt-id	ENSG	ENST	ENSP
P42892-1	ENSG00000117298.16	ENST00000374893.11	ENSP00000364028.6
P42892-2	ENSG00000117298.16	ENST00000357071.8	ENSP00000349581.4
P42892-3	ENSG00000117298.16	ENST00000415912.6	ENSP00000405088.2
P42892-4	ENSG00000117298.16	ENST00000264205.10	ENSP00000264205.6

UniProt-id	NM ID	NP ID
P42892-1	NM_001397.2	NP_001388.1
P42892-2	NM_001113347.1	NP_001106818.1
P42892-3	NM_001113348.1	NP_001106819.1
P42892-4	NM_001113349.1	NP_001106820.1

Amino acid sequences of our canonical and alternatively spliced ECE1

accession_id	Protein sequence
P42892-1	MRGVWPPPVSALLSALGMSTYKRATLDEEDLVDSLSEGDAYPNGLQVNFHSPRSGQRCWAARTQVEKRLVVLVVLLAAGLVACLAALGIQ YQTRSPSVCLSEACVSVTSSILSSMDPTVDPCHDFFSYACGGWIKANPVPDGHSRWGTFSNLWEHNQAIIKHLLENSTASVSEAERKAQV YYRACMNETRIEELRAKPLMELIERLGGWNITGPWAKDNFQDTLQVVTAHYRTSPFFSVYVSADSKNSNSNVIQVDQSGLGLPSRDYYLN KTENEKVLTGYLNYMVQLGKLLGGGDEEAIRPQMQQILDFETALANITIPQEKRRDEELIYHKVTAAELQTLAPAINWLPFLNTIFYPVE INESEPIVVYDKEYLEQISTLINTTDRCLLNNYMIWNLVRKTSSFLDQRFQDADEKFMEVMYGTKKTCLPRWKFCVSDTENNLGFALGPM FVKATFAEDSKSIATEIILEIKKAFEESLSTLKWMDEETRKSAKEKADAIYNMIGYPNFIMDPKELDKVFNDYTAVPDLYFENAMRFFNF SWRVTADQLRKAPNRDQWSMTPPMVNAYYSPTKNEIVFPAGILQAPFYTRSSPKALNFGGIGVVVGHELTHAFDDQGREYDKDGNLRPWW KNSSVEAFKRQTECMVEQYSNYSVNGEPVNGRHTLGENIADNGGLKAAYRAYQNWVKKNGAEHSLPTLGLTNNQLFFLGFAQVWCSVRTP
P42892-2	MPLQGLGLQRNPFLQGKRGPGLTSSPPLLPPSLQVNFHSPRSGQRCWAARTQVEKRLVVLVVLLAAGLVACLAALGIQYQTRSPSVCLSE ACVSVTSSILSSMDPTVDPCHDFFSYACGGWIKANPVPDGHSRWGTFSNLWEHNQAIIKHLLENSTASVSEAERKAQVYYRACMNETRIE ELRAKPLMELIERLGGWNITGPWAKDNFQDTLQVVTAHYRTSPFFSVYVSADSKNSNSNVIQVDQSGLGLPSRDYYLNKTENEKVLTGYL NYMVQLGKLLGGGDEEAIRPQMQQILDFETALANITIPQEKRRDEELIYHKVTAAELQTLAPAINWLPFLNTIFYPVEINESEPIVVYDK EYLEQISTLINTTDRCLLNNYMIWNLVRKTSSFLDQRFQDADEKFMEVMYGTKKTCLPRWKFCVSDTENNLGFALGPMFVKATFAEDSKS IATEIILEIKKAFEESLSTLKWMDEETRKSAKEKADAIYNMIGYPNFIMDPKELDKVFNDYTAVPDLYFENAMRFFNFSWRVTADQLRKA PNRDQWSMTPPMVNAYYSPTKNEIVFPAGILQAPFYTRSSPKALNFGGIGVVVGHELTHAFDDQGREYDKDGNLRPWWKNSSVEAFKRQT ECMVEQYSNYSVNGEPVNGRHTLGENIADNGGLKAAYRAYQNWVKKNGAEHSLPTLGLTNNQLFFLGFAQVWCSVRTPESSHEGLITDPH
P42892-3	MMSTYKRATLDEEDLVDSLSEGDAYPNGLQVNFHSPRSGQRCWAARTQVEKRLVVLVVLLAAGLVACLAALGIQYQTRSPSVCLSEACVS VTSSILSSMDPTVDPCHDFFSYACGGWIKANPVPDGHSRWGTFSNLWEHNQAIIKHLLENSTASVSEAERKAQVYYRACMNETRIEELRA KPLMELIERLGGWNITGPWAKDNFQDTLQVVTAHYRTSPFFSVYVSADSKNSNSNVIQVDQSGLGLPSRDYYLNKTENEKVLTGYLNYMV QLGKLLGGGDEEAIRPQMQQILDFETALANITIPQEKRRDEELIYHKVTAAELQTLAPAINWLPFLNTIFYPVEINESEPIVVYDKEYLE QISTLINTTDRCLLNNYMIWNLVRKTSSFLDQRFQDADEKFMEVMYGTKKTCLPRWKFCVSDTENNLGFALGPMFVKATFAEDSKSIATE IILEIKKAFEESLSTLKWMDEETRKSAKEKADAIYNMIGYPNFIMDPKELDKVFNDYTAVPDLYFENAMRFFNFSWRVTADQLRKAPNRD QWSMTPPMVNAYYSPTKNEIVFPAGILQAPFYTRSSPKALNFGGIGVVVGHELTHAFDDQGREYDKDGNLRPWWKNSSVEAFKRQTECMV EQYSNYSVNGEPVNGRHTLGENIADNGGLKAAYRAYQNWVKKNGAEHSLPTLGLTNNQLFFLGFAQVWCSVRTPESSHEGLITDPHSPSR
P42892-4	MEALRESVLHLALQMSTYKRATLDEEDLVDSLSEGDAYPNGLQVNFHSPRSGQRCWAARTQVEKRLVVLVVLLAAGLVACLAALGIQYQT RSPSVCLSEACVSVTSSILSSMDPTVDPCHDFFSYACGGWIKANPVPDGHSRWGTFSNLWEHNQAIIKHLLENSTASVSEAERKAQVYYR ACMNETRIEELRAKPLMELIERLGGWNITGPWAKDNFQDTLQVVTAHYRTSPFFSVYVSADSKNSNSNVIQVDQSGLGLPSRDYYLNKTE NEKVLTGYLNYMVQLGKLLGGGDEEAIRPQMQQILDFETALANITIPQEKRRDEELIYHKVTAAELQTLAPAINWLPFLNTIFYPVEINE SEPIVVYDKEYLEQISTLINTTDRCLLNNYMIWNLVRKTSSFLDQRFQDADEKFMEVMYGTKKTCLPRWKFCVSDTENNLGFALGPMFVK ATFAEDSKSIATEIILEIKKAFEESLSTLKWMDEETRKSAKEKADAIYNMIGYPNFIMDPKELDKVFNDYTAVPDLYFENAMRFFNFSWR VTADQLRKAPNRDQWSMTPPMVNAYYSPTKNEIVFPAGILQAPFYTRSSPKALNFGGIGVVVGHELTHAFDDQGREYDKDGNLRPWWKNS SVEAFKRQTECMVEQYSNYSVNGEPVNGRHTLGENIADNGGLKAAYRAYQNWVKKNGAEHSLPTLGLTNNQLFFLGFAQVWCSVRTPESS

Protein Functional Features

Main function of this protein. (from UniProt)

ECE1 (go to UniProt):P42892

Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
P42892	Topological domain	1	68	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=1;End=44
P42892	Topological domain	1	68	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=1;End=17
P42892	Topological domain	1	68	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Substitution;Start=1;End=17

Gene Isoform Structures and Expression Levels for ECE1

Gene structures of our canonical and alternative spliced genes of ECE1
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Expression levels of gene isoforms across GTEx.

Expression levels of gene isoforms across TCGA.

Protein Structures

PDB and CIF files of the predicted protein structures
* Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

3D view using mol* of P42892-1

3D view using mol* of P42892-2

3D view using mol* of P42892-3

3D view using mol* of P42892-4

pLDDT Score Distribution

pLDDT score distribution of the predicted protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

pLDDT distribution across the protein length of P42892-1

pLDDT distribution across the protein length of P42892-2

pLDDT distribution across the protein length of P42892-3

pLDDT distribution across the protein length of P42892-4

Ramachandran Plot of Protein Structures

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide.

Ramachandran plot of P42892-1

Ramachandran plot of P42892-2

Ramachandran plot of P42892-4

Potential Active Site Information

The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite.

UniProt-id	Site score	Size	D score	Volume	Exposure	Enclosure	Contact	Phobic	Philic	Balance	Don/Acc	Residues
P42892-1	1.056	100	1.106	266.168	0.578	0.714	0.941	0.748	0.807	0.928	1.141	106,107,110,111,113,114,133,137,146,148,151,152,15 5,585,586,589,592,596,600,709,712,713,715
P42892-2	1.065	97	1.111	217.119	0.515	0.743	0.978	1.024	0.799	1.281	0.564	462,463,466,469,633,657,660,661,663,664,665,667,66 8,671,695,730,733,734,735,736,754,755,756,757,758
P42892-3	1.052	96	1.084	258.965	0.536	0.752	1.019	0.928	0.883	1.051	0.727	87,90,91,94,95,97,98,117,121,132,135,136,139,568,5 69,570,572,573,575,576,580,581,693,696,697,699
P42892-4	1.039	122	1.042	365.295	0.579	0.757	1.014	0.65	1.079	0.602	0.862	100,104,107,108,110,111,130,134,145,148,149,452,45 3,454,457,580,581,582,583,585,586,587,588,589,593, 594,706,709,710,712

Protein Structure and Feature Comparision

Protein Structure Comparision Using Template Modeling Scores (TM-score).

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green)

3D view using mol* of P42892-1_P42892-1_3dwb_A.pdb

Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of P42892-1_3dwb_A_P42892-2.pdb

3D view using mol* of P42892-1_3dwb_A_P42892-3.pdb

3D view using mol* of P42892-1_3dwb_A_P42892-4.pdb

Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green)

3D view using mol* of P42892-1_P42892-2.pdb

3D view using mol* of P42892-1_P42892-3.pdb

3D view using mol* of P42892-1_P42892-4.pdb

Protein Feature Comparison of the protein sequendary structures among the protiens.

./stats/secondary_structure/figure/P42892-1_vs_P42892-2.png

./stats/secondary_structure/figure/P42892-1_vs_P42892-3.png

./stats/secondary_structure/figure/P42892-1_vs_P42892-4.png

Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.

./stats/relative_asa/P42892-1_vs_P42892-2.png

./stats/relative_asa/P42892-1_vs_P42892-3.png

./stats/relative_asa/P42892-1_vs_P42892-4.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id

Subsection

Start

End

Funcitonal feature

Splicing information

Interactors from STRING.

Gene name

Interactors

Related Drugs to ECE1

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
P42892	ECE1	DB07171	5-(2-hydroxyethyl)nonane-1,9-diol	experimental

Related Diseases to ECE1

Previous studies relating to the alternative splicing of ECE1 and disease information from the MeSH term (PubMed)

Gene	PMID	Title	Abstract	MeSH ID	MeSH term
ECE1	7695628	Cloning and sequencing of a human endothelin converting enzyme in renal adenocarcinoma (ACHN) cells producing endothelin-2.	Endothelin (ET)-2 is a 21 residue vasoactive peptide which is biosynthesized from big ET-2(1-38) by a specific cleavage at Trp21-Val22 with an ET converting enzyme (ECE). To identify an ECE in ACHN (human renal adenocarcinoma) cells which produce ET-2, we have cloned and sequenced a novel cDNA encoding a human ECE in ACHN (hAECE). It encodes a 770 amino acid protein with a zinc-binding motif and a single membrane spanning region. The sequences of nucleic acids and amino acids from Leu45 to Trp770 of hAECE are identical to those from Leu33 to Trp758 of a human ECE in HUVEC (hHECE). The sequences in the amino-terminal moiety are divergent between hAECE and hHECE. Based on the difference of the amino-terminal amino acid sequences, ECEs reported so far, can be classified into two isoforms. These results strongly suggest that an alternative splicing might occur in the 5'-terminal region of the ECE pre-mRNA.	D000230	Adenocarcinoma
ECE1	7695628	Cloning and sequencing of a human endothelin converting enzyme in renal adenocarcinoma (ACHN) cells producing endothelin-2.	Endothelin (ET)-2 is a 21 residue vasoactive peptide which is biosynthesized from big ET-2(1-38) by a specific cleavage at Trp21-Val22 with an ET converting enzyme (ECE). To identify an ECE in ACHN (human renal adenocarcinoma) cells which produce ET-2, we have cloned and sequenced a novel cDNA encoding a human ECE in ACHN (hAECE). It encodes a 770 amino acid protein with a zinc-binding motif and a single membrane spanning region. The sequences of nucleic acids and amino acids from Leu45 to Trp770 of hAECE are identical to those from Leu33 to Trp758 of a human ECE in HUVEC (hHECE). The sequences in the amino-terminal moiety are divergent between hAECE and hHECE. Based on the difference of the amino-terminal amino acid sequences, ECEs reported so far, can be classified into two isoforms. These results strongly suggest that an alternative splicing might occur in the 5'-terminal region of the ECE pre-mRNA.	D007680	Kidney Neoplasms

Clinically important variants in ECE1

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance