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:ZNF451

Protein Summary

Gene summary

Gene name: ZNF451
ASpdb.0 ID: 26036
	Gene
Gene symbol	ZNF451
Gene ID	26036
Gene name	zinc finger protein 451
Synonyms	COASTER\|ZATT\|dJ417I1.1
Cytomap	6p12.1
Type of gene	protein-coding
Description	E3 SUMO-protein ligase ZNF451E3 SUMO-protein transferase ZNF451coactivator for steroid receptorszinc finger protein associated with TDP2 and TOP2
Modification date	20240403
UniProtAcc	Q9Y4E5

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	ZNF451	GO:0005634	nucleus	24324267
Gene	ZNF451	GO:0016605	PML body	36373674
Gene	ZNF451	GO:0016925	protein sumoylation	26524494
Gene	ZNF451	GO:0061665	SUMO ligase activity	26524494
Gene	ZNF451	GO:0140416	transcription regulator inhibitor activity	24324267

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
Q9Y4E5-1	Q9Y4E5-1_5d2m_G.pdb	5D2M	X-ray	2.4	G	30	50

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

Q9Y4E5

ZNF451

Q9Y4E5-1

Q9Y4E5-4

1061

559

1061

Substitution

ENIKRKDHIDYQKDKVALTLARLARHVEVEKQQKEEKNRAFREKIDFQHAHGLQELEFIRGHSDTEAARLCVDQWLKMPGLKTGTINCGTKSSFRRGGHTWVSGKPILCPIMHCNKEFDNGHLLLGHLKRFDHSPCDPTITLHGPFFSSFACVVCYKKFVTQQQYRDHLFDKEATDDGHNNNLLPQIIQCFACPNCFLLFSRKEECSKHMSGKNHFHQSFKLGDNKGIAHPISFPSFAKKLLISLCKDVPFQVKCVACHKTLRSHMELTAHFRVHCRNAGPVAVAEKSITQVAEKFILRGYCPDCNQVFVDETSTQNHKQNSGHKVRVINSVEESVLLYCHSSEGNKDPSSDLHLLLDQSKFSSLKRTMSIKESSSLECIAIPKKKMNLKDKSHEGVACVQKEKSVVKTWFCECNQRFPSEDAVEKHVFSANTMGYKCVVCGKVCDDSGVIRLHMSRIHGGAHLNNFLFWCRTCKKELTRKDTIMAHVTEFHNGHRYFYEMDEVEGETLPSSSTTLDNLTANKPSSAITVIDHSPANSSPRGKWQCRICEDMFDSQEYVKQHCMSLASHKFHRYSCAHCRKPFHKIETLYRHCQDEHDNEIKIKYFCGLCDLIFNVEEAFLSHYEEHHSIDYVFVSEKTETSIKTEDDFPVIETSNQLTCGCRESYICKVNRKEDYSRCLQIMLDKGKLWFRCSLCSATAQNLTDMNTHIHQVHKEKSDEEEQQYVIKCGTCTKAFHDPESAQQHFHRKHCFLQKPSVAHFGSEKSNLYKFTASASHTERKLKQAINYSKSLDMEKGVENDLSYQNIEEEIVELPDLDYLRTMTHIVFVDFDNWSNFFGHLPGHLNQGTFIWGFQGGNTNWKPPLNCKIYNYLNRIGCFFLHPRCSKRKDAADFAICMHAGRLDEQLPKQIPFTILSGDQGFLELENQFKKTQRPAHILNPHHLEGDMMCALLNSISDTTKECDSDDNMGAKNTSIGEEFISTEDVELEEAIRRSLEEM

RMPESKVPSSENHRPEMCSSCNVPLPIGDSSSFSGSCSSSPERIVSQTSSVENPLENQKNDQNNSDTKISETETLKSSQNFQTLPSSPLLVPQESLASSEVKENLRIDSSSASQHGRDAILYLQTQVAEMSRVIRDLQSRSCFRFHHSRPSENSSVPWDISTSKEENLSTVEEETDYKSPSADDKGQPSDPSQSSFTGLLKRMEQRGVIKRVTLQSEAESCEGKPDCVTSKKRLVPPLHPLLRIATTEVFKDPADCHPSSFMGHRVYPVAKDTSPFQPNPPAEGPIVEALEHSKRGNTTSPLDSTSKEMEVMGCRFYHAASIAARAASYMAYMTQYQRKLWEDMEDLVHDPEFDRGKARCIISDGMDAGLWQLCTTRDIMDSVVRVMAMAIDYRRQAWLRLTSLTKKTQEKISHLPFDGTSLFGQDVKAVVAEDNNIKENDYKDHKYYNQHRYFYSHDQKAHYHNRGYSKGDWYKPRNHPYRYRKKGDSPERHGYKN

559

Multiple sequence alignment of our canonical and alternatively spliced ZNF451

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of ZNF451

UniProt-id	ENSG	ENST	ENSP
Q9Y4E5-1	ENSG00000112200.17	ENST00000370706.9	ENSP00000359740.4
Q9Y4E5-4	ENSG00000112200.17	ENST00000370708.8	ENSP00000359742.4

UniProt-id	NM ID	NP ID
Q9Y4E5-1	NM_001031623.2	NP_001026794.1

Amino acid sequences of our canonical and alternatively spliced ZNF451

accession_id	Protein sequence
Q9Y4E5-1	MGDPGSEIIESVPPAGPEASESTTDENEDDIQFVSEGPLRPVLEYIDLVSSDDEEPSTSYTDENIKRKDHIDYQKDKVALTLARLARHVE VEKQQKEEKNRAFREKIDFQHAHGLQELEFIRGHSDTEAARLCVDQWLKMPGLKTGTINCGTKSSFRRGGHTWVSGKPILCPIMHCNKEF DNGHLLLGHLKRFDHSPCDPTITLHGPFFSSFACVVCYKKFVTQQQYRDHLFDKEATDDGHNNNLLPQIIQCFACPNCFLLFSRKEECSK HMSGKNHFHQSFKLGDNKGIAHPISFPSFAKKLLISLCKDVPFQVKCVACHKTLRSHMELTAHFRVHCRNAGPVAVAEKSITQVAEKFIL RGYCPDCNQVFVDETSTQNHKQNSGHKVRVINSVEESVLLYCHSSEGNKDPSSDLHLLLDQSKFSSLKRTMSIKESSSLECIAIPKKKMN LKDKSHEGVACVQKEKSVVKTWFCECNQRFPSEDAVEKHVFSANTMGYKCVVCGKVCDDSGVIRLHMSRIHGGAHLNNFLFWCRTCKKEL TRKDTIMAHVTEFHNGHRYFYEMDEVEGETLPSSSTTLDNLTANKPSSAITVIDHSPANSSPRGKWQCRICEDMFDSQEYVKQHCMSLAS HKFHRYSCAHCRKPFHKIETLYRHCQDEHDNEIKIKYFCGLCDLIFNVEEAFLSHYEEHHSIDYVFVSEKTETSIKTEDDFPVIETSNQL TCGCRESYICKVNRKEDYSRCLQIMLDKGKLWFRCSLCSATAQNLTDMNTHIHQVHKEKSDEEEQQYVIKCGTCTKAFHDPESAQQHFHR KHCFLQKPSVAHFGSEKSNLYKFTASASHTERKLKQAINYSKSLDMEKGVENDLSYQNIEEEIVELPDLDYLRTMTHIVFVDFDNWSNFF GHLPGHLNQGTFIWGFQGGNTNWKPPLNCKIYNYLNRIGCFFLHPRCSKRKDAADFAICMHAGRLDEQLPKQIPFTILSGDQGFLELENQ
Q9Y4E5-4	MGDPGSEIIESVPPAGPEASESTTDENEDDIQFVSEGPLRPVLEYIDLVSSDDEEPSTSYTDRMPESKVPSSENHRPEMCSSCNVPLPIG DSSSFSGSCSSSPERIVSQTSSVENPLENQKNDQNNSDTKISETETLKSSQNFQTLPSSPLLVPQESLASSEVKENLRIDSSSASQHGRD AILYLQTQVAEMSRVIRDLQSRSCFRFHHSRPSENSSVPWDISTSKEENLSTVEEETDYKSPSADDKGQPSDPSQSSFTGLLKRMEQRGV IKRVTLQSEAESCEGKPDCVTSKKRLVPPLHPLLRIATTEVFKDPADCHPSSFMGHRVYPVAKDTSPFQPNPPAEGPIVEALEHSKRGNT TSPLDSTSKEMEVMGCRFYHAASIAARAASYMAYMTQYQRKLWEDMEDLVHDPEFDRGKARCIISDGMDAGLWQLCTTRDIMDSVVRVMA MAIDYRRQAWLRLTSLTKKTQEKISHLPFDGTSLFGQDVKAVVAEDNNIKENDYKDHKYYNQHRYFYSHDQKAHYHNRGYSKGDWYKPRN

Protein Functional Features

Main function of this protein. (from UniProt)

ZNF451 (go to UniProt):Q9Y4E5

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
Q9Y4E5	Zinc finger	169	195	Note=C2H2-type 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042	Type=Substitution;Start=63;End=1061
Q9Y4E5	Zinc finger	253	277	Note=C2H2-type 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042	Type=Substitution;Start=63;End=1061
Q9Y4E5	Zinc finger	315	337	Note=C2H2-type 3;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042	Type=Substitution;Start=63;End=1061
Q9Y4E5	Zinc finger	362	386	Note=C2H2-type 4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042	Type=Substitution;Start=63;End=1061
Q9Y4E5	Zinc finger	498	521	Note=C2H2-type 5;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042	Type=Substitution;Start=63;End=1061
Q9Y4E5	Zinc finger	531	554	Note=C2H2-type 6;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042	Type=Substitution;Start=63;End=1061
Q9Y4E5	Zinc finger	606	631	Note=C2H2-type 7%3B atypical;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042	Type=Substitution;Start=63;End=1061
Q9Y4E5	Zinc finger	636	659	Note=C2H2-type 8;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042	Type=Substitution;Start=63;End=1061
Q9Y4E5	Zinc finger	667	690	Note=C2H2-type 9;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042	Type=Substitution;Start=63;End=1061
Q9Y4E5	Zinc finger	753	776	Note=C2H2-type 10;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042	Type=Substitution;Start=63;End=1061
Q9Y4E5	Zinc finger	789	812	Note=C2H2-type 11;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00042	Type=Substitution;Start=63;End=1061
Q9Y4E5	Region	1	344	Note=Important for interaction with SUMO1 and SUMO2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18656483;Dbxref=PMID:18656483	Type=Substitution;Start=63;End=1061
Q9Y4E5	Region	1	246	Note=Sufficient for E3 SUMO-protein ligase activity;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26524493;Dbxref=PMID:26524493	Type=Substitution;Start=63;End=1061
Q9Y4E5	Region	168	525	Note=Important for interaction with SMAD4;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:24324267;Dbxref=PMID:24324267	Type=Substitution;Start=63;End=1061
Q9Y4E5	Region	1050	1061	Note=Important for ubiquitin binding;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18656483;Dbxref=PMID:18656483	Type=Substitution;Start=63;End=1061

Gene Isoform Structures and Expression Levels for ZNF451

Gene structures of our canonical and alternative spliced genes of ZNF451
* 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 Q9Y4E5-1

3D view using mol* of Q9Y4E5-4

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 Q9Y4E5-1

pLDDT distribution across the protein length of Q9Y4E5-4

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 Q9Y4E5-1

Ramachandran plot of Q9Y4E5-4

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
Q9Y4E5-1	1.013	128	1.045	429.779	0.609	0.693	0.929	0.709	0.953	0.744	0.802	214,215,216,227,244,245,246,247,248,249,297,298,29 9,302,303,306,363,368,403,404,405,406,407,408,409, 411,414,415,418,419
Q9Y4E5-4	0.9	83	0.923	181.447	0.698	0.609	0.743	0.35	0.916	0.382	1.528	208,209,210,211,212,310,311,313,314,317,318,319,32 0,321,322,323,324,326,380,447

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 Q9Y4E5-1_Q9Y4E5-1_5d2m_G.pdb

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

3D view using mol* of Q9Y4E5-1_5d2m_G_Q9Y4E5-4.pdb

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

3D view using mol* of Q9Y4E5-1_Q9Y4E5-4.pdb

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

./stats/secondary_structure/figure/Q9Y4E5-1_vs_Q9Y4E5-4.png

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

./stats/relative_asa/Q9Y4E5-1_vs_Q9Y4E5-4.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
Q9Y4E5	Region	1	344	Note=Important for interaction with SUMO1 and SUMO2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:18656483;Dbxref=PMID:18656483	Type=Substitution;Start=63;End=1061
Q9Y4E5	Region	168	525	Note=Important for interaction with SMAD4;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:24324267;Dbxref=PMID:24324267	Type=Substitution;Start=63;End=1061

Interactors from STRING.

Gene name

Interactors

Related Drugs to ZNF451

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to ZNF451

Previous studies relating to the alternative splicing of ZNF451 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in ZNF451

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance