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

Home

Download

Statistics

Examples

Help

Contact

	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:IMPDH1

Protein Summary

Gene summary

Gene name: IMPDH1
ASpdb.0 ID: 3614
	Gene
Gene symbol	IMPDH1
Gene ID	3614
Gene name	inosine monophosphate dehydrogenase 1
Synonyms	IMPD\|IMPD1\|IMPDH-I\|LCA11\|RP10\|sWSS2608
Cytomap	7q32.1
Type of gene	protein-coding
Description	inosine-5'-monophosphate dehydrogenase 1IMP (inosine 5'-monophosphate) dehydrogenase 1IMP (inosine monophosphate) dehydrogenase 1IMPD 1IMPDH 1
Modification date	20240403
UniProtAcc	P20839

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	IMPDH1	GO:0003676	nucleic acid binding	14766016
Gene	IMPDH1	GO:0003677	DNA binding	14766016
Gene	IMPDH1	GO:0005634	nucleus	14766016
Gene	IMPDH1	GO:0005737	cytoplasm	14766016

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
P20839-1	P20839-1_1jcn_A.pdb	1JCN	X-ray	2.5	A	10	499

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

P20839

IMPDH1

P20839-1

P20839-2

514

489

108

Deletion

none

P20839

IMPDH1

P20839-1

P20839-3

514

563

Substitution

MEGPLTPPPLQGGGAAAVPEPGARQHPGHETAAQRYSARLLQAGYEPESM

P20839

IMPDH1

P20839-1

P20839-4

514

509

104

108

Deletion

none

103

P20839

IMPDH1

P20839-1

P20839-5

514

589

Substitution

MEGPLTPPPLQGGGAAAVPEPGARQHPGHETAAQRYSARLLQAGYEPESCFLLELSSVVLLAGVGVQMDRLRRASM

P20839

IMPDH1

P20839-1

P20839-6

514

599

Substitution

MEGPLTPPPLQGGGAAAVPEPGARQHPGHETAAQRYSARLLQAGYEPESPRLDLATHPTTPRSELSSVVLLAGVGVQMDRLRRASM

P20839

IMPDH1

P20839-1

P20839-7

514

566

Substitution

MADYLISGGTGYVPEDGLTAQQLFASADGLTYN

MEGPLTPPPLQGGGAAAVPEPGARQHPGHETAAQRYSARLLQAGYEPESPRLDLATHPTTPRSELSSVVLLAGVGVQMDRLRRAS

Multiple sequence alignment of our canonical and alternatively spliced IMPDH1

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of IMPDH1

UniProt-id	ENSG	ENST	ENSP
P20839-2	ENSG00000106348.19	ENST00000496200.5	ENSP00000420803.1
P20839-3	ENSG00000106348.19	ENST00000348127.11	ENSP00000265385.8
P20839-4	ENSG00000106348.19	ENST00000480861.5	ENSP00000420185.1
P20839-5	ENSG00000106348.19	ENST00000354269.9	ENSP00000346219.5
P20839-6	ENSG00000106348.19	ENST00000338791.11	ENSP00000345096.6
P20839-7	ENSG00000106348.19	ENST00000419067.6	ENSP00000399400.2

UniProt-id	NM ID	NP ID
P20839-1	NM_001142573.1	NP_001136045.1
P20839-2	NM_001142575.1	NP_001136047.1
P20839-3	NM_183243.2	NP_899066.1
P20839-4	NM_001142574.1	NP_001136046.1
P20839-5	NM_001102605.1	NP_001096075.1
P20839-6	NM_000883.3	NP_000874.2
P20839-7	NM_001142576.1	NP_001136048.1

Amino acid sequences of our canonical and alternatively spliced IMPDH1

accession_id	Protein sequence
P20839-1	MADYLISGGTGYVPEDGLTAQQLFASADGLTYNDFLILPGFIDFIADEVDLTSALTRKITLKTPLISSPMDTVTEADMAIAMALMGGIGF IHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLEAKMRHGFSGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMT PRIELVVAPAGVTLKEANEILQRSKKGKLPIVNDCDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDV IVLDSSQGNSVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGSICITQEVMACGRPQGTAVYKVAEYARRFGVP IIADGGIQTVGHVVKALALGASTVMMGSLLAATTEAPGEYFFSDGVRLKKYRGMGSLDAMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDK
P20839-2	MADYLISGGTGYVPEDGLTAQQLFASADGLTYNDFLILPGFIDFIADEVDLTSALTRKITLKTPLISSPMDTVTEADMAIAMAKFEQGFI TDPVVLSPSHTVGDVLEAKMRHGFSGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIELVVAPAGVTLKEANEILQRSK KGKLPIVNDCDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIVLDSSQGNSVYQIAMVHYIKQKYP HLQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGSICITQEVMACGRPQGTAVYKVAEYARRFGVPIIADGGIQTVGHVVKALALGASTVM MGSLLAATTEAPGEYFFSDGVRLKKYRGMGSLDAMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQKFVPYLIAGIQHGCQDIGARS
P20839-3	MEGPLTPPPLQGGGAAAVPEPGARQHPGHETAAQRYSARLLQAGYEPESMADYLISGGTGYVPEDGLTAQQLFASADGLTYNDFLILPGF IDFIADEVDLTSALTRKITLKTPLISSPMDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVL EAKMRHGFSGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIELVVAPAGVTLKEANEILQRSKKGKLPIVNDCDELVAI IARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIVLDSSQGNSVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAK NLIDAGVDGLRVGMGCGSICITQEVMACGRPQGTAVYKVAEYARRFGVPIIADGGIQTVGHVVKALALGASTVMMGSLLAATTEAPGEYF FSDGVRLKKYRGMGSLDAMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQKFVPYLIAGIQHGCQDIGARSLSVLRSMMYSGELKFE
P20839-4	MADYLISGGTGYVPEDGLTAQQLFASADGLTYNDFLILPGFIDFIADEVDLTSALTRKITLKTPLISSPMDTVTEADMAIAMALMGGIGF IHHNCTPEFQANEKFEQGFITDPVVLSPSHTVGDVLEAKMRHGFSGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIEL VVAPAGVTLKEANEILQRSKKGKLPIVNDCDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIVLDS SQGNSVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGSICITQEVMACGRPQGTAVYKVAEYARRFGVPIIADG GIQTVGHVVKALALGASTVMMGSLLAATTEAPGEYFFSDGVRLKKYRGMGSLDAMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQK
P20839-5	MEGPLTPPPLQGGGAAAVPEPGARQHPGHETAAQRYSARLLQAGYEPESCFLLELSSVVLLAGVGVQMDRLRRASMADYLISGGTGYVPE DGLTAQQLFASADGLTYNDFLILPGFIDFIADEVDLTSALTRKITLKTPLISSPMDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVR KVKKFEQGFITDPVVLSPSHTVGDVLEAKMRHGFSGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIELVVAPAGVTLK EANEILQRSKKGKLPIVNDCDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIVLDSSQGNSVYQIA MVHYIKQKYPHLQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGSICITQEVMACGRPQGTAVYKVAEYARRFGVPIIADGGIQTVGHVVK ALALGASTVMMGSLLAATTEAPGEYFFSDGVRLKKYRGMGSLDAMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQKFVPYLIAGIQ
P20839-6	MEGPLTPPPLQGGGAAAVPEPGARQHPGHETAAQRYSARLLQAGYEPESPRLDLATHPTTPRSELSSVVLLAGVGVQMDRLRRASMADYL ISGGTGYVPEDGLTAQQLFASADGLTYNDFLILPGFIDFIADEVDLTSALTRKITLKTPLISSPMDTVTEADMAIAMALMGGIGFIHHNC TPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLEAKMRHGFSGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIEL VVAPAGVTLKEANEILQRSKKGKLPIVNDCDELVAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIVLDS SQGNSVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGSICITQEVMACGRPQGTAVYKVAEYARRFGVPIIADG GIQTVGHVVKALALGASTVMMGSLLAATTEAPGEYFFSDGVRLKKYRGMGSLDAMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQK
P20839-7	MEGPLTPPPLQGGGAAAVPEPGARQHPGHETAAQRYSARLLQAGYEPESPRLDLATHPTTPRSELSSVVLLAGVGVQMDRLRRASDFLIL PGFIDFIADEVDLTSALTRKITLKTPLISSPMDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVG DVLEAKMRHGFSGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIELVVAPAGVTLKEANEILQRSKKGKLPIVNDCDEL VAIIARTDLKKNRDYPLASKDSQKQLLCGAAVGTREDDKYRLDLLTQAGVDVIVLDSSQGNSVYQIAMVHYIKQKYPHLQVIGGNVVTAA QAKNLIDAGVDGLRVGMGCGSICITQEVMACGRPQGTAVYKVAEYARRFGVPIIADGGIQTVGHVVKALALGASTVMMGSLLAATTEAPG EYFFSDGVRLKKYRGMGSLDAMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQKFVPYLIAGIQHGCQDIGARSLSVLRSMMYSGEL

Protein Functional Features

Main function of this protein. (from UniProt)

IMPDH1 (go to UniProt):P20839

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

Gene Isoform Structures and Expression Levels for IMPDH1

Gene structures of our canonical and alternative spliced genes of IMPDH1
* 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 P20839-1

3D view using mol* of P20839-2

3D view using mol* of P20839-3

3D view using mol* of P20839-4

3D view using mol* of P20839-5

3D view using mol* of P20839-6

3D view using mol* of P20839-7

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 P20839-1

pLDDT distribution across the protein length of P20839-2

pLDDT distribution across the protein length of P20839-3

pLDDT distribution across the protein length of P20839-4

pLDDT distribution across the protein length of P20839-5

pLDDT distribution across the protein length of P20839-6

pLDDT distribution across the protein length of P20839-7

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 P20839-1

Ramachandran plot of P20839-2

Ramachandran plot of P20839-3

Ramachandran plot of P20839-6

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
P20839-1	1.175	144	0.96	190.708	0.258	0.96	1.296	0.593	1.705	0.348	0.406	68,69,70,276,303,305,322,324,325,326,327,328,329,3 30,331,333,341,343,364,365,366,367,368,385,386,387 ,388,389,411,413,414,415,429,430,441,442
P20839-2	1.168	137	0.929	182.476	0.308	0.949	1.265	0.277	1.782	0.156	0.279	68,70,251,278,297,299,300,301,302,303,304,305,306, 308,312,339,340,341,342,343,360,361,362,363,364,38 6,388,389,390,404,405,416,417
P20839-3	1.175	153	0.951	192.08	0.261	0.96	1.318	0.506	1.734	0.292	0.353	117,118,119,325,352,371,373,374,375,376,377,378,37 9,380,382,413,414,415,416,417,434,435,436,437,438, 460,462,463,464,478,479,491
P20839-4	1.173	134	0.975	191.737	0.309	0.956	1.291	0.551	1.653	0.333	0.348	68,69,70,271,298,317,319,320,321,322,323,324,325,3 26,359,360,361,362,363,380,381,382,383,384,406,408 ,409,410,424,425,436,437
P20839-5	1.171	140	0.955	199.969	0.289	0.954	1.306	0.465	1.708	0.272	0.354	143,144,145,351,378,397,399,400,401,402,403,404,40 5,406,408,439,440,441,442,443,460,461,462,463,464, 486,488,489,490,504,505,517
P20839-6	1.176	139	0.943	183.848	0.319	0.961	1.302	0.357	1.76	0.203	0.467	153,154,155,361,388,407,409,410,411,412,413,414,41 5,416,418,449,450,451,452,453,470,471,472,473,474, 496,498,499,500,514,515,526,527
P20839-7	1.098	193	0.936	311.444	0.408	0.845	1.071	0.439	1.567	0.28	0.46	83,84,85,120,121,122,328,355,374,376,377,378,379,3 80,381,382,383,385,386,394,395,399,415,416,417,418 ,419,420,424,428,437,438,439,440,441,463,465,466,4 67,481,482,493,494

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 P20839-1_P20839-1_1jcn_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 P20839-1_1jcn_A_P20839-2.pdb

3D view using mol* of P20839-1_1jcn_A_P20839-3.pdb

3D view using mol* of P20839-1_1jcn_A_P20839-4.pdb

3D view using mol* of P20839-1_1jcn_A_P20839-5.pdb

3D view using mol* of P20839-1_1jcn_A_P20839-6.pdb

3D view using mol* of P20839-1_1jcn_A_P20839-7.pdb

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

3D view using mol* of P20839-1_P20839-2.pdb

3D view using mol* of P20839-1_P20839-3.pdb

3D view using mol* of P20839-1_P20839-4.pdb

3D view using mol* of P20839-1_P20839-5.pdb

3D view using mol* of P20839-1_P20839-6.pdb

3D view using mol* of P20839-1_P20839-7.pdb

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

./stats/secondary_structure/figure/P20839-1_vs_P20839-2.png

./stats/secondary_structure/figure/P20839-1_vs_P20839-3.png

./stats/secondary_structure/figure/P20839-1_vs_P20839-4.png

./stats/secondary_structure/figure/P20839-1_vs_P20839-5.png

./stats/secondary_structure/figure/P20839-1_vs_P20839-6.png

./stats/secondary_structure/figure/P20839-1_vs_P20839-7.png

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

./stats/relative_asa/P20839-1_vs_P20839-2.png

./stats/relative_asa/P20839-1_vs_P20839-3.png

./stats/relative_asa/P20839-1_vs_P20839-4.png

./stats/relative_asa/P20839-1_vs_P20839-5.png

./stats/relative_asa/P20839-1_vs_P20839-6.png

./stats/relative_asa/P20839-1_vs_P20839-7.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 IMPDH1

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
P20839	IMPDH1	DB00157	NADH	approved, nutraceutical
P20839	IMPDH1	DB01033	Mercaptopurine	approved	inhibitor
P20839	IMPDH1	DB03948	6-Chloropurine Riboside, 5'-Monophosphate	experimental
P20839	IMPDH1	DB00688	Mycophenolate mofetil	approved, investigational	inhibitor, inducer
P20839	IMPDH1	DB00811	Ribavirin	approved	inhibitor
P20839	IMPDH1	DB06408	Taribavirin	investigational
P20839	IMPDH1	DB06103	VX-148	investigational
P20839	IMPDH1	DB01024	Mycophenolic acid	approved, investigational	inhibitor

Related Diseases to IMPDH1

Previous studies relating to the alternative splicing of IMPDH1 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in IMPDH1

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance