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:INPP5B

Protein Summary

Gene summary

Gene name: INPP5B
ASpdb.0 ID: 3633
	Gene
Gene symbol	INPP5B
Gene ID	3633
Gene name	inositol polyphosphate-5-phosphatase B
Synonyms	5PTase
Cytomap	1p34.3
Type of gene	protein-coding
Description	type II inositol 1,4,5-trisphosphate 5-phosphataseinositol polyphosphate-5-phosphatase, 75kDaphosphoinositide 5-phosphatase
Modification date	20240403
UniProtAcc	P32019

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	INPP5B	GO:0004439	phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity	7721860
Gene	INPP5B	GO:0005829	cytosol	7721860
Gene	INPP5B	GO:0016020	membrane	7721860
Gene	INPP5B	GO:0046856	phosphatidylinositol dephosphorylation	7721860
Gene	INPP5B	GO:0052658	inositol-1,4,5-trisphosphate 5-phosphatase activity	7721860

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
P32019-1	P32019-1_4cml_A.pdb	4CML	X-ray	2.3	A	339	643

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

P32019

INPP5B

P32019-1

P32019-2

993

913

178

257

Deletion

none

177

P32019

INPP5B

P32019-1

P32019-3

993

749

244

Deletion

none

P32019

INPP5B

P32019-1

P32019-4

993

828

810

828

Substitution

TLMPVWTGDDGSQLDSPME

LAYLAAYCFETQLVTKSLI

810

828

P32019

INPP5B

P32019-1

P32019-4

993

828

829

993

Deletion

none

828

Multiple sequence alignment of our canonical and alternatively spliced INPP5B

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of INPP5B

UniProt-id	ENSG	ENST	ENSP
P32019-1	ENSG00000204084.14	ENST00000373026.5	ENSP00000362117.1
P32019-2	ENSG00000204084.14	ENST00000373024.8	ENSP00000362115.3
P32019-3	ENSG00000204084.14	ENST00000373027.5	ENSP00000362118.1

UniProt-id	NM ID	NP ID
P32019-2	NM_005540.2	NP_005531.2
P32019-3	NM_001297434.1	NP_001284363.1

Amino acid sequences of our canonical and alternatively spliced INPP5B

accession_id	Protein sequence
P32019-1	MDQSVAIQETLAEGEYCVIAVQGVLCEGDSRQSRLLGLVRYRLEHGGQEHALFLYTHRRMAITGDDVSLDQIVPVSRDFTLEEVSPDGEL YILGSDVTVQLDTAELSLVFQLPFGSQTRMFLHEVARACPGFDSATRDPEFLWLSRYRCAELELEMPTPRGCNSALVTWPGYATIGGGRY PSRKKRWGLEEARPQGAGSVLFWGGAMEKTGFRLMERAHGGGFVWGRSARDGRRDEELEEAGREMSAAAGSRERNTAGGSNFDGLRPNGK GVPMDQSSRGQDKPESLQPRQNKSKSEITDMVRSSTITVSDKAHILSMQKFGLRDTIVKSHLLQKEEDYTYIQNFRFFAGTYNVNGQSPK ECLRLWLSNGIQAPDVYCVGFQELDLSKEAFFFHDTPKEEEWFKAVSEGLHPDAKYAKVKLIRLVGIMLLLYVKQEHAAYISEVEAETVG TGIMGRMGNKGGVAIRFQFHNTSICVVNSHLAAHIEEYERRNQDYKDICSRMQFCQPDPSLPPLTISNHDVILWLGDLNYRIEELDVEKV KKLIEEKDFQMLYAYDQLKIQVAAKTVFEGFTEGELTFQPTYKYDTGSDDWDTSEKCRAPAWCDRILWKGKNITQLSYQSHMALKTSDHK PVSSVFDIGVRVVNDELYRKTLEEIVRSLDKMENANIPSVSLSKREFCFQNVKYMQLKVESFTIHNGQVPCHFEFINKPDEESYCKQWLN ANPSRGFLLPDSDVEIDLELFVNKMTATKLNSGEDKIEDILVLHLDRGKDYFLSVSGNYLPSCFGSPIHTLCYMREPILDLPLETISELT LMPVWTGDDGSQLDSPMEIPKELWMMVDYLYRNAVQQEDLFQQPGLRSEFEHIRDCLDTGMIDNLSASNHSVAEALLLFLESLPEPVICY STYHNCLECSGNYTASKQVISTLPIFHKNVFHYLMAFLRELLKNSAKNHLDENILASIFGSLLLRNPAGHQKLDMTEKKKAQEFIHQFLC
P32019-2	MDQSVAIQETLAEGEYCVIAVQGVLCEGDSRQSRLLGLVRYRLEHGGQEHALFLYTHRRMAITGDDVSLDQIVPVSRDFTLEEVSPDGEL YILGSDVTVQLDTAELSLVFQLPFGSQTRMFLHEVARACPGFDSATRDPEFLWLSRYRCAELELEMPTPRGCNSALVTWPGYATIGGGGS NFDGLRPNGKGVPMDQSSRGQDKPESLQPRQNKSKSEITDMVRSSTITVSDKAHILSMQKFGLRDTIVKSHLLQKEEDYTYIQNFRFFAG TYNVNGQSPKECLRLWLSNGIQAPDVYCVGFQELDLSKEAFFFHDTPKEEEWFKAVSEGLHPDAKYAKVKLIRLVGIMLLLYVKQEHAAY ISEVEAETVGTGIMGRMGNKGGVAIRFQFHNTSICVVNSHLAAHIEEYERRNQDYKDICSRMQFCQPDPSLPPLTISNHDVILWLGDLNY RIEELDVEKVKKLIEEKDFQMLYAYDQLKIQVAAKTVFEGFTEGELTFQPTYKYDTGSDDWDTSEKCRAPAWCDRILWKGKNITQLSYQS HMALKTSDHKPVSSVFDIGVRVVNDELYRKTLEEIVRSLDKMENANIPSVSLSKREFCFQNVKYMQLKVESFTIHNGQVPCHFEFINKPD EESYCKQWLNANPSRGFLLPDSDVEIDLELFVNKMTATKLNSGEDKIEDILVLHLDRGKDYFLSVSGNYLPSCFGSPIHTLCYMREPILD LPLETISELTLMPVWTGDDGSQLDSPMEIPKELWMMVDYLYRNAVQQEDLFQQPGLRSEFEHIRDCLDTGMIDNLSASNHSVAEALLLFL ESLPEPVICYSTYHNCLECSGNYTASKQVISTLPIFHKNVFHYLMAFLRELLKNSAKNHLDENILASIFGSLLLRNPAGHQKLDMTEKKK
P32019-3	MSAAAGSRERNTAGGSNFDGLRPNGKGVPMDQSSRGQDKPESLQPRQNKSKSEITDMVRSSTITVSDKAHILSMQKFGLRDTIVKSHLLQ KEEDYTYIQNFRFFAGTYNVNGQSPKECLRLWLSNGIQAPDVYCVGFQELDLSKEAFFFHDTPKEEEWFKAVSEGLHPDAKYAKVKLIRL VGIMLLLYVKQEHAAYISEVEAETVGTGIMGRMGNKGGVAIRFQFHNTSICVVNSHLAAHIEEYERRNQDYKDICSRMQFCQPDPSLPPL TISNHDVILWLGDLNYRIEELDVEKVKKLIEEKDFQMLYAYDQLKIQVAAKTVFEGFTEGELTFQPTYKYDTGSDDWDTSEKCRAPAWCD RILWKGKNITQLSYQSHMALKTSDHKPVSSVFDIGVRVVNDELYRKTLEEIVRSLDKMENANIPSVSLSKREFCFQNVKYMQLKVESFTI HNGQVPCHFEFINKPDEESYCKQWLNANPSRGFLLPDSDVEIDLELFVNKMTATKLNSGEDKIEDILVLHLDRGKDYFLSVSGNYLPSCF GSPIHTLCYMREPILDLPLETISELTLMPVWTGDDGSQLDSPMEIPKELWMMVDYLYRNAVQQEDLFQQPGLRSEFEHIRDCLDTGMIDN LSASNHSVAEALLLFLESLPEPVICYSTYHNCLECSGNYTASKQVISTLPIFHKNVFHYLMAFLRELLKNSAKNHLDENILASIFGSLLL
P32019-4	MDQSVAIQETLAEGEYCVIAVQGVLCEGDSRQSRLLGLVRYRLEHGGQEHALFLYTHRRMAITGDDVSLDQIVPVSRDFTLEEVSPDGEL YILGSDVTVQLDTAELSLVFQLPFGSQTRMFLHEVARACPGFDSATRDPEFLWLSRYRCAELELEMPTPRGCNSALVTWPGYATIGGGRY PSRKKRWGLEEARPQGAGSVLFWGGAMEKTGFRLMERAHGGGFVWGRSARDGRRDEELEEAGREMSAAAGSRERNTAGGSNFDGLRPNGK GVPMDQSSRGQDKPESLQPRQNKSKSEITDMVRSSTITVSDKAHILSMQKFGLRDTIVKSHLLQKEEDYTYIQNFRFFAGTYNVNGQSPK ECLRLWLSNGIQAPDVYCVGFQELDLSKEAFFFHDTPKEEEWFKAVSEGLHPDAKYAKVKLIRLVGIMLLLYVKQEHAAYISEVEAETVG TGIMGRMGNKGGVAIRFQFHNTSICVVNSHLAAHIEEYERRNQDYKDICSRMQFCQPDPSLPPLTISNHDVILWLGDLNYRIEELDVEKV KKLIEEKDFQMLYAYDQLKIQVAAKTVFEGFTEGELTFQPTYKYDTGSDDWDTSEKCRAPAWCDRILWKGKNITQLSYQSHMALKTSDHK PVSSVFDIGVRVVNDELYRKTLEEIVRSLDKMENANIPSVSLSKREFCFQNVKYMQLKVESFTIHNGQVPCHFEFINKPDEESYCKQWLN ANPSRGFLLPDSDVEIDLELFVNKMTATKLNSGEDKIEDILVLHLDRGKDYFLSVSGNYLPSCFGSPIHTLCYMREPILDLPLETISELL

Protein Functional Features

Main function of this protein. (from UniProt)

INPP5B (go to UniProt):P32019

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
P32019	Domain	22	148	Note=PH	Type=Deletion;Start=1;End=244
P32019	Domain	821	993	Note=Rho-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00172	Type=Substitution;Start=810;End=828
P32019	Domain	821	993	Note=Rho-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00172	Type=Deletion;Start=829;End=993
P32019	Region	224	302	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=178;End=257
P32019	Region	224	302	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=244
P32019	Compositional bias	228	247	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=178;End=257
P32019	Compositional bias	228	247	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=1;End=244

Gene Isoform Structures and Expression Levels for INPP5B

Gene structures of our canonical and alternative spliced genes of INPP5B
* 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 P32019-1

3D view using mol* of P32019-2

3D view using mol* of P32019-3

3D view using mol* of P32019-4

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 P32019-1

pLDDT distribution across the protein length of P32019-2

pLDDT distribution across the protein length of P32019-3

pLDDT distribution across the protein length of P32019-4

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 P32019-1

Ramachandran plot of P32019-2

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
P32019-1	0.982	312	1.011	1036.889	0.658	0.656	0.837	0.395	0.99	0.399	0.948	1,2,3,5,6,21,22,26,31,35,60,61,62,83,84,85,86,87,8 8,89,90,91,92,93,94,95,96,97,98,109,111,113,114,11 5,116,117,118,119,319,320,321,322,323,324,325,327, 328,659,660,661,662,663,664,666,667,668,675,767,76 8,769,770,771,772
P32019-2	0.99	231	0.999	641.753	0.656	0.683	0.854	0.364	1.078	0.338	0.73	1,2,3,20,21,22,57,59,60,61,62,83,84,85,86,88,89,90 ,91,92,93,94,95,96,97,98,111,113,114,115,116,117,1 18,119,319,320,323,337,338,339,340,341,353,355,356 ,358,359,361,362,363,364
P32019-3	0.931	79	0.932	184.191	0.484	0.703	1.003	0.784	0.997	0.786	1.153	549,568,570,571,572,573,574,575,576,577,578,579,58 1,582,584,680,681,682
P32019-4	0.994	109	1.024	389.648	0.661	0.669	0.822	0.351	0.972	0.361	0.884	1,2,3,5,6,21,22,57,58,59,60,61,62,113,114,115,116, 117,118,445,447,504,505,506,507,508,509,511,512,51 3

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 P32019-1_P32019-1_4cml_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 P32019-1_4cml_A_P32019-2.pdb

3D view using mol* of P32019-1_4cml_A_P32019-3.pdb

3D view using mol* of P32019-1_4cml_A_P32019-4.pdb

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

3D view using mol* of P32019-1_P32019-2.pdb

3D view using mol* of P32019-1_P32019-3.pdb

3D view using mol* of P32019-1_P32019-4.pdb

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

./stats/secondary_structure/figure/P32019-1_vs_P32019-2.png

./stats/secondary_structure/figure/P32019-1_vs_P32019-3.png

./stats/secondary_structure/figure/P32019-1_vs_P32019-4.png

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

./stats/relative_asa/P32019-1_vs_P32019-2.png

./stats/relative_asa/P32019-1_vs_P32019-3.png

./stats/relative_asa/P32019-1_vs_P32019-4.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 INPP5B

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
P32019	INPP5B	DB03158	D-Myo-Inositol-1,4-Bisphosphate	experimental

Related Diseases to INPP5B

Previous studies relating to the alternative splicing of INPP5B and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in INPP5B

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance