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:FNBP1

Protein Summary

Gene summary

Gene name: FNBP1
ASpdb.0 ID: 23048
	Gene
Gene symbol	FNBP1
Gene ID	23048
Gene name	formin binding protein 1
Synonyms	FBP17
Cytomap	9q34.11
Type of gene	protein-coding
Description	formin-binding protein 1formin-binding protein 17
Modification date	20240403
UniProtAcc	Q96RU3

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	FNBP1	GO:0005886	plasma membrane	-
Gene	FNBP1	GO:0043231	intracellular membrane-bounded organelle	-

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
Q96RU3-1	Q96RU3-1_2efl_A.pdb	2EFL	X-ray	2.61	A	2	288

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

Q96RU3

FNBP1

Q96RU3-1

Q96RU3-2

617

616

391

395

Deletion

none

390

Q96RU3

FNBP1

Q96RU3-1

Q96RU3-2

617

616

617

Substitution

GAKTYI

611

616

Q96RU3

FNBP1

Q96RU3-1

Q96RU3-3

617

592

330

358

Deletion

none

329

Q96RU3

FNBP1

Q96RU3-1

Q96RU3-3

617

592

616

617

Substitution

GAKTYI

587

592

Q96RU3

FNBP1

Q96RU3-1

Q96RU3-4

617

551

329

394

Deletion

none

328

Q96RU3

FNBP1

Q96RU3-1

Q96RU3-5

617

612

391

395

Deletion

none

390

Multiple sequence alignment of our canonical and alternatively spliced FNBP1

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of FNBP1

UniProt-id	ENSG	ENST	ENSP
Q96RU3-1	ENSG00000187239.19	ENST00000446176.7	ENSP00000413625.1
Q96RU3-2	ENSG00000187239.19	ENST00000703532.1	ENSP00000515358.1
Q96RU3-3	ENSG00000187239.19	ENST00000355681.3	ENSP00000347907.3

UniProt-id	NM ID	NP ID
Q96RU3-1	NM_015033.2	NP_055848.1
Q96RU3-2	XM_005251823.2	XP_005251880.1
Q96RU3-5	XM_005251824.2	XP_005251881.1

Amino acid sequences of our canonical and alternatively spliced FNBP1

accession_id	Protein sequence
Q96RU3-1	MSWGTELWDQFDNLEKHTQWGIDILEKYIKFVKERTEIELSYAKQLRNLSKKYQPKKNSKEEEEYKYTSCKAFISNLNEMNDYAGQHEVI SENMASQIIVDLARYVQELKQERKSNFHDGRKAQQHIETCWKQLESSKRRFERDCKEADRAQQYFEKMDADINVTKADVEKARQQAQIRH QMAEDSKADYSSILQKFNHEQHEYYHTHIPNIFQKIQEMEERRIVRMGESMKTYAEVDRQVIPIIGKCLDGIVKAAESIDQKNDSQLVIE AYKSGFEPPGDIEFEDYTQPMKRTVSDNSLSNSRGEGKPDLKFGGKSKGKLWPFIKKNKLMSLLTSPHQPPPPPPASASPSAVPNGPQSP KQQKEPLSHRFNEFMTSKPKIHCFRSLKRGLSLKLGATPEDFSNLPPEQRRKKLQQKVDELNKEIQKEMDQRDAITKMKDVYLKNPQMGD PASLDHKLAEVSQNIEKLRVETQKFEAWLAEVEGRLPARSEQARRQSGLYDSQNPPTVNNCAQDRESPDGSYTEEQSQESEMKVLATDFD
Q96RU3-2	MSWGTELWDQFDNLEKHTQWGIDILEKYIKFVKERTEIELSYAKQLRNLSKKYQPKKNSKEEEEYKYTSCKAFISNLNEMNDYAGQHEVI SENMASQIIVDLARYVQELKQERKSNFHDGRKAQQHIETCWKQLESSKRRFERDCKEADRAQQYFEKMDADINVTKADVEKARQQAQIRH QMAEDSKADYSSILQKFNHEQHEYYHTHIPNIFQKIQEMEERRIVRMGESMKTYAEVDRQVIPIIGKCLDGIVKAAESIDQKNDSQLVIE AYKSGFEPPGDIEFEDYTQPMKRTVSDNSLSNSRGEGKPDLKFGGKSKGKLWPFIKKNKLMSLLTSPHQPPPPPPASASPSAVPNGPQSP KQQKEPLSHRFNEFMTSKPKIHCFRSLKRGGATPEDFSNLPPEQRRKKLQQKVDELNKEIQKEMDQRDAITKMKDVYLKNPQMGDPASLD HKLAEVSQNIEKLRVETQKFEAWLAEVEGRLPARSEQARRQSGLYDSQNPPTVNNCAQDRESPDGSYTEEQSQESEMKVLATDFDDEFDD
Q96RU3-3	MSWGTELWDQFDNLEKHTQWGIDILEKYIKFVKERTEIELSYAKQLRNLSKKYQPKKNSKEEEEYKYTSCKAFISNLNEMNDYAGQHEVI SENMASQIIVDLARYVQELKQERKSNFHDGRKAQQHIETCWKQLESSKRRFERDCKEADRAQQYFEKMDADINVTKADVEKARQQAQIRH QMAEDSKADYSSILQKFNHEQHEYYHTHIPNIFQKIQEMEERRIVRMGESMKTYAEVDRQVIPIIGKCLDGIVKAAESIDQKNDSQLVIE AYKSGFEPPGDIEFEDYTQPMKRTVSDNSLSNSRGEGKPDLKFGGKSKGKLWPFIKKNKSPKQQKEPLSHRFNEFMTSKPKIHCFRSLKR GLSLKLGATPEDFSNLPPEQRRKKLQQKVDELNKEIQKEMDQRDAITKMKDVYLKNPQMGDPASLDHKLAEVSQNIEKLRVETQKFEAWL AEVEGRLPARSEQARRQSGLYDSQNPPTVNNCAQDRESPDGSYTEEQSQESEMKVLATDFDDEFDDEEPLPAIGTCKALYTFEGQNEGTI
Q96RU3-4	MSWGTELWDQFDNLEKHTQWGIDILEKYIKFVKERTEIELSYAKQLRNLSKKYQPKKNSKEEEEYKYTSCKAFISNLNEMNDYAGQHEVI SENMASQIIVDLARYVQELKQERKSNFHDGRKAQQHIETCWKQLESSKRRFERDCKEADRAQQYFEKMDADINVTKADVEKARQQAQIRH QMAEDSKADYSSILQKFNHEQHEYYHTHIPNIFQKIQEMEERRIVRMGESMKTYAEVDRQVIPIIGKCLDGIVKAAESIDQKNDSQLVIE AYKSGFEPPGDIEFEDYTQPMKRTVSDNSLSNSRGEGKPDLKFGGKSKGKLWPFIKKNLGATPEDFSNLPPEQRRKKLQQKVDELNKEIQ KEMDQRDAITKMKDVYLKNPQMGDPASLDHKLAEVSQNIEKLRVETQKFEAWLAEVEGRLPARSEQARRQSGLYDSQNPPTVNNCAQDRE SPDGSYTEEQSQESEMKVLATDFDDEFDDEEPLPAIGTCKALYTFEGQNEGTISVVEGETLYVIEEDKGDGWTRIRRNEDEEGYVPTSYV
Q96RU3-5	MSWGTELWDQFDNLEKHTQWGIDILEKYIKFVKERTEIELSYAKQLRNLSKKYQPKKNSKEEEEYKYTSCKAFISNLNEMNDYAGQHEVI SENMASQIIVDLARYVQELKQERKSNFHDGRKAQQHIETCWKQLESSKRRFERDCKEADRAQQYFEKMDADINVTKADVEKARQQAQIRH QMAEDSKADYSSILQKFNHEQHEYYHTHIPNIFQKIQEMEERRIVRMGESMKTYAEVDRQVIPIIGKCLDGIVKAAESIDQKNDSQLVIE AYKSGFEPPGDIEFEDYTQPMKRTVSDNSLSNSRGEGKPDLKFGGKSKGKLWPFIKKNKLMSLLTSPHQPPPPPPASASPSAVPNGPQSP KQQKEPLSHRFNEFMTSKPKIHCFRSLKRGGATPEDFSNLPPEQRRKKLQQKVDELNKEIQKEMDQRDAITKMKDVYLKNPQMGDPASLD HKLAEVSQNIEKLRVETQKFEAWLAEVEGRLPARSEQARRQSGLYDSQNPPTVNNCAQDRESPDGSYTEEQSQESEMKVLATDFDDEFDD

Protein Functional Features

Main function of this protein. (from UniProt)

FNBP1 (go to UniProt):Q96RU3

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
Q96RU3	Region	1	335	Note=Interaction with microtubules;Ontology_term=ECO:0000250;evidence=ECO:0000250	Type=Deletion;Start=330;End=358
Q96RU3	Region	1	335	Note=Interaction with microtubules;Ontology_term=ECO:0000250;evidence=ECO:0000250	Type=Deletion;Start=329;End=394
Q96RU3	Region	251	617	Note=Required for self-association and induction of membrane tubulation	Type=Deletion;Start=391;End=395
Q96RU3	Region	251	617	Note=Required for self-association and induction of membrane tubulation	Type=Substitution;Start=616;End=617
Q96RU3	Region	251	617	Note=Required for self-association and induction of membrane tubulation	Type=Deletion;Start=330;End=358
Q96RU3	Region	251	617	Note=Required for self-association and induction of membrane tubulation	Type=Substitution;Start=616;End=617
Q96RU3	Region	251	617	Note=Required for self-association and induction of membrane tubulation	Type=Deletion;Start=329;End=394
Q96RU3	Region	251	617	Note=Required for self-association and induction of membrane tubulation	Type=Deletion;Start=391;End=395
Q96RU3	Region	333	366	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=330;End=358
Q96RU3	Region	333	366	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=329;End=394
Q96RU3	Region	495	617	Note=Interaction with PDE6G;Ontology_term=ECO:0000250;evidence=ECO:0000250	Type=Substitution;Start=616;End=617
Q96RU3	Region	495	617	Note=Interaction with PDE6G;Ontology_term=ECO:0000250;evidence=ECO:0000250	Type=Substitution;Start=616;End=617
Q96RU3	Region	514	617	Note=Required for interaction with TNKS;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14596906;Dbxref=PMID:14596906	Type=Substitution;Start=616;End=617
Q96RU3	Region	514	617	Note=Required for interaction with TNKS;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14596906;Dbxref=PMID:14596906	Type=Substitution;Start=616;End=617
Q96RU3	Region	535	617	Note=Interaction with DNM1 and DNM3;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15252009;Dbxref=PMID:15252009	Type=Substitution;Start=616;End=617
Q96RU3	Region	535	617	Note=Interaction with DNM1 and DNM3;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15252009;Dbxref=PMID:15252009	Type=Substitution;Start=616;End=617
Q96RU3	Region	550	617	"Note=Interaction with ARHGAP17%2C DAAM1%2C DIAPH1 and DIAPH2;Ontology_term=ECO:0000269	ECO:0000269;evidence=ECO:0000269\|PubMed:11431473
Q96RU3	Region	550	617	"Note=Interaction with ARHGAP17%2C DAAM1%2C DIAPH1 and DIAPH2;Ontology_term=ECO:0000269	ECO:0000269;evidence=ECO:0000269\|PubMed:11431473
Q96RU3	Compositional bias	336	351	Note=Pro residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=330;End=358
Q96RU3	Compositional bias	336	351	Note=Pro residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=329;End=394

Gene Isoform Structures and Expression Levels for FNBP1

Gene structures of our canonical and alternative spliced genes of FNBP1
* 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 Q96RU3-1

3D view using mol* of Q96RU3-2

3D view using mol* of Q96RU3-3

3D view using mol* of Q96RU3-4

3D view using mol* of Q96RU3-5

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 Q96RU3-1

pLDDT distribution across the protein length of Q96RU3-2

pLDDT distribution across the protein length of Q96RU3-3

pLDDT distribution across the protein length of Q96RU3-4

pLDDT distribution across the protein length of Q96RU3-5

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 Q96RU3-1

Ramachandran plot of Q96RU3-2

Ramachandran plot of Q96RU3-3

Ramachandran plot of Q96RU3-5

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
Q96RU3-1	0.979	91	0.984	329.28	0.547	0.717	0.972	0.717	1.051	0.682	0.682	8,9,10,11,12,13,121,124,125,127,128,131,197,201,20 4,205,209,381,384
Q96RU3-2	1.017	167	1.023	362.894	0.436	0.723	0.967	0.437	1.075	0.407	1.371	63,270,271,272,273,274,326,327,328,329,330,400,403 ,404,406,407,408,410,411,414,415,474,478
Q96RU3-3	0.858	67	0.878	183.162	0.613	0.615	0.814	0.613	0.798	0.769	1.57	520,521,523,551,552,553,555,581,585,586,587,588,58 9,590,591
Q96RU3-4	0.624	27	0.606	100.156	0.801	0.551	0.685	0.63	0.652	0.966	2.526	483,484,486,514,515,516,544,545,546,548,549
Q96RU3-5	0.666	31	0.67	63.455	0.762	0.543	0.73	0.834	0.548	1.521	0.294	147,150,151,154,158,168,171,172,175,176,179

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 Q96RU3-1_Q96RU3-1_2efl_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 Q96RU3-1_2efl_A_Q96RU3-2.pdb

3D view using mol* of Q96RU3-1_2efl_A_Q96RU3-3.pdb

3D view using mol* of Q96RU3-1_2efl_A_Q96RU3-4.pdb

3D view using mol* of Q96RU3-1_2efl_A_Q96RU3-5.pdb

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

3D view using mol* of Q96RU3-1_Q96RU3-2.pdb

3D view using mol* of Q96RU3-1_Q96RU3-3.pdb

3D view using mol* of Q96RU3-1_Q96RU3-4.pdb

3D view using mol* of Q96RU3-1_Q96RU3-5.pdb

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

./stats/secondary_structure/figure/Q96RU3-1_vs_Q96RU3-2.png

./stats/secondary_structure/figure/Q96RU3-1_vs_Q96RU3-3.png

./stats/secondary_structure/figure/Q96RU3-1_vs_Q96RU3-4.png

./stats/secondary_structure/figure/Q96RU3-1_vs_Q96RU3-5.png

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

./stats/relative_asa/Q96RU3-1_vs_Q96RU3-2.png

./stats/relative_asa/Q96RU3-1_vs_Q96RU3-3.png

./stats/relative_asa/Q96RU3-1_vs_Q96RU3-4.png

./stats/relative_asa/Q96RU3-1_vs_Q96RU3-5.png

Protein-Protein Interaction

Interactors from UniProt.

Accession_id	Subsection	Start	End	Funcitonal feature	Splicing information
Q96RU3	Region	1	335	Note=Interaction with microtubules;Ontology_term=ECO:0000250;evidence=ECO:0000250	Type=Deletion;Start=330;End=358
Q96RU3	Region	1	335	Note=Interaction with microtubules;Ontology_term=ECO:0000250;evidence=ECO:0000250	Type=Deletion;Start=329;End=394
Q96RU3	Region	495	617	Note=Interaction with PDE6G;Ontology_term=ECO:0000250;evidence=ECO:0000250	Type=Substitution;Start=616;End=617
Q96RU3	Region	495	617	Note=Interaction with PDE6G;Ontology_term=ECO:0000250;evidence=ECO:0000250	Type=Substitution;Start=616;End=617
Q96RU3	Region	514	617	Note=Required for interaction with TNKS;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14596906;Dbxref=PMID:14596906	Type=Substitution;Start=616;End=617
Q96RU3	Region	514	617	Note=Required for interaction with TNKS;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:14596906;Dbxref=PMID:14596906	Type=Substitution;Start=616;End=617
Q96RU3	Region	535	617	Note=Interaction with DNM1 and DNM3;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15252009;Dbxref=PMID:15252009	Type=Substitution;Start=616;End=617
Q96RU3	Region	535	617	Note=Interaction with DNM1 and DNM3;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15252009;Dbxref=PMID:15252009	Type=Substitution;Start=616;End=617
Q96RU3	Region	550	617	"Note=Interaction with ARHGAP17%2C DAAM1%2C DIAPH1 and DIAPH2;Ontology_term=ECO:0000269	ECO:0000269;evidence=ECO:0000269\|PubMed:11431473
Q96RU3	Region	550	617	"Note=Interaction with ARHGAP17%2C DAAM1%2C DIAPH1 and DIAPH2;Ontology_term=ECO:0000269	ECO:0000269;evidence=ECO:0000269\|PubMed:11431473

Interactors from STRING.

Gene name

Interactors

Related Drugs to FNBP1

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to FNBP1

Previous studies relating to the alternative splicing of FNBP1 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in FNBP1

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance