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:CNKSR2

Protein Summary

Gene summary

Gene name: CNKSR2
ASpdb.0 ID: 22866
	Gene
Gene symbol	CNKSR2
Gene ID	22866
Gene name	connector enhancer of kinase suppressor of Ras 2
Synonyms	CNK2\|KSR2\|MAGUIN\|MRXSHG
Cytomap	Xp22.12
Type of gene	protein-coding
Description	connector enhancer of kinase suppressor of ras 2CNK homolog protein 2connector enhancer of KSR2membrane-associated guanylate kinase-interacting protein
Modification date	20240305
UniProtAcc	Q8WXI2

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	CNKSR2	GO:0005886	plasma membrane	14597674
Gene	CNKSR2	GO:0019901	protein kinase binding	14597674
Gene	CNKSR2	GO:0035556	intracellular signal transduction	14597674

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
Q8WXI2-1	Q8WXI2-1_3bs5_B.pdb	3BS5	X-ray	2.0	B	6	80

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

Q8WXI2

CNKSR2

Q8WXI2-1

Q8WXI2-2

1034

898

899

1034

Deletion

none

898

Q8WXI2

CNKSR2

Q8WXI2-1

Q8WXI2-4

1034

849

271

319

Deletion

none

270

Q8WXI2

CNKSR2

Q8WXI2-1

Q8WXI2-4

1034

849

899

1034

Deletion

none

849

Q8WXI2

CNKSR2

Q8WXI2-1

Q8WXI2-5

1034

1004

435

464

Deletion

none

434

Multiple sequence alignment of our canonical and alternatively spliced CNKSR2

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of CNKSR2

UniProt-id	ENSG	ENST	ENSP
Q8WXI2-1	ENSG00000149970.16	ENST00000379510.5	ENSP00000368824.3
Q8WXI2-2	ENSG00000149970.16	ENST00000642359.1	ENSP00000496709.1
Q8WXI2-4	ENSG00000149970.16	ENST00000543067.6	ENSP00000444633.1
Q8WXI2-5	ENSG00000149970.16	ENST00000425654.7	ENSP00000397906.2

UniProt-id	NM ID	NP ID
Q8WXI2-1	NM_014927.4	NP_055742.2
Q8WXI2-2	NM_001168648.2	NP_001162119.1
Q8WXI2-4	NM_001168649.2	NP_001162120.1
Q8WXI2-5	NM_001168647.2	NP_001162118.1

Amino acid sequences of our canonical and alternatively spliced CNKSR2

accession_id	Protein sequence
Q8WXI2-1	MALIMEPVSKWSPSQVVDWMKGLDDCLQQYIKNFEREKISGDQLLRITHQELEDLGVSRIGHQELILEAVDLLCALNYGLETENLKTLSH KLNASAKNLQNFITGRRRSGHYDGRTSRKLPNDFLTSVVDLIGAAKSLLAWLDRSPFAAVTDYSVTRNNVIQLCLELTTIVQQDCTVYET ENKILHVCKTLSGVCDHIISLSSDPLVSQSAHLEVIQLANIKPSEGLGMYIKSTYDGLHVITGTTENSPADRCKKIHAGDEVIQVNHQTV VGWQLKNLVNALREDPSGVILTLKKRPQSMLTSAPALLKNMRWKPLALQPLIPRSPTSSVATPSSTISTPTKRDSSALQDLYIPPPPAEP YIPRDEKGNLPCEDLRGHMVGKPVHKGSESPNSFLDQEYRKRFNIVEEDTVLYCYEYEKGRSSSQGRRESTPTYGKLRPISMPVEYNWVG DYEDPNKMKRDSRRENSLLRYMSNEKIAQEEYMFQRNSKKDTGKKSKKKGDKSNSPTHYSLLPSLQMDALRQDIMGTPVPETTLYHTFQQ SSLQHKSKKKNKGPIAGKSKRRISCKDLGRGDCEGWLWKKKDAKSYFSQKWKKYWFVLKDASLYWYINEEDEKAEGFISLPEFKIDRASE CRKKYAFKACHPKIKSFYFAAEHLDDMNRWLNRINMLTAGYAERERIKQEQDYWSESDKEEADTPSTPKQDSPPPPYDTYPRPPSMSCAS PYVEAKHSRLSSTETSQSQSSHEEFRQEVTGSSAVSPIRKTASQRRSWQDLIETPLTSSGLHYLQTLPLEDSVFSDSAAISPEHRRQSTL PTQKCHLQDHYGPYPLAESERMQVLNGNGGKPRSFTLPRDSGFNHCCLNAPVSACDPQDDVQPPEVEEEEEEEEEEGEAAGENIGEKSES REEKLGDSLQDLYRALEQASLSPLGEHRISTKMEYKLSFIKRCNDPVMNEKLHRLRILKSTLKAREGEVAIIDKVLDNPDLTSKEFQQWK
Q8WXI2-2	MALIMEPVSKWSPSQVVDWMKGLDDCLQQYIKNFEREKISGDQLLRITHQELEDLGVSRIGHQELILEAVDLLCALNYGLETENLKTLSH KLNASAKNLQNFITGRRRSGHYDGRTSRKLPNDFLTSVVDLIGAAKSLLAWLDRSPFAAVTDYSVTRNNVIQLCLELTTIVQQDCTVYET ENKILHVCKTLSGVCDHIISLSSDPLVSQSAHLEVIQLANIKPSEGLGMYIKSTYDGLHVITGTTENSPADRCKKIHAGDEVIQVNHQTV VGWQLKNLVNALREDPSGVILTLKKRPQSMLTSAPALLKNMRWKPLALQPLIPRSPTSSVATPSSTISTPTKRDSSALQDLYIPPPPAEP YIPRDEKGNLPCEDLRGHMVGKPVHKGSESPNSFLDQEYRKRFNIVEEDTVLYCYEYEKGRSSSQGRRESTPTYGKLRPISMPVEYNWVG DYEDPNKMKRDSRRENSLLRYMSNEKIAQEEYMFQRNSKKDTGKKSKKKGDKSNSPTHYSLLPSLQMDALRQDIMGTPVPETTLYHTFQQ SSLQHKSKKKNKGPIAGKSKRRISCKDLGRGDCEGWLWKKKDAKSYFSQKWKKYWFVLKDASLYWYINEEDEKAEGFISLPEFKIDRASE CRKKYAFKACHPKIKSFYFAAEHLDDMNRWLNRINMLTAGYAERERIKQEQDYWSESDKEEADTPSTPKQDSPPPPYDTYPRPPSMSCAS PYVEAKHSRLSSTETSQSQSSHEEFRQEVTGSSAVSPIRKTASQRRSWQDLIETPLTSSGLHYLQTLPLEDSVFSDSAAISPEHRRQSTL
Q8WXI2-4	MALIMEPVSKWSPSQVVDWMKGLDDCLQQYIKNFEREKISGDQLLRITHQELEDLGVSRIGHQELILEAVDLLCALNYGLETENLKTLSH KLNASAKNLQNFITGRRRSGHYDGRTSRKLPNDFLTSVVDLIGAAKSLLAWLDRSPFAAVTDYSVTRNNVIQLCLELTTIVQQDCTVYET ENKILHVCKTLSGVCDHIISLSSDPLVSQSAHLEVIQLANIKPSEGLGMYIKSTYDGLHVITGTTENSPADRCKKIHAGDEVIQVNHQTV PLIPRSPTSSVATPSSTISTPTKRDSSALQDLYIPPPPAEPYIPRDEKGNLPCEDLRGHMVGKPVHKGSESPNSFLDQEYRKRFNIVEED TVLYCYEYEKGRSSSQGRRESTPTYGKLRPISMPVEYNWVGDYEDPNKMKRDSRRENSLLRYMSNEKIAQEEYMFQRNSKKDTGKKSKKK GDKSNSPTHYSLLPSLQMDALRQDIMGTPVPETTLYHTFQQSSLQHKSKKKNKGPIAGKSKRRISCKDLGRGDCEGWLWKKKDAKSYFSQ KWKKYWFVLKDASLYWYINEEDEKAEGFISLPEFKIDRASECRKKYAFKACHPKIKSFYFAAEHLDDMNRWLNRINMLTAGYAERERIKQ EQDYWSESDKEEADTPSTPKQDSPPPPYDTYPRPPSMSCASPYVEAKHSRLSSTETSQSQSSHEEFRQEVTGSSAVSPIRKTASQRRSWQ DLIETPLTSSGLHYLQTLPLEDSVFSDSAAISPEHRRQSTLPTQKCHLQDHYGPYPLAESERMQVLNGNGGKPRSFTLPRDSGFNHCCLN
Q8WXI2-5	MALIMEPVSKWSPSQVVDWMKGLDDCLQQYIKNFEREKISGDQLLRITHQELEDLGVSRIGHQELILEAVDLLCALNYGLETENLKTLSH KLNASAKNLQNFITGRRRSGHYDGRTSRKLPNDFLTSVVDLIGAAKSLLAWLDRSPFAAVTDYSVTRNNVIQLCLELTTIVQQDCTVYET ENKILHVCKTLSGVCDHIISLSSDPLVSQSAHLEVIQLANIKPSEGLGMYIKSTYDGLHVITGTTENSPADRCKKIHAGDEVIQVNHQTV VGWQLKNLVNALREDPSGVILTLKKRPQSMLTSAPALLKNMRWKPLALQPLIPRSPTSSVATPSSTISTPTKRDSSALQDLYIPPPPAEP YIPRDEKGNLPCEDLRGHMVGKPVHKGSESPNSFLDQEYRKRFNIVEEDTVLYCYEYEKGRSSSQGRRESTPTYENSLLRYMSNEKIAQE EYMFQRNSKKDTGKKSKKKGDKSNSPTHYSLLPSLQMDALRQDIMGTPVPETTLYHTFQQSSLQHKSKKKNKGPIAGKSKRRISCKDLGR GDCEGWLWKKKDAKSYFSQKWKKYWFVLKDASLYWYINEEDEKAEGFISLPEFKIDRASECRKKYAFKACHPKIKSFYFAAEHLDDMNRW LNRINMLTAGYAERERIKQEQDYWSESDKEEADTPSTPKQDSPPPPYDTYPRPPSMSCASPYVEAKHSRLSSTETSQSQSSHEEFRQEVT GSSAVSPIRKTASQRRSWQDLIETPLTSSGLHYLQTLPLEDSVFSDSAAISPEHRRQSTLPTQKCHLQDHYGPYPLAESERMQVLNGNGG KPRSFTLPRDSGFNHCCLNAPVSACDPQDDVQPPEVEEEEEEEEEEGEAAGENIGEKSESREEKLGDSLQDLYRALEQASLSPLGEHRIS TKMEYKLSFIKRCNDPVMNEKLHRLRILKSTLKAREGEVAIIDKVLDNPDLTSKEFQQWKQMYLDLFLDICQNTTSNDPLSISSEVDVIT

Protein Functional Features

Main function of this protein. (from UniProt)

CNKSR2 (go to UniProt):Q8WXI2

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
Q8WXI2	Domain	215	297	Note=PDZ;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00143	Type=Deletion;Start=271;End=319
Q8WXI2	Domain	332	515	Note=DUF1170	Type=Deletion;Start=435;End=464
Q8WXI2	Region	864	905	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=899;End=1034
Q8WXI2	Region	864	905	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=899;End=1034
Q8WXI2	Coiled coil	875	904	Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=899;End=1034
Q8WXI2	Coiled coil	875	904	Ontology_term=ECO:0000255;evidence=ECO:0000255	Type=Deletion;Start=899;End=1034
Q8WXI2	Compositional bias	891	905	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=899;End=1034
Q8WXI2	Compositional bias	891	905	Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=899;End=1034

Gene Isoform Structures and Expression Levels for CNKSR2

Gene structures of our canonical and alternative spliced genes of CNKSR2
* 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 Q8WXI2-1

3D view using mol* of Q8WXI2-2

3D view using mol* of Q8WXI2-4

3D view using mol* of Q8WXI2-5

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 Q8WXI2-1

pLDDT distribution across the protein length of Q8WXI2-2

pLDDT distribution across the protein length of Q8WXI2-4

pLDDT distribution across the protein length of Q8WXI2-5

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 Q8WXI2-1

Ramachandran plot of Q8WXI2-2

Ramachandran plot of Q8WXI2-4

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
Q8WXI2-1	1.056	124	1.126	556.346	0.661	0.675	0.851	1.223	0.671	1.823	1.114	125,128,129,132,135,136,139,140,161,164,165,166,16 8,169,171,172,765,766,768,769,771,772,774,775,776, 777,780,781,783,784
Q8WXI2-2	1.039	375	1.089	1319.521	0.633	0.691	0.866	0.982	0.814	1.206	0.934	23,24,27,61,64,65,68,69,71,72,74,75,76,78,79,83,87 ,88,91,118,119,120,125,128,129,132,133,135,136,137 ,139,140,141,143,144,161,164,165,168,171,172,173,1 74,175,177,180,232,233,234,235,236,237,238,239,240 ,242,261,262,263,271,272,273,274,275,276,294,296,7 66,768,771,772,774,775,776,777,778,780,781,782,783 ,784
Q8WXI2-4	1.049	762	1.086	2051.14	0.472	0.727	0.939	0.951	0.891	1.068	1.062	1,2,3,4,5,6,7,8,11,15,18,19,72,73,75,76,77,79,80,8 1,83,125,128,129,132,135,136,137,139,140,141,143,1 44,145,146,147,148,149,154,157,158,161,164,168,171 ,172,206,209,210,211,212,213,214,215,216,217,218,2 21,226,227,229,230,231,232,236,238,239,240,241,242 ,243,255,256,257,258,259,260,261,262,263,264,265,2 66,267,268,269,272,304,305,306,307,717,718,719,720 ,721,722,723,724,725,726,727,728,729,730,731,732
Q8WXI2-5	1.045	466	1.097	1571.626	0.595	0.696	0.842	0.71	0.8	0.887	0.976	68,71,72,75,76,79,80,83,125,128,129,132,133,136,13 7,139,140,141,143,144,145,146,148,149,157,158,161, 165,166,168,169,171,172,211,230,232,233,234,235,23 6,238,240,242,243,244,245,246,250,251,254,256,257, 258,259,260,261,263,271,294,295,296,297,298,299,30 2,304,305,306,307,308,309,310,311,313,314,315,735, 736,737,738,739,741,742,743,744,745,746,751,754,75 6

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 Q8WXI2-1_Q8WXI2-1_3bs5_B.pdb

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

3D view using mol* of Q8WXI2-1_3bs5_B_Q8WXI2-2.pdb

3D view using mol* of Q8WXI2-1_3bs5_B_Q8WXI2-4.pdb

3D view using mol* of Q8WXI2-1_3bs5_B_Q8WXI2-5.pdb

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

3D view using mol* of Q8WXI2-1_Q8WXI2-2.pdb

3D view using mol* of Q8WXI2-1_Q8WXI2-4.pdb

3D view using mol* of Q8WXI2-1_Q8WXI2-5.pdb

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

./stats/secondary_structure/figure/Q8WXI2-1_vs_Q8WXI2-2.png

./stats/secondary_structure/figure/Q8WXI2-1_vs_Q8WXI2-4.png

./stats/secondary_structure/figure/Q8WXI2-1_vs_Q8WXI2-5.png

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

./stats/relative_asa/Q8WXI2-1_vs_Q8WXI2-2.png

./stats/relative_asa/Q8WXI2-1_vs_Q8WXI2-4.png

./stats/relative_asa/Q8WXI2-1_vs_Q8WXI2-5.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 CNKSR2

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to CNKSR2

Previous studies relating to the alternative splicing of CNKSR2 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in CNKSR2

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance