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:DEPDC5

Protein Summary

Gene summary

Gene name: DEPDC5
ASpdb.0 ID: 9681
	Gene
Gene symbol	DEPDC5
Gene ID	9681
Gene name	DEP domain containing 5, GATOR1 subcomplex subunit
Synonyms	DEE111\|DEP.5\|FFEVF\|FFEVF1\|FPEVF
Cytomap	22q12.2-q12.3
Type of gene	protein-coding
Description	GATOR1 complex protein DEPDC5DEP domain-containing protein 5GATOR complex protein DEPDC5
Modification date	20240403
UniProtAcc	O75140

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	DEPDC5	GO:0005096	GTPase activator activity	23723238
Gene	DEPDC5	GO:0005764	lysosome	23723238
Gene	DEPDC5	GO:0005765	lysosomal membrane	28199306
Gene	DEPDC5	GO:0031267	small GTPase binding	29590090\|35338845
Gene	DEPDC5	GO:0031463	Cul3-RING ubiquitin ligase complex	29769719
Gene	DEPDC5	GO:0034198	cellular response to amino acid starvation	29590090\|35338845
Gene	DEPDC5	GO:0044877	protein-containing complex binding	23723238
Gene	DEPDC5	GO:1904262	negative regulation of TORC1 signaling	29590090\|35338845
Gene	DEPDC5	GO:1990130	GATOR1 complex	23723238\|29590090\|35338845

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
O75140-10	O75140-10_6ces_D.pdb	6CES	EM	4.0	D	38	1597

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

O75140

DEPDC5

O75140-10

O75140-2

1603

559

556

559

Substitution

DVLE

EHLG

556

559

O75140

DEPDC5

O75140-10

O75140-2

1603

559

560

1603

Deletion

none

559

O75140

DEPDC5

O75140-10

O75140-4

1603

1581

1089

1110

Deletion

none

1088

O75140

DEPDC5

O75140-10

O75140-8

1603

1503

624

701

Deletion

none

623

O75140

DEPDC5

O75140-10

O75140-8

1603

1503

1089

1110

Deletion

none

1010

Multiple sequence alignment of our canonical and alternatively spliced DEPDC5

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of DEPDC5

UniProt-id	ENSG	ENST	ENSP
O75140-10	ENSG00000100150.20	ENST00000382112.8	ENSP00000371546.4
O75140-10	ENSG00000100150.20	ENST00000651528.2	ENSP00000498382.1
O75140-2	ENSG00000100150.20	ENST00000400242.8	ENSP00000383101.3
O75140-2	ENSG00000100150.20	ENST00000646755.1	ENSP00000496532.1
O75140-4	ENSG00000100150.20	ENST00000400249.7	ENSP00000383108.3
O75140-4	ENSG00000100150.20	ENST00000644331.1	ENSP00000494406.1
O75140-8	ENSG00000100150.20	ENST00000535622.6	ENSP00000440210.1

UniProt-id	NM ID	NP ID
O75140-10	NM_001242896.1	NP_001229825.1
O75140-2	NM_001007188.2	NP_001007189.1
O75140-8	NM_001242897.1	NP_001229826.1
O75140-8	XM_011530563.2	XP_011528865.1

Amino acid sequences of our canonical and alternatively spliced DEPDC5

accession_id	Protein sequence
O75140-10	MRTTKVYKLVIHKKGFGGSDDELVVNPKVFPHIKLGDIVEIAHPNDEYSPLLLQVKSLKEDLQKETISVDQTVTQVFRLRPYQDVYVNVV DPKDVTLDLVELTFKDQYIGRGDMWRLKKSLVSTCAYITQKVEFAGIRAQAGELWVKNEKVMCGYISEDTRVVFRSTSAMVYIFIQMSCE MWDFDIYGDLYFEKAVNGFLADLFTKWKEKNCSHEVTVVLFSRTFYDAKSVDEFPEINRASIRQDHKGRFYEDFYKVVVQNERREEWTSL LVTIKKLFIQYPVLVRLEQAEGFPQGDNSTSAQGNYLEAINLSFNVFDKHYINRNFDRTGQMSVVITPGVGVFEVDRLLMILTKQRMIDN GIGVDLVCMGEQPLHAVPLFKLHNRSAPRDSRLGDDYNIPHWINHSFYTSKSQLFCNSFTPRIKLAGKKPASEKAKNGRDTSLGSPKESE NALPIQVDYDAYDAQVFRLPGPSRAQCLTTCRSVRERESHSRKSASSCDVSSSPSLPSRTLPTEEVRSQASDDSSLGKSANILMIPHPHL HQYEVSSSLGYTSTRDVLENMMEPPQRDSSAPGRFHVGSAESMLHVRPGGYTPQRALINPFAPSRMPMKLTSNRRRWMHTFPVGPSGEAI QIHHQTRQNMAELQGSGQRDPTHSSAELLELAYHEAAGRHSNSRQPGDGMSFLNFSGTEELSVGLLSNSGAGMNPRTQNKDSLEDSVSTS PDPILTLSAPPVVPGFCCTVGVDWKSLTTPACLPLTTDYFPDRQGLQNDYTEGCYDLLPEADIDRRDEDGVQMTAQQVFEEFICQRLMQG YQIIVQPKTQKPNPAVPPPLSSSPLYSRGLVSRNRPEEEDQYWLSMGRTFHKVTLKDKMITVTRYLPKYPYESAQIHYTYSLCPSHSDSE FVSCWVEFSHERLEEYKWNYLDQYICSAGSEDFSLIESLKFWRTRFLLLPACVTATKRITEGEAHCDIYGDRPRADEDEWQLLDGFVRFV EGLNRIRRRHRSDRMMRKGTAMKGLQMTGPISTHSLESTAPPVGKKGTSALSALLEMEASQKCLGEQQAAVHGGKSSAQSAESSSVAMTP TYMDSPRKDGAFFMEFVRSPRTASSAFYPQVSVDQTATPMLDGTSLGICTGQSMDRGNSQTFGNSQNIGEQGYSSTNSSDSSSQQLVASS LTSSSTLTEILEAMKHPSTGVQLLSEQKGLSPYCFISAEVVHWLVNHVEGIQTQAMAIDIMQKMLEEQLITHASGEAWRTFIYGFYFYKI VTDKEPDRVAMQQPATTWHTAGVDDFASFQRKWFEVAFVAEELVHSEIPAFLLPWLPSRPASYASRHSSFSRSFGGRSQAAALLAATVPE QRTVTLDVDVNNRTDRLEWCSCYYHGNFSLNAAFEIKLHWMAVTAAVLFEMVQGWHRKATSCGFLLVPVLEGPFALPSYLYGDPLRAQLF IPLNISCLLKEGSEHLFDSFEPETYWDRMHLFQEAIAHRFGFVQDKYSASAFNFPAENKPQYIHVTGTVFLQLPYSKRKFSGQQRRRRNS
O75140-2	MRTTKVYKLVIHKKGFGGSDDELVVNPKVFPHIKLGDIVEIAHPNDEYSPLLLQVKSLKEDLQKETISVDQTVTQVFRLRPYQDVYVNVV DPKDVTLDLVELTFKDQYIGRGDMWRLKKSLVSTCAYITQKVEFAGIRAQAGELWVKNEKVMCGYISEDTRVVFRSTSAMVYIFIQMSCE MWDFDIYGDLYFEKAVNGFLADLFTKWKEKNCSHEVTVVLFSRTFYDAKSVDEFPEINRASIRQDHKGRFYEDFYKVVVQNERREEWTSL LVTIKKLFIQYPVLVRLEQAEGFPQGDNSTSAQGNYLEAINLSFNVFDKHYINRNFDRTGQMSVVITPGVGVFEVDRLLMILTKQRMIDN GIGVDLVCMGEQPLHAVPLFKLHNRSAPRDSRLGDDYNIPHWINHSFYTSKSQLFCNSFTPRIKLAGKKPASEKAKNGRDTSLGSPKESE NALPIQVDYDAYDAQVFRLPGPSRAQCLTTCRSVRERESHSRKSASSCDVSSSPSLPSRTLPTEEVRSQASDDSSLGKSANILMIPHPHL
O75140-4	MRTTKVYKLVIHKKGFGGSDDELVVNPKVFPHIKLGDIVEIAHPNDEYSPLLLQVKSLKEDLQKETISVDQTVTQVFRLRPYQDVYVNVV DPKDVTLDLVELTFKDQYIGRGDMWRLKKSLVSTCAYITQKVEFAGIRAQAGELWVKNEKVMCGYISEDTRVVFRSTSAMVYIFIQMSCE MWDFDIYGDLYFEKAVNGFLADLFTKWKEKNCSHEVTVVLFSRTFYDAKSVDEFPEINRASIRQDHKGRFYEDFYKVVVQNERREEWTSL LVTIKKLFIQYPVLVRLEQAEGFPQGDNSTSAQGNYLEAINLSFNVFDKHYINRNFDRTGQMSVVITPGVGVFEVDRLLMILTKQRMIDN GIGVDLVCMGEQPLHAVPLFKLHNRSAPRDSRLGDDYNIPHWINHSFYTSKSQLFCNSFTPRIKLAGKKPASEKAKNGRDTSLGSPKESE NALPIQVDYDAYDAQVFRLPGPSRAQCLTTCRSVRERESHSRKSASSCDVSSSPSLPSRTLPTEEVRSQASDDSSLGKSANILMIPHPHL HQYEVSSSLGYTSTRDVLENMMEPPQRDSSAPGRFHVGSAESMLHVRPGGYTPQRALINPFAPSRMPMKLTSNRRRWMHTFPVGPSGEAI QIHHQTRQNMAELQGSGQRDPTHSSAELLELAYHEAAGRHSNSRQPGDGMSFLNFSGTEELSVGLLSNSGAGMNPRTQNKDSLEDSVSTS PDPILTLSAPPVVPGFCCTVGVDWKSLTTPACLPLTTDYFPDRQGLQNDYTEGCYDLLPEADIDRRDEDGVQMTAQQVFEEFICQRLMQG YQIIVQPKTQKPNPAVPPPLSSSPLYSRGLVSRNRPEEEDQYWLSMGRTFHKVTLKDKMITVTRYLPKYPYESAQIHYTYSLCPSHSDSE FVSCWVEFSHERLEEYKWNYLDQYICSAGSEDFSLIESLKFWRTRFLLLPACVTATKRITEGEAHCDIYGDRPRADEDEWQLLDGFVRFV EGLNRIRRRHRSDRMMRKGTAMKGLQMTGPISTHSLESTAPPVGKKGTSALSALLEMEASQKCLGEQQAAVHGGKSSAQSAESSSVAMTP TYMDSPRKVSVDQTATPMLDGTSLGICTGQSMDRGNSQTFGNSQNIGEQGYSSTNSSDSSSQQLVASSLTSSSTLTEILEAMKHPSTGVQ LLSEQKGLSPYCFISAEVVHWLVNHVEGIQTQAMAIDIMQKMLEEQLITHASGEAWRTFIYGFYFYKIVTDKEPDRVAMQQPATTWHTAG VDDFASFQRKWFEVAFVAEELVHSEIPAFLLPWLPSRPASYASRHSSFSRSFGGRSQAAALLAATVPEQRTVTLDVDVNNRTDRLEWCSC YYHGNFSLNAAFEIKLHWMAVTAAVLFEMVQGWHRKATSCGFLLVPVLEGPFALPSYLYGDPLRAQLFIPLNISCLLKEGSEHLFDSFEP ETYWDRMHLFQEAIAHRFGFVQDKYSASAFNFPAENKPQYIHVTGTVFLQLPYSKRKFSGQQRRRRNSTSSTNQNMFCEERVGYNWAYNT
O75140-8	MRTTKVYKLVIHKKGFGGSDDELVVNPKVFPHIKLGDIVEIAHPNDEYSPLLLQVKSLKEDLQKETISVDQTVTQVFRLRPYQDVYVNVV DPKDVTLDLVELTFKDQYIGRGDMWRLKKSLVSTCAYITQKVEFAGIRAQAGELWVKNEKVMCGYISEDTRVVFRSTSAMVYIFIQMSCE MWDFDIYGDLYFEKAVNGFLADLFTKWKEKNCSHEVTVVLFSRTFYDAKSVDEFPEINRASIRQDHKGRFYEDFYKVVVQNERREEWTSL LVTIKKLFIQYPVLVRLEQAEGFPQGDNSTSAQGNYLEAINLSFNVFDKHYINRNFDRTGQMSVVITPGVGVFEVDRLLMILTKQRMIDN GIGVDLVCMGEQPLHAVPLFKLHNRSAPRDSRLGDDYNIPHWINHSFYTSKSQLFCNSFTPRIKLAGKKPASEKAKNGRDTSLGSPKESE NALPIQVDYDAYDAQVFRLPGPSRAQCLTTCRSVRERESHSRKSASSCDVSSSPSLPSRTLPTEEVRSQASDDSSLGKSANILMIPHPHL HQYEVSSSLGYTSTRDVLENMMEPPQRDSSAPGRFHVGSAESMLHVRPGGYTPQRALINPFAPSRMPMKLTSNRRRWMHTFPVGMNPRTQ NKDSLEDSVSTSPDPILTLSAPPVVPGFCCTVGVDWKSLTTPACLPLTTDYFPDRQGLQNDYTEGCYDLLPEADIDRRDEDGVQMTAQQV FEEFICQRLMQGYQIIVQPKTQKPNPAVPPPLSSSPLYSRGLVSRNRPEEEDQYWLSMGRTFHKVTLKDKMITVTRYLPKYPYESAQIHY TYSLCPSHSDSEFVSCWVEFSHERLEEYKWNYLDQYICSAGSEDFSLIESLKFWRTRFLLLPACVTATKRITEGEAHCDIYGDRPRADED EWQLLDGFVRFVEGLNRIRRRHRSDRMMRKGTAMKGLQMTGPISTHSLESTAPPVGKKGTSALSALLEMEASQKCLGEQQAAVHGGKSSA QSAESSSVAMTPTYMDSPRKVSVDQTATPMLDGTSLGICTGQSMDRGNSQTFGNSQNIGEQGYSSTNSSDSSSQQLVASSLTSSSTLTEI LEAMKHPSTGVQLLSEQKGLSPYCFISAEVVHWLVNHVEGIQTQAMAIDIMQKMLEEQLITHASGEAWRTFIYGFYFYKIVTDKEPDRVA MQQPATTWHTAGVDDFASFQRKWFEVAFVAEELVHSEIPAFLLPWLPSRPASYASRHSSFSRSFGGRSQAAALLAATVPEQRTVTLDVDV NNRTDRLEWCSCYYHGNFSLNAAFEIKLHWMAVTAAVLFEMVQGWHRKATSCGFLLVPVLEGPFALPSYLYGDPLRAQLFIPLNISCLLK EGSEHLFDSFEPETYWDRMHLFQEAIAHRFGFVQDKYSASAFNFPAENKPQYIHVTGTVFLQLPYSKRKFSGQQRRRRNSTSSTNQNMFC

Protein Functional Features

Main function of this protein. (from UniProt)

DEPDC5 (go to UniProt):O75140

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
O75140	Domain	1187	1262	Note=DEP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00066	Type=Deletion;Start=560;End=1603
O75140	Region	696	720	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=560;End=1603
O75140	Region	696	720	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=624;End=701
O75140	Region	1135	1165	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Deletion;Start=560;End=1603

Gene Isoform Structures and Expression Levels for DEPDC5

Gene structures of our canonical and alternative spliced genes of DEPDC5
* 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 O75140-10

3D view using mol* of O75140-2

3D view using mol* of O75140-4

3D view using mol* of O75140-8

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 O75140-10

pLDDT distribution across the protein length of O75140-2

pLDDT distribution across the protein length of O75140-4

pLDDT distribution across the protein length of O75140-8

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 O75140-10

Ramachandran plot of O75140-2

Ramachandran plot of O75140-8

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
O75140-10	1.071	1113	0.985	2543.345	0.453	0.804	1.047	0.369	1.342	0.275	0.683	99,101,108,109,110,111,114,145,163,165,170,172,215 ,261,315,316,317,318,319,320,321,322,323,324,325,3 28,329,330,331,332,352,356,357,358,359,360,361,362 ,363,364,365,401,402,403,404,405,406,613,614,617,6 18,620,621,622,630,631,632,633,634,739,743,745,746 ,749,750,751,752,753,808,809,811,856,883,884,885,8 87,894,896,897,898,899,900,902,903,904,905,906,907 ,908,909,910,911,912,913,915,916,918,924,934,935,9 37,938,940,941,942,943,945,1299,1319,1347,1348,135 0,1351,1371,1373,1375,1377,1378,1379,1382,1383,138 4,1387,1389,1420,1421,1422,1423,1424,1425,1426,142 7,1428,1429,1430,1431,1432,1433,1434,1436,1437,143 8,1439,1440,1470,1474,1484,1485,1486,1487,1488,148 9,1490,1491,1492,1493,1494,1495,1496,1497,1498,149 9,1500,1501,1502,1512,1514,1515,1516,1517,1518,151 9,1540,1541,1542,1543,1547,1552,1553,1555
O75140-2	1.004	105	0.925	371.812	0.537	0.704	0.968	0.089	1.342	0.067	1.226	246,344,347,381,382,383,384,387,388,389,390,391,39 2,393,394,395,396,536,537,538,539,540
O75140-4	1.067	261	0.966	649.642	0.417	0.799	1.085	0.149	1.392	0.107	0.675	105,106,204,207,208,211,212,213,214,215,257,259,26 0,261,262,263,264,265,266,267,325,327,328,894,895, 896,1401,1402,1403,1404,1405,1413,1414,1415,1416,1 417,1486,1526,1527,1528,1529,1530,1531,1532,1533,1 534,1535,1537,1543,1544,1546,1547
O75140-8	1.048	303	0.989	724.759	0.434	0.77	1.056	0.223	1.265	0.176	0.77	105,106,201,204,205,207,208,211,212,213,214,215,25 7,260,261,262,263,264,265,266,267,268,271,325,327, 328,816,817,818,1323,1324,1325,1326,1327,1335,1336 ,1337,1338,1339,1408,1448,1449,1450,1451,1452,1454 ,1455,1456,1457,1459,1465,1466,1468,1469

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 O75140-10_O75140-10_6ces_D.pdb

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

3D view using mol* of O75140-10_6ces_D_O75140-2.pdb

3D view using mol* of O75140-10_6ces_D_O75140-4.pdb

3D view using mol* of O75140-10_6ces_D_O75140-8.pdb

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

3D view using mol* of O75140-10_O75140-2.pdb

3D view using mol* of O75140-10_O75140-4.pdb

3D view using mol* of O75140-10_O75140-8.pdb

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

./stats/secondary_structure/figure/O75140-10_vs_O75140-2.png

./stats/secondary_structure/figure/O75140-10_vs_O75140-4.png

./stats/secondary_structure/figure/O75140-10_vs_O75140-8.png

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

./stats/relative_asa/O75140-10_vs_O75140-2.png

./stats/relative_asa/O75140-10_vs_O75140-4.png

./stats/relative_asa/O75140-10_vs_O75140-8.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 DEPDC5

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession

Gene name

DrugBank ID

Drug name

Drug group

Actions

Related Diseases to DEPDC5

Previous studies relating to the alternative splicing of DEPDC5 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in DEPDC5

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance