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:NDRG2

Protein Summary

Gene summary

Gene name: NDRG2
ASpdb.0 ID: 57447
	Gene
Gene symbol	NDRG2
Gene ID	57447
Gene name	NDRG family member 2
Synonyms	SYLD
Cytomap	14q11.2
Type of gene	protein-coding
Description	protein NDRG2N-myc downstream regulator 2N-myc downstream-regulated gene 2 proteinNDR1-related protein NDR2cytoplasmic protein Ndr1syld709613 protein
Modification date	20240407
UniProtAcc	Q9UN36

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	NDRG2	GO:0005794	Golgi apparatus	-

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
Q9UN36-1	Q9UN36-1_2xmr_A.pdb	2XMR	X-ray	2.0	A	40	318

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
Q9UN36	NDRG2	Q9UN36-1	Q9UN36-2	371	357	26	39	Deletion	none	none	25	25
Q9UN36	NDRG2	Q9UN36-1	Q9UN36-3	371	360	262	272	Deletion	none	none	261	261
Q9UN36	NDRG2	Q9UN36-1	Q9UN36-4	371	328	26	39	Deletion	none	none	25	25
Q9UN36	NDRG2	Q9UN36-1	Q9UN36-4	371	328	157	185	Deletion	none	none	142	142
Q9UN36	NDRG2	Q9UN36-1	Q9UN36-5	371	341	26	39	Deletion	none	none	25	25
Q9UN36	NDRG2	Q9UN36-1	Q9UN36-5	371	341	272	287	Deletion	none	none	257	257
Q9UN36	NDRG2	Q9UN36-1	Q9UN36-6	371	367	1	1	Substitution	M	MENGGSMQATM	1	11
Q9UN36	NDRG2	Q9UN36-1	Q9UN36-6	371	367	26	39	Deletion	none	none	35	35

Multiple sequence alignment of our canonical and alternatively spliced NDRG2

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of NDRG2

UniProt-id	ENSG	ENST	ENSP
Q9UN36-1	ENSG00000165795.25	ENST00000298687.9	ENSP00000298687.5
Q9UN36-1	ENSG00000165795.25	ENST00000397851.6	ENSP00000380949.2
Q9UN36-1	ENSG00000165795.25	ENST00000397853.7	ENSP00000380951.3
Q9UN36-1	ENSG00000165795.25	ENST00000397858.5	ENSP00000380956.1
Q9UN36-1	ENSG00000165795.25	ENST00000556147.6	ENSP00000451712.1
Q9UN36-2	ENSG00000165795.25	ENST00000350792.7	ENSP00000344620.3
Q9UN36-2	ENSG00000165795.25	ENST00000360463.7	ENSP00000353649.3
Q9UN36-2	ENSG00000165795.25	ENST00000553503.5	ENSP00000452306.1
Q9UN36-2	ENSG00000165795.25	ENST00000554143.5	ENSP00000452006.1
Q9UN36-2	ENSG00000165795.25	ENST00000555158.5	ENSP00000452038.1
Q9UN36-3	ENSG00000165795.25	ENST00000397847.6	ENSP00000380945.2
Q9UN36-4	ENSG00000165795.25	ENST00000298684.9	ENSP00000298684.5
Q9UN36-5	ENSG00000165795.25	ENST00000397844.6	ENSP00000380943.2
Q9UN36-6	ENSG00000165795.25	ENST00000403829.7	ENSP00000385889.3

UniProt-id	NM ID	NP ID
Q9UN36-1	NM_001320329.1	NP_001307258.1
Q9UN36-1	NM_201535.1	NP_963293.1
Q9UN36-1	NM_201537.1	NP_963831.1
Q9UN36-1	NM_201539.1	NP_963833.1
Q9UN36-1	NM_201540.1	NP_963834.1
Q9UN36-2	NM_001282213.1	NP_001269142.1
Q9UN36-2	NM_001282214.1	NP_001269143.1
Q9UN36-2	NM_016250.2	NP_057334.1
Q9UN36-2	NM_201536.1	NP_963294.1
Q9UN36-2	NM_201538.1	NP_963832.1
Q9UN36-2	NM_201541.1	NP_963835.1
Q9UN36-3	NM_001282215.1	NP_001269144.1
Q9UN36-5	NM_001282212.1	NP_001269141.1
Q9UN36-6	NM_001282211.1	NP_001269140.1

Amino acid sequences of our canonical and alternatively spliced NDRG2

accession_id	Protein sequence
Q9UN36-1	MAELQEVQITEEKPLLPGQTPEAAKEAELAARILLDQGQTHSVETPYGSVTFTVYGTPKPKRPAILTYHDVGLNYKSCFQPLFQFEDMQE IIQNFVRVHVDAPGMEEGAPVFPLGYQYPSLDQLADMIPCVLQYLNFSTIIGVGVGAGAYILARYALNHPDTVEGLVLINIDPNAKGWMD WAAHKLTGLTSSIPEMILGHLFSQEELSGNSELIQKYRNIITHAPNLDNIELYWNSYNNRRDLNFERGGDITLRCPVMLVVGDQAPHEDA VVECNSKLDPTQTSFLKMADSGGQPQLTQPGKLTEAFKYFLQGMGYMASSCMTRLSRSRTASLTSAASVDGNRSRSRTLSQSSESGTLSS
Q9UN36-2	MAELQEVQITEEKPLLPGQTPEAAKTHSVETPYGSVTFTVYGTPKPKRPAILTYHDVGLNYKSCFQPLFQFEDMQEIIQNFVRVHVDAPG MEEGAPVFPLGYQYPSLDQLADMIPCVLQYLNFSTIIGVGVGAGAYILARYALNHPDTVEGLVLINIDPNAKGWMDWAAHKLTGLTSSIP EMILGHLFSQEELSGNSELIQKYRNIITHAPNLDNIELYWNSYNNRRDLNFERGGDITLRCPVMLVVGDQAPHEDAVVECNSKLDPTQTS
Q9UN36-3	MAELQEVQITEEKPLLPGQTPEAAKEAELAARILLDQGQTHSVETPYGSVTFTVYGTPKPKRPAILTYHDVGLNYKSCFQPLFQFEDMQE IIQNFVRVHVDAPGMEEGAPVFPLGYQYPSLDQLADMIPCVLQYLNFSTIIGVGVGAGAYILARYALNHPDTVEGLVLINIDPNAKGWMD WAAHKLTGLTSSIPEMILGHLFSQEELSGNSELIQKYRNIITHAPNLDNIELYWNSYNNRRDLNFERGGDITLRCPVMLVVECNSKLDPT QTSFLKMADSGGQPQLTQPGKLTEAFKYFLQGMGYMASSCMTRLSRSRTASLTSAASVDGNRSRSRTLSQSSESGTLSSGPPGHTMEVSC
Q9UN36-4	MAELQEVQITEEKPLLPGQTPEAAKTHSVETPYGSVTFTVYGTPKPKRPAILTYHDVGLNYKSCFQPLFQFEDMQEIIQNFVRVHVDAPG MEEGAPVFPLGYQYPSLDQLADMIPCVLQYLNFSTIIGVGVGAGAYILARYALTGLTSSIPEMILGHLFSQEELSGNSELIQKYRNIITH APNLDNIELYWNSYNNRRDLNFERGGDITLRCPVMLVVGDQAPHEDAVVECNSKLDPTQTSFLKMADSGGQPQLTQPGKLTEAFKYFLQG
Q9UN36-5	MAELQEVQITEEKPLLPGQTPEAAKTHSVETPYGSVTFTVYGTPKPKRPAILTYHDVGLNYKSCFQPLFQFEDMQEIIQNFVRVHVDAPG MEEGAPVFPLGYQYPSLDQLADMIPCVLQYLNFSTIIGVGVGAGAYILARYALNHPDTVEGLVLINIDPNAKGWMDWAAHKLTGLTSSIP EMILGHLFSQEELSGNSELIQKYRNIITHAPNLDNIELYWNSYNNRRDLNFERGGDITLRCPVMLVVGDQAPHEDAVMADSGGQPQLTQP
Q9UN36-6	MENGGSMQATMAELQEVQITEEKPLLPGQTPEAAKTHSVETPYGSVTFTVYGTPKPKRPAILTYHDVGLNYKSCFQPLFQFEDMQEIIQN FVRVHVDAPGMEEGAPVFPLGYQYPSLDQLADMIPCVLQYLNFSTIIGVGVGAGAYILARYALNHPDTVEGLVLINIDPNAKGWMDWAAH KLTGLTSSIPEMILGHLFSQEELSGNSELIQKYRNIITHAPNLDNIELYWNSYNNRRDLNFERGGDITLRCPVMLVVGDQAPHEDAVVEC NSKLDPTQTSFLKMADSGGQPQLTQPGKLTEAFKYFLQGMGYMASSCMTRLSRSRTASLTSAASVDGNRSRSRTLSQSSESGTLSSGPPG

Protein Functional Features

Main function of this protein. (from UniProt)

NDRG2 (go to UniProt):Q9UN36

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
Q9UN36	Region	1	21	Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256\|SAM:MobiDB-lite	Type=Substitution;Start=1;End=1

Gene Isoform Structures and Expression Levels for NDRG2

Gene structures of our canonical and alternative spliced genes of NDRG2
* 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 Q9UN36-1

3D view using mol* of Q9UN36-2

3D view using mol* of Q9UN36-3

3D view using mol* of Q9UN36-4

3D view using mol* of Q9UN36-5

3D view using mol* of Q9UN36-6

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 Q9UN36-1

pLDDT distribution across the protein length of Q9UN36-2

pLDDT distribution across the protein length of Q9UN36-3

pLDDT distribution across the protein length of Q9UN36-4

pLDDT distribution across the protein length of Q9UN36-5

pLDDT distribution across the protein length of Q9UN36-6

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 Q9UN36-1

Ramachandran plot of Q9UN36-4

Ramachandran plot of Q9UN36-6

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
Q9UN36-1	0.876	76	0.882	296.695	0.736	0.634	0.713	0.097	0.977	0.099	0.548	172,174,175,176,177,180,183,184,187,195,196,199,20 0,204,207,218,234,237,240,266,267,269,270,273
Q9UN36-2	0.985	167	1.019	449.673	0.641	0.651	0.838	0.667	0.958	0.696	1.005	73,76,77,233,242,244,261,262,266,267,268,269,270,2 71,272,273,288,290,291,292,294,295,296,299,300,306 ,308,309,310,351,352,353,354,355,357
Q9UN36-3	1.076	120	1.146	345.401	0.557	0.7	0.901	1.389	0.656	2.117	1.388	256,257,258,269,270,271,272,273,274,275,291,294,29 5,298,299,301,302,303,311,312,313,314,354,355,356, 357,358,360
Q9UN36-4	0.996	164	0.994	421.89	0.553	0.693	0.882	0.277	1.11	0.249	1.515	32,33,106,108,109,111,112,115,116,118,119,123,124, 140,141,144,145,146,148,149,150,151,153,185,188,18 9,191,192,195,196
Q9UN36-5	0.974	213	1.008	630.091	0.641	0.635	0.803	0.427	0.959	0.445	0.988	154,157,158,159,160,162,166,169,170,173,177,181,18 2,184,185,186,188,189,190,193,204,220,223,226,228, 229,230,231,232,233,234,238,239,240,241,242,243,24 5,247,252,253,255,256,280,283,284,334,335,336,337
Q9UN36-6	0.967	102	0.956	232.211	0.551	0.648	0.912	0.505	1.145	0.441	0.488	28,29,30,31,32,51,52,53,55,71,72,75,76,79,80,85,86 ,88,89,91,92,93,95

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 Q9UN36-1_Q9UN36-1_2xmr_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 Q9UN36-1_2xmr_A_Q9UN36-2.pdb

3D view using mol* of Q9UN36-1_2xmr_A_Q9UN36-3.pdb

3D view using mol* of Q9UN36-1_2xmr_A_Q9UN36-4.pdb

3D view using mol* of Q9UN36-1_2xmr_A_Q9UN36-5.pdb

3D view using mol* of Q9UN36-1_2xmr_A_Q9UN36-6.pdb

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

3D view using mol* of Q9UN36-1_Q9UN36-2.pdb

3D view using mol* of Q9UN36-1_Q9UN36-3.pdb

3D view using mol* of Q9UN36-1_Q9UN36-4.pdb

3D view using mol* of Q9UN36-1_Q9UN36-5.pdb

3D view using mol* of Q9UN36-1_Q9UN36-6.pdb

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

./stats/secondary_structure/figure/Q9UN36-1_vs_Q9UN36-2.png