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:OPRK1

Protein Summary

Gene summary

Gene name: OPRK1
ASpdb.0 ID: 4986
	Gene
Gene symbol	OPRK1
Gene ID	4986
Gene name	opioid receptor kappa 1
Synonyms	K-OR-1\|KOP\|KOR\|KOR-1\|KOR1\|OPRK
Cytomap	8q11.23
Type of gene	protein-coding
Description	kappa-type opioid receptorOpiate receptor, kappa-1kappa opioid receptor
Modification date	20240411
UniProtAcc	P41145

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

Partner	Gene	GO ID	GO term	PubMed ID
Gene	OPRK1	GO:0004985	G protein-coupled opioid receptor activity	22437504
Gene	OPRK1	GO:0005654	nucleoplasm	-
Gene	OPRK1	GO:0005829	cytosol	-
Gene	OPRK1	GO:0005886	plasma membrane	-
Gene	OPRK1	GO:0006955	immune response	8755601
Gene	OPRK1	GO:0016020	membrane	22437504
Gene	OPRK1	GO:0031635	adenylate cyclase-inhibiting opioid receptor signaling pathway	22437504
Gene	OPRK1	GO:0038003	G protein-coupled opioid receptor signaling pathway	8755601
Gene	OPRK1	GO:0038048	dynorphin receptor activity	8755601
Gene	OPRK1	GO:0051607	defense response to virus	8755601

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
P41145-1	P41145-1_4djh_A.pdb	4DJH	X-ray	2.9	A	55	347

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

P41145

OPRK1

P41145-1

P41145-2

380

291

Deletion

none

Multiple sequence alignment of our canonical and alternatively spliced OPRK1

Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of OPRK1

UniProt-id	ENSG	ENST	ENSP
P41145-1	ENSG00000082556.14	ENST00000265572.8	ENSP00000265572.3
P41145-1	ENSG00000082556.14	ENST00000520287.5	ENSP00000429706.1
P41145-2	ENSG00000082556.14	ENST00000524278.5	ENSP00000430923.1

UniProt-id	NM ID	NP ID
P41145-1	NM_000912.4	NP_000903.2
P41145-2	NM_001282904.1	NP_001269833.1

Amino acid sequences of our canonical and alternatively spliced OPRK1

accession_id	Protein sequence
P41145-1	MDSPIQIFRGEPGPTCAPSACLPPNSSAWFPGWAEPDSNGSAGSEDAQLEPAHISPAIPVIITAVYSVVFVVGLVGNSLVMFVIIRYTKM KTATNIYIFNLALADALVTTTMPFQSTVYLMNSWPFGDVLCKIVISIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPLKAKIINI CIWLLSSSVGISAIVLGGTKVREDVDVIECSLQFPDDDYSWWDLFMKICVFIFAFVIPVLIIIVCYTLMILRLKSVRLLSGSREKDRNLR RITRLVLVVVAVFVVCWTPIHIFILVEALGSTSHSTAALSSYYFCIALGYTNSSLNPILYAFLDENFKRCFRDFCFPLKMRMERQSTSRV
P41145-2	MKTATNIYIFNLALADALVTTTMPFQSTVYLMNSWPFGDVLCKIVISIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPLKAKIIN ICIWLLSSSVGISAIVLGGTKVREDVDVIECSLQFPDDDYSWWDLFMKICVFIFAFVIPVLIIIVCYTLMILRLKSVRLLSGSREKDRNL RRITRLVLVVVAVFVVCWTPIHIFILVEALGSTSHSTAALSSYYFCIALGYTNSSLNPILYAFLDENFKRCFRDFCFPLKMRMERQSTSR

Protein Functional Features

Main function of this protein. (from UniProt)

OPRK1 (go to UniProt):P41145

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
P41145	Topological domain	1	57	Note=Extracellular	Type=Deletion;Start=1;End=89
P41145	Transmembrane	58	85	Note=Helical%3B Name%3D1	Type=Deletion;Start=1;End=89
P41145	Topological domain	86	95	Note=Cytoplasmic	Type=Deletion;Start=1;End=89

Gene Isoform Structures and Expression Levels for OPRK1

Gene structures of our canonical and alternative spliced genes of OPRK1
* 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 P41145-1

3D view using mol* of P41145-2

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 P41145-1

pLDDT distribution across the protein length of P41145-2

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 P41145-1

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
P41145-1	1.199	205	1.217	368.725	0.357	0.961	1.249	1.805	0.92	1.961	1.499	26,27,28,29,30,31,108,111,115,118,124,134,135,138, 139,141,142,209,210,211,212,214,223,226,227,230,23 1,287,290,291,294,297,312,313,315,316,319,320,322, 323
P41145-2	1.12	136	1.172	375.928	0.5	0.794	1.02	1.67	0.749	2.23	0.376	5,6,9,12,60,63,64,67,150,153,157,182,183,185,186,1 89,190,191,193,194,233,237,240,241,243,244,245,246 ,247,249

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 P41145-1_P41145-1_4djh_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 P41145-1_4djh_A_P41145-2.pdb

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

3D view using mol* of P41145-1_P41145-2.pdb

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

./stats/secondary_structure/figure/P41145-1_vs_P41145-2.png

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

./stats/relative_asa/P41145-1_vs_P41145-2.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 OPRK1

Drugs targeting this gene/protein.
(DrugBank)

UniProt accession	Gene name	DrugBank ID	Drug name	Drug group	Actions
P41145	OPRK1	DB09173	Butyrfentanyl	illicit	agonist
P41145	OPRK1	DB01238	Aripiprazole	approved, investigational	ligand
P41145	OPRK1	DB06230	Nalmefene	approved, investigational, withdrawn	partial agonist
P41145	OPRK1	DB06148	Mianserin	approved, investigational	agonist
P41145	OPRK1	DB06409	Morphine glucuronide	investigational
P41145	OPRK1	DB01221	Ketamine	approved, vet_approved	agonist
P41145	OPRK1	DB06738	Ketobemidone	investigational	agonist
P41145	OPRK1	DB05046	V1003	investigational
P41145	OPRK1	DB06288	Amisulpride	approved, investigational	agonist
P41145	OPRK1	DB06800	Methylnaltrexone	approved	antagonist
P41145	OPRK1	DB06274	Alvimopan	approved, investigational	antagonist
P41145	OPRK1	DB09272	Eluxadoline	approved, investigational	agonist
P41145	OPRK1	DB01439	3-Methylthiofentanyl	experimental, illicit	agonist
P41145	OPRK1	DB01452	Diamorphine	approved, illicit, investigational	agonist
P41145	OPRK1	DB05104	Asimadoline	investigational
P41145	OPRK1	DB01497	Etorphine	illicit, vet_approved	agonist
P41145	OPRK1	DB01535	Carfentanil	illicit, investigational, vet_approved	agonist
P41145	OPRK1	DB01548	Diprenorphine	illicit, vet_approved	antagonist
P41145	OPRK1	DB05155	CR665	investigational
P41145	OPRK1	DB01565	Dihydromorphine	experimental, illicit	agonist
P41145	OPRK1	DB01571	3-Methylfentanyl	illicit	agonist
P41145	OPRK1	DB09209	Pholcodine	approved, illicit	antagonist
P41145	OPRK1	DB05443	ADL 10-0101	investigational
P41145	OPRK1	DB01209	Dezocine	approved, investigational	antagonist
P41145	OPRK1	DB06204	Tapentadol	approved	agonist
P41145	OPRK1	DB11130	Opium	approved, illicit	agonist
P41145	OPRK1	DB00854	Levorphanol	approved	agonist
P41145	OPRK1	DB00844	Nalbuphine	approved	agonist
P41145	OPRK1	DB00836	Loperamide	approved	agonist
P41145	OPRK1	DB00825	Levomenthol	approved	agonist
P41145	OPRK1	DB00813	Fentanyl	approved, illicit, investigational, vet_approved	agonist
P41145	OPRK1	DB11938	Difelikefalin	approved, investigational	agonist
P41145	OPRK1	DB00708	Sufentanil	approved, investigational
P41145	OPRK1	DB00704	Naltrexone	approved, investigational, vet_approved	antagonist
P41145	OPRK1	DB00652	Pentazocine	approved, vet_approved	agonist
P41145	OPRK1	DB00647	Dextropropoxyphene	approved, illicit, investigational, withdrawn	antagonist
P41145	OPRK1	DB00611	Butorphanol	approved, illicit, vet_approved	agonist
P41145	OPRK1	DB00555	Lamotrigine	approved, investigational	inhibitor
P41145	OPRK1	DB00514	Dextromethorphan	approved	agonist
P41145	OPRK1	DB00497	Oxycodone	approved, illicit, investigational	agonist
P41145	OPRK1	DB00454	Meperidine	approved
P41145	OPRK1	DB00396	Progesterone	approved, vet_approved	activator, potentiator
P41145	OPRK1	DB00370	Mirtazapine	approved	agonist
P41145	OPRK1	DB00327	Hydromorphone	approved, illicit	agonist
P41145	OPRK1	DB00321	Amitriptyline	approved	agonist
P41145	OPRK1	DB00318	Codeine	approved, illicit	agonist
P41145	OPRK1	DB00295	Morphine	approved, investigational	agonist
P41145	OPRK1	DB00289	Atomoxetine	approved	partial agonist
P41145	OPRK1	DB12543	Samidorphan	approved, investigational	partial agonist
P41145	OPRK1	DB00899	Remifentanil	approved	agonist
P41145	OPRK1	DB11691	Naldemedine	approved, investigational	antagonist
P41145	OPRK1	DB00193	Tramadol	approved, investigational	agonist
P41145	OPRK1	DB00921	Buprenorphine	approved, illicit, investigational, vet_approved	antagonist
P41145	OPRK1	DB14146	Loxicodegol	investigational	agonist
P41145	OPRK1	DB01183	Naloxone	approved, vet_approved	antagonist
P41145	OPRK1	DB11186	Pentoxyverine	approved, investigational, withdrawn	agonist

Related Diseases to OPRK1

Previous studies relating to the alternative splicing of OPRK1 and disease information from the MeSH term (PubMed)

Gene

PMID

Title

Abstract

MeSH ID

MeSH term

Clinically important variants in OPRK1

(ClinVar, 04/20/2024)

accession_id

uniprot_id

gene_name

Type

Variant

Clinical_significance