6LN1 | pdb_00006ln1

A natural inhibitor of DYRK1A for treatment of diabetes mellitus

• PDB DOI: https://doi.org/10.2210/pdb6LN1/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-28 Released: 2021-10-06 
• Deposition Author(s): Li, H., Chen, L.X., Zheng, M.Z., Zhang, Q.Z., Zhang, C.L., Wu, C.R., Yang, K.Y., Song, Z.R., Wang, Q.Q., Li, C., Zhou, Y.R., Chen, J.C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

A natural DYRK1A inhibitor as a potential stimulator for beta-cell proliferation in diabetes.

Zheng, M., Zhang, Q., Zhang, C., Wu, C., Yang, K., Song, Z., Wang, Q., Li, C., Zhou, Y., Chen, J., Li, H., Chen, L.

(2021) Clin Transl Med 11: e494-e494

• PubMed: 34323401 
• DOI: https://doi.org/10.1002/ctm2.494
• Primary Citation of Related Structures:  
  6LN1

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Organizational Affiliation: 
• Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji-Rongcheng Center for Biomedicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 81.48 kDa 
• Atom Count: 5,610 
• Modeled Residue Count: 673 
• Deposited Residue Count: 694 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 1A	A, B	347	Homo sapiens	Mutation(s): 0  Gene Names: DYRK1A, DYRK, MNB, MNBH EC: 2.7.12.1 (PDB Primary Data), 2.7.11.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13627 (Homo sapiens) Explore Q13627  Go to UniProtKB:  Q13627
PHAROS:  Q13627 GTEx:  ENSG00000157540

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EKU (Subject of Investigation/LOI)	C [auth A], D [auth B]	1,3,5,8-tetrakis(oxidanyl)xanthen-9-one C13 H8 O6 MPXAWSABMVLIBU-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
EKU	BindingDB:  6LN1	Kd: 60 (nM) from 1 assay(s)
		IC50: 266 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.467	α = 90
b = 133.467	β = 90
c = 92.238	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Li, H., Chen, L.X., Zheng, M.Z., Zhang, Q.Z., Zhang, C.L., Wu, C.R., Yang, K.Y., Song, Z.R., Wang, Q.Q., Li, C., Zhou, Y.R., Chen, J.C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81773594, 81773869, 81773637,U1803122

Revision History  

• Version 1.0: 2021-10-06
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary