9CY5 | pdb_00009cy5

Dyrk1a bound to a competitive inhibitor

PDB DOI: https://doi.org/10.2210/pdb9CY5/pdb

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

Deposited: 2024-08-01 Released: 2025-10-22
Deposition Author(s): Montfort, W.R.
Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.259 (Depositor), 0.207 (DCC)
R-Value Work:
0.200 (Depositor)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Dyrk1a bound to a competitive inhibitor

Montfort, W.R.

To be published.

Macromolecule Content

Total Structure Weight: 85.9 kDa
Atom Count: 5,865
Modeled Residue Count: 681
Deposited Residue Count: 730
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 1A	A, B	365	Homo sapiens	Mutation(s): 0 Gene Names: DYRK1A, DYRK, MNB, MNBH EC: 2.7.11.23 (PDB Primary Data), 2.7.12.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13627 (Homo sapiens) Explore Q13627 Go to UniProtKB: Q13627
PHAROS: Q13627 GTEx: ENSG00000157540
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13627
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A04 (Subject of Investigation/LOI) Query on A1A04 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	(4P)-4-{(4M)-4-[3-fluoro-4-(4-methylpiperazin-1-yl)phenyl]quinazolin-6-yl}pyridin-2-amine C₂₄ H₂₃ F N₆ IRBNSGDBRRBWDJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.259 (Depositor), 0.207 (DCC)
R-Value Work: 0.200 (Depositor)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.886	α = 90
b = 84.646	β = 90
c = 148.799	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM2	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	AG067926

Revision History (Full details and data files)

Version 1.0: 2025-10-22
Type: Initial release

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