8C3G

Crystal structure of DYRK1A in complex with AZ191

PDB DOI: https://doi.org/10.2210/pdb8C3G/pdb

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

Deposited: 2022-12-23 Released: 2024-01-10
Deposition Author(s): Grygier, P., Pustelny, K., Dubin, G., Czarna, A.
Funding Organization(s): Polish National Science Centre, National Center for Research and Development (Poland)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.237
R-Value Work: 0.194
R-Value Observed: 0.196

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural perspective on the design of selective DYRK1B inhibitors

Grygier, P., Pustelny, K., Dubin, G., Czarna, A.

To be published.

Macromolecule Content

Total Structure Weight: 177.14 kDa
Atom Count: 11,918
Modelled Residue Count: 1,355
Deposited Residue Count: 1,484
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 1A	A, B, C, D	371	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13627
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QS0 (Subject of Investigation/LOI) Query on QS0 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain E [auth A] SDF format, chain JA [auth D] SDF format, chain T [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain T [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain T [auth B]	AA [auth C], E [auth A], JA [auth D], T [auth B]	N-[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]-4-(1-methylpyrrolo[2,3-c]pyridin-3-yl)pyrimidin-2-amine C₂₄ H₂₇ N₇ O ZYVXTMKTGDARKR-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain E [auth A] Focus chain JA [auth D] Focus chain T [auth B] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A] Focus chain JA [auth D] Focus chain T [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain PA [auth D] SDF format, chain Y [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain Y [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain Y [auth B]	PA [auth D], Y [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain PA [auth D] Focus chain Y [auth B] Interactions & Density Focus chain PA [auth D] Focus chain Y [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain P [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain BA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain Z [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain Z [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain Z [auth C]	BA [auth C] CA [auth C] DA [auth C] EA [auth C] F [auth A] BA [auth C], CA [auth C], DA [auth C], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], Q [auth A], R [auth A], S [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Z [auth C]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
QS0	BindingDB: 8C3G	Ki: 4.4 (nM) from 1 assay(s)
		Kd: 2.6 (nM) from 1 assay(s)
		IC50: min: 17, max: 3.00e+4 (nM) from 5 assay(s)