7DH3

The co-crystal structure of DYRK2 with a small molecule inhibitor 5

PDB DOI: https://doi.org/10.2210/pdb7DH3/pdb

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2020-11-12 Released: 2021-11-17
Deposition Author(s): Wei, T., Xiao, J.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.217
R-Value Work: 0.194
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The co-crystal structure of DYRK2 with a small molecule inhibitor 5

Wei, T., Xiao, J.

To be published.

Macromolecule Content

Total Structure Weight: 38.23 kDa
Atom Count: 2,742
Modelled Residue Count: 326
Deposited Residue Count: 326
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 2	A	326	Homo sapiens	Mutation(s): 0 Gene Names: DYRK2 EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92630 (Homo sapiens) Explore Q92630 Go to UniProtKB: Q92630
PHAROS: Q92630 GTEx: ENSG00000127334
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92630
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H7C (Subject of Investigation/LOI) Query on H7C Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2,7-dimethoxy-9-piperidin-4-ylsulfanyl-acridine C₂₀ H₂₂ N₂ O₂ S ZXEZPSYSBIFZGE-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.217
R-Value Work: 0.194
R-Value Observed: 0.195
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.56	α = 90
b = 128.83	β = 90
c = 132.45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PDB_EXTRACT	data extraction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-11-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2021-11-17
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.