6HDP | pdb_00006hdp

Human DYRK2 bound to Scorzodihydrostilbene A

PDB DOI: https://doi.org/10.2210/pdb6HDP/pdb

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

Deposited: 2018-08-18 Released: 2019-08-28
Deposition Author(s): Elkins, J.M., Soundararajan, M., Proksch, P., Meijer, L., Vollmar, M., Krojer, T., Bountra, C., Edwards, A.M., Arrowsmith, C., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.238 (Depositor), 0.237 (DCC)
R-Value Work:
0.184 (Depositor), 0.192 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

DYRK2 bound to Scorzodihydrostilbene A

Elkins, J.M., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 50.01 kDa
Atom Count: 3,498
Modeled Residue Count: 409
Deposited Residue Count: 429
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity tyrosine-phosphorylation-regulated kinase 2	A	429	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92630
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FZ5 Query on FZ5 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	Scorzodihydrostilbene A C₂₃ H₂₈ O₁₀ YRCZOJOYJCLBDV-DODNOZFWSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 2 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
PTR Query on PTR	A	TYR	Phosphorylation	C₉ H₁₂ N O₆ P
SEP Query on SEP	A	SER	Phosphorylation	C₃ H₈ N O₆ P

Binding Affinity Annotations
ID	Source	Binding Affinity
FZ5	BindingDB: 6HDP	IC50: 1.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.238 (Depositor), 0.237 (DCC)
R-Value Work: 0.184 (Depositor), 0.192 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.527	α = 90
b = 84.527	β = 90
c = 148.372	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-08-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-08-28
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary