6HDR | pdb_00006hdr

Human DYRK2 bound to Curcumin

PDB DOI: https://doi.org/10.2210/pdb6HDR/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., Vollmar, M., Krojer, T., Bountra, C., Edwards, A.M., Arrowsmith, C., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.243 (Depositor), 0.242 (DCC)
R-Value Work:
0.190 (Depositor), 0.192 (DCC)
R-Value Observed:
0.192 (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 Curcumin

Elkins, J.M., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 50.22 kDa
Atom Count: 3,394
Modeled Residue Count: 407
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CC9 Query on CC9 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]	curcumin C₂₁ H₂₀ O₆ VFLDPWHFBUODDF-FCXRPNKRSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DTD Query on DTD 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]	DITHIANE DIOL C₄ H₈ O₂ S₂ YPGMOWHXEQDBBV-IMJSIDKUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PO4 Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [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

Binding Affinity Annotations
ID	Source	Binding Affinity
CC9	BindingDB: 6HDR	Kd: 1.45e+4 (nM) from 1 assay(s)
CC9	BindingDB: 6HDR	IC50: min: 2.5, max: 1058 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.243 (Depositor), 0.242 (DCC)
R-Value Work: 0.190 (Depositor), 0.192 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.642	α = 90
b = 83.642	β = 90
c = 148.916	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, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary