6S1J | pdb_00006s1j

Crystal Structure of DYRK1A with small molecule inhibitor

PDB DOI: https://doi.org/10.2210/pdb6S1J/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-06-18 Released: 2019-06-26
Deposition Author(s): Sorrell, F.J., Henderson, S.H., Redondo, C., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Elkins, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free:
0.176 (Depositor), 0.179 (DCC)
R-Value Work:
0.155 (Depositor), 0.158 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Kinase Scaffold Repurposing in the Public Domain

Sorrell, F.J., Henderson, S.H., Elkins, J.M., Ward, S.

To be published.

Macromolecule Content

Total Structure Weight: 43.2 kDa
Atom Count: 3,172
Modeled Residue Count: 341
Deposited Residue Count: 361
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 1A	A	361	Homo sapiens	Mutation(s): 0 Gene Names: DYRK1A, DYRK, MNB, MNBH EC: 2.7.12.1 (PDB Primary Data), 2.7.11.23 (UniProt)
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KRK (Subject of Investigation/LOI) Query on KRK 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]	3-[2-[(3~{S})-3-fluoranylpyrrolidin-1-yl]pyrimidin-4-yl]pyrazolo[1,5-b]pyridazine C₁₄ H₁₃ F N₆ CTKSUQYBSSCMMB-JTQLQIEISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], L [auth A], M [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] H [auth A] C [auth A], D [auth A], E [auth A], F [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free: 0.176 (Depositor), 0.179 (DCC)
R-Value Work: 0.155 (Depositor), 0.158 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.202	α = 90
b = 69.671	β = 117.54
c = 67.44	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-06-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-06-26
Type: Initial release
Version 1.1: 2019-08-21
Changes: Data collection
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary

6S1J | pdb_00006s1j

Crystal Structure of DYRK1A with small molecule inhibitor

Literature

Kinase Scaffold Repurposing in the Public Domain

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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