7REE | pdb_00007ree

High-resolution crystal structure of human JAK2 kinase domain (JH1) bound to YM2-059

PDB DOI: https://doi.org/10.2210/pdb7REE/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Mammalia sp. MMA-2019
Mutation(s): No

Deposited: 2021-07-12 Released: 2021-09-01
Deposition Author(s): Karim, M.R., Schonbrunn, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free:
0.205 (Depositor), 0.210 (DCC)
R-Value Work:
0.173 (Depositor), 0.180 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

High-resolution crystal structure of human JAK2 kinase domain (JH1) bound to YM2-059.

Karim, M.R., Schonbrunn, E.

To be published.

Macromolecule Content

Total Structure Weight: 35.54 kDa
Atom Count: 2,814
Modeled Residue Count: 291
Deposited Residue Count: 297
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK2	A	297	Homo sapiens	Mutation(s): 0 Gene Names: JAK2 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for O60674 (Homo sapiens) Explore O60674 Go to UniProtKB: O60674
PHAROS: O60674 GTEx: ENSG00000096968
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60674
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4LY (Subject of Investigation/LOI) Query on 4LY 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-(4-{2-[3,5-difluoro-4-(1-methyl-1,2,3,6-tetrahydropyridin-4-yl)anilino]-7H-pyrrolo[2,3-d]pyrimidin-4-yl}-1H-pyrazol-1-yl)-1-(ethanesulfonyl)azetidin-3-yl]acetonitrile C₂₈ H₂₉ F₂ N₉ O₂ S MXGPFEUZRMBECL-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [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: 1.38 Å
R-Value Free: 0.205 (Depositor), 0.210 (DCC)
R-Value Work: 0.173 (Depositor), 0.180 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.05	α = 90
b = 69.095	β = 97.87
c = 49.787	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-09-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-09-01
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection
Version 1.3: 2024-11-13
Changes: Structure summary

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 R01GM157729.