7RN6 | pdb_00007rn6

High-resolution crystal structure of human JAK2 kinase domain (JH1) bound to type-II inhibitor BBT594

PDB DOI: https://doi.org/10.2210/pdb7RN6/pdb

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

Deposited: 2021-07-29 Released: 2021-11-03
Deposition Author(s): Karim, M.R., Schonbrunn, E.
Funding Organization(s): Department of Health & Human Services (HHS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.214 (Depositor), 0.220 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.190 (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 type-II inhibitor BBT594

Karim, M.R., Schonbrunn, E.

To be published.

Macromolecule Content

Total Structure Weight: 35.63 kDa
Atom Count: 2,495
Modeled Residue Count: 274
Deposited Residue Count: 298
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	298	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
046 (Subject of Investigation/LOI) Query on 046 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]	5-{[6-(acetylamino)pyrimidin-4-yl]oxy}-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}-2,3-dihydro-1H-indole-1-carboxamide C₂₈ H₃₀ F₃ N₇ O₃ VQLNKQZLPGLOSI-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [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: 1.50 Å
R-Value Free: 0.214 (Depositor), 0.220 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.338	α = 90
b = 69.54	β = 98.81
c = 50.733	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 & Funding Information

Deposition Data

Released Date: 2021-11-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Health & Human Services (HHS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2021-11-03
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.