2XA4 | pdb_00002xa4

Inhibitors of Jak2 Kinase domain

PDB DOI: https://doi.org/10.2210/pdb2XA4/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-03-26 Released: 2010-12-15
Deposition Author(s): Read, J., Green, I., Pollard, H., Howard, T., Mott, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.245 (Depositor), 0.255 (DCC)
R-Value Work:
0.197 (Depositor), 0.206 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Discovery of 5-Chloro-N2-[(1S)-1-(5-Fluoropyrimidin-2-Yl) Ethyl]-N4-(5-Methyl-1H-Pyrazol-3-Yl)Pyrimidine-2,4-Diamine (Azd1480) as a Novel Inhibitor of the Jak/Stat Pathway

Ioannidis, S., Lamb, M.L., Wang, T., Almeida, L., Block, M.H., Davies, A.M., Peng, B., Su, M., Zhang, H., Hoffmann, E., Rivard, C., Green, I., Howard, T., Pollard, H., Read, J., Alimzhanov, M., Bebernitz, G., Bell, K., Ye, M., Huszar, D., Zinda, M.

(2011) J Med Chem 54: 262

PubMed: 21138246 Search on PubMed
DOI: https://doi.org/10.1021/jm1011319
Primary Citation Related Structures:
2XA4

PubMed Abstract:
The myeloproliferative neoplasms, polycythemia vera, essential thrombocythemia, and idiopathic myelofibrosis are a heterogeneous but related group of hematological malignancies characterized by clonal expansion of one or more myeloid lineages. The discovery of the Jak2 V617F gain of function mutation highlighted Jak2 as a potential therapeutic target in the MPNs. Herein, we disclose the discovery of a series of pyrazol-3-yl pyrimidin-4-amines and the identification of 9e (AZD1480) as a potent Jak2 inhibitor. 9e inhibits signaling and proliferation of Jak2 V617F cell lines in vitro, demonstrates in vivo efficacy in a TEL-Jak2 model, has excellent physical properties and preclinical pharmacokinetics, and is currently being evaluated in Phase I clinical trials.

Organizational Affiliation

Department of Cancer Chemistry, AstraZeneca R&D, Boston, Massachusetts, United States. stephanos.ioannidis@astrazeneca.com

Macromolecule Content

Total Structure Weight: 70.86 kDa
Atom Count: 4,871
Modeled Residue Count: 555
Deposited Residue Count: 596
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE-PROTEIN KINASE JAK2	A, B	298	Homo sapiens	Mutation(s): 2 EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60674
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AZ5 Query on AZ5 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	5-CHLORO-N2-[(1S)-1-(5-FLUOROPYRIMIDIN-2-YL)ETHYL]-N4-(5-METHYL-1H-PYRAZOL-3-YL)PYRIMIDINE-2,4-DIAMINE C₁₄ H₁₄ Cl F N₈ PDOQBOJDRPLBQU-QMMMGPOBSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.245 (Depositor), 0.255 (DCC)
R-Value Work: 0.197 (Depositor), 0.206 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.854	α = 90
b = 126.741	β = 97.04
c = 134.342	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-12-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-12-15
Type: Initial release
Version 1.1: 2011-10-12
Changes: Database references, Derived calculations, Refinement description, Version format compliance
Version 1.2: 2015-04-01
Changes: Database references
Version 1.3: 2018-03-07
Changes: Source and taxonomy
Version 1.4: 2019-05-08
Changes: Data collection, Derived calculations, Experimental preparation
Version 1.5: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Other, Structure summary