9NWX | pdb_00009nwx

Discovery of a Small Molecule ITK and Pan-TRK Kinase Inhibitor (PF-07245303) for the Potential Topical Treatment of Atopic Dermatitis

PDB DOI: https://doi.org/10.2210/pdb9NWX/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Linospadix microcaryus
Mutation(s): No

Deposited: 2025-03-24 Released: 2025-11-19
Deposition Author(s): Liu, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.227 (Depositor), 0.219 (DCC)
R-Value Work:
0.182 (Depositor), 0.182 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Discovery of a Small Molecule ITK and Pan-TRK Kinase Inhibitor (PF-07245303) for the Potential Topical Treatment of Atopic Dermatitis

Liu, S.

To be published.

Macromolecule Content

Total Structure Weight: 31.1 kDa
Atom Count: 2,538
Modeled Residue Count: 264
Deposited Residue Count: 269
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 ITK/TSK	A	269	Homo sapiens	Mutation(s): 0 Gene Names: ITK, EMT, LYK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q08881 (Homo sapiens) Explore Q08881 Go to UniProtKB: Q08881
PHAROS: Q08881 GTEx: ENSG00000113263
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08881
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1B66 (Subject of Investigation/LOI) Query on A1B66 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]	(2S)-N-methyl-N-{6-methyl-2-[(4aS,5aR)-5a-methyl-1,4,4a,5,5a,6-hexahydrocyclopropa[f]indazol-3-yl]-1H-1,3-benzimidazol-5-yl}-2-(morpholin-4-yl)propanamide C₂₅ H₃₂ N₆ O₂ DVXKDRBZBOJVGG-JAUXOLPYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.227 (Depositor), 0.219 (DCC)
R-Value Work: 0.182 (Depositor), 0.182 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.23	α = 90
b = 68.67	β = 106.94
c = 49.51	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-11-19
Type: Initial release

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.