4AOJ | pdb_00004aoj

Human TrkA in complex with the inhibitor AZ-23

PDB DOI: https://doi.org/10.2210/pdb4AOJ/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2012-03-28 Released: 2012-08-15
Deposition Author(s): Wang, T., Lamb, M.L., Block, M.H., Davies, A.M., Han, Y., Hoffmann, E., Ioannidis, S., Josey, J.A., Liu, Z., Lyne, P.D., MacIntyre, T., Mohr, P.J., Omer, C.A., Sjogren, T., Thress, K., Wang, B., Wang, H., Yu, D., Zhang, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.242 (Depositor), 0.233 (DCC)
R-Value Work:
0.220 (Depositor), 0.212 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Discovery of Disubstituted Imidazo[4,5-B]Pyridines and Purines as Potent Trka Inhibitors

Wang, T., Lamb, M.L., Block, M.H., Davies, A.M., Han, Y., Hoffmann, E., Ioannidis, S., Josey, J.A., Liu, Z., Lyne, P.D., Macintyre, T., Mohr, P.J., Omer, C.A., Sjogren, T., Thress, K., Wang, B., Wang, H., Yu, D., Zhang, H.

(2012) ACS Med Chem Lett 3: 705

PubMed: 24900538 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/ml300074j
Primary Citation Related Structures:
4AOJ

PubMed Abstract:
Trk receptor tyrosine kinases have been implicated in cancer and pain. A crystal structure of TrkA with AZ-23 (1a) was obtained, and scaffold hopping resulted in two 5/6-bicyclic series comprising either imidazo[4,5-b]pyridines or purines. Further optimization of these two fusion series led to compounds with subnanomolar potencies against TrkA kinase in cellular assays. Antitumor effects in a TrkA-driven mouse allograft model were demonstrated with compounds 2d and 3a.

Organizational Affiliation

Oncology Innovative Medicines Unit, AstraZeneca R&D Boston , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.

Macromolecule Content

Total Structure Weight: 112.26 kDa
Atom Count: 6,412
Modeled Residue Count: 779
Deposited Residue Count: 987
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR	A, B, C	329	Homo sapiens	Mutation(s): 0 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04629 (Homo sapiens) Explore P04629 Go to UniProtKB: P04629
PHAROS: P04629 GTEx: ENSG00000198400
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04629
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V4Z Query on V4Z Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B], J [auth C]	5-chloranyl-N2-[(1S)-1-(5-fluoranylpyridin-2-yl)ethyl]-N4-(3-propan-2-yloxy-1H-pyrazol-5-yl)pyrimidine-2,4-diamine C₁₇ H₁₉ Cl F N₇ O LBVKEEFIPBQIMD-JTQLQIEISA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain J [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] H [auth B] I [auth B] K [auth C] E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
V4Z	BindingDB: 4AOJ	Ki: min: 0.36, max: 3.7 (nM) from 2 assay(s)
		Kd: 0.2 (nM) from 1 assay(s)
		IC50: min: 0.26, max: 9.9 (nM) from 9 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.242 (Depositor), 0.233 (DCC)
R-Value Work: 0.220 (Depositor), 0.212 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.727	α = 90
b = 158.419	β = 90
c = 152.577	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-08-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-15
Type: Initial release
Version 1.1: 2012-10-31
Changes: Database references
Version 1.2: 2014-06-18
Changes: Database references
Version 1.3: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description