6TIA | pdb_00006tia

IRAK4 IN COMPLEX WITH inhibitor

PDB DOI: https://doi.org/10.2210/pdb6TIA/pdb

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

Deposited: 2019-11-22 Released: 2020-10-28
Deposition Author(s): Xue, Y., Aagaard, A., Degorce, S.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.261 (Depositor), 0.268 (DCC)
R-Value Work:
0.216 (Depositor)
R-Value Observed:
0.218 (Depositor)

Starting Model: other
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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

Improving metabolic stability and removing aldehyde oxidase liability in a 5-azaquinazoline series of IRAK4 inhibitors.

Degorce, S.L., Aagaard, A., Anjum, R., Cumming, I.A., Diene, C.R., Fallan, C., Johnson, T., Leuchowius, K.J., Orton, A.L., Pearson, S., Robb, G.R., Rosen, A., Scarfe, G.B., Scott, J.S., Smith, J.M., Steward, O.R., Terstiege, I., Tucker, M.J., Turner, P., Wilkinson, S.D., Wrigley, G.L., Xue, Y.

(2020) Bioorg Med Chem 28: 115815-115815

PubMed: 33091850 Search on PubMed
DOI: https://doi.org/10.1016/j.bmc.2020.115815
Primary Citation Related Structures:
6THW, 6THX, 6THZ, 6TI8, 6TIA

PubMed Abstract:
In this article, we report our efforts towards improving in vitro human clearance in a series of 5-azaquinazolines through a series of C4 truncations and C2 expansions. Extensive DMPK studies enabled us to tackle high Aldehyde Oxidase (AO) metabolism and unexpected discrepancies in human hepatocyte and liver microsomal intrinsic clearance. Our efforts culminated with the discovery of 5-azaquinazoline 35, which also displayed exquisite selectivity for IRAK4, and showed synergistic in vitro activity against MyD88/CD79 double mutant ABC-DLBCL in combination with the covalent BTK inhibitor acalabrutinib.

Organizational Affiliation

Medicinal Chemistry, Research and Early Development, Oncology R&D, AstraZeneca, Boston, 35 Gatehouse Drive, Waltham, MA 02451, United States. Electronic address: sebastien.degorce@astrazeneca.com.

Macromolecule Content

Total Structure Weight: 73.87 kDa
Atom Count: 5,064
Modeled Residue Count: 575
Deposited Residue Count: 616
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 receptor-associated kinase 4	A, B	308	Homo sapiens	Mutation(s): 0 Gene Names: IRAK4 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWZ3 (Homo sapiens) Explore Q9NWZ3 Go to UniProtKB: Q9NWZ3
PHAROS: Q9NWZ3 GTEx: ENSG00000198001
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NWZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ND2 (Subject of Investigation/LOI) Query on ND2 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	4-(1-methylcyclopropyl)oxy-~{N}-[1-(1-methylpiperidin-4-yl)pyrazol-4-yl]-6-(1-methylpyrazol-4-yl)pyrido[3,2-d]pyrimidin-2-amine C₂₄ H₂₉ N₉ O WGMWEVJCHUDPID-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A, B	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER
TPO Query on TPO	A, B	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.261 (Depositor), 0.268 (DCC)
R-Value Work: 0.216 (Depositor)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.9	α = 90
b = 140.57	β = 90
c = 56.02	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-10-28

Deposition Author(s):

Xue, Y.

Aagaard, A.

Degorce, S.L.

Revision History (Full details and data files)

Version 1.0: 2020-10-28
Type: Initial release
Version 1.1: 2020-11-04
Changes: Database references
Version 1.2: 2024-05-01
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary