4Y73

Crystal structure of IRAK4 kinase domain with inhibitor

PDB DOI: https://doi.org/10.2210/pdb4Y73/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: unidentified baculovirus
Mutation(s): No

Deposited: 2015-02-13 Released: 2015-05-20
Deposition Author(s): Lesburg, C.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.217
R-Value Work: 0.195
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery of 5-Amino-N-(1H-pyrazol-4-yl)pyrazolo[1,5-a]pyrimidine-3-carboxamide Inhibitors of IRAK4.

Lim, J., Altman, M.D., Baker, J., Brubaker, J.D., Chen, H., Chen, Y., Fischmann, T., Gibeau, C., Kleinschek, M.A., Leccese, E., Lesburg, C., Maclean, J.K., Moy, L.Y., Mulrooney, E.F., Presland, J., Rakhilina, L., Smith, G.F., Steinhuebel, D., Yang, R.

(2015) ACS Med Chem Lett 6: 683-688

PubMed: 26101574 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.5b00107
Primary Citation of Related Structures:
4Y73

PubMed Abstract:

Macromolecule Content

Total Structure Weight: 137.74 kDa
Atom Count: 9,744
Modelled Residue Count: 1,168
Deposited Residue Count: 1,208
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 receptor-associated kinase 4	A, B, C, D	302	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NWZ3
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XPY Query on XPY Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain H [auth D] SDF format, chain E [auth A] SDF format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C]	E [auth A], F [auth B], G [auth C], H [auth D]	5-{[(1R,2S)-2-aminocyclohexyl]amino}-N-[1-methyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]pyrazolo[1,5-a]pyrimidine-3-carboxamide C₁₈ H₂₁ F₃ N₈ O LAXFSYWLDNVHAQ-NWDGAFQWSA-N		Ligand Interaction

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

Binding Affinity Annotations
ID	Source	Binding Affinity
XPY	Binding MOAD: 4Y73	IC50: 0.3 (nM) from 1 assay(s)
XPY	BindingDB: 4Y73	IC50: min: 0.3, max: 9 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.217
R-Value Work: 0.195
R-Value Observed: 0.196
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.86	α = 90
b = 138.75	β = 124.59
c = 88.02	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-05-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-05-20
Type: Initial release
Version 1.1: 2015-07-15
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.