3CGO | pdb_00003cgo

IRAK-4 Inhibitors (Part II)- A structure based assessment of imidazo[1,2 a]pyridine binding

PDB DOI: https://doi.org/10.2210/pdb3CGO/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-03-06 Released: 2008-06-03
Deposition Author(s): Ceska, T.A., Platt, A., Fortunato, M., Dickson, K.M., Beevers, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.318 (Depositor), 0.300 (DCC)
R-Value Work:
0.243 (Depositor), 0.218 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

IRAK-4 inhibitors. Part II: A structure-based assessment of imidazo[1,2-a]pyridine binding

Buckley, G.M., Ceska, T.A., Fraser, J.L., Gowers, L., Groom, C.R., Higueruelo, A.P., Jenkins, K., Mack, S.R., Morgan, T., Parry, D.M., Pitt, W.R., Rausch, O., Richard, M.D., Sabin, V.

(2008) Bioorg Med Chem Lett 18: 3291-3295

PubMed: 18482836 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2008.04.039
Primary Citation Related Structures:
3CGF, 3CGO

PubMed Abstract:
A potent IRAK-4 inhibitor was identified through routine project cross screening. The binding mode was inferred using a combination of in silico docking into an IRAK-4 homology model, surrogate crystal structure analysis and chemical analogue SAR.

Organizational Affiliation

UCB, Granta Park, Great Abington, Cambridge CB21 6GS, UK.

Macromolecule Content

Total Structure Weight: 42.48 kDa
Atom Count: 2,784
Modeled Residue Count: 332
Deposited Residue Count: 365
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 10	A	365	Homo sapiens	Mutation(s): 0 Gene Names: MAPK10, JNK3, JNK3A, PRKM10 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens) Explore P53779 Go to UniProtKB: P53779
PHAROS: P53779 GTEx: ENSG00000109339
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53779
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JNO Query on JNO 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]	2-{4-[(4-imidazo[1,2-a]pyridin-3-ylpyrimidin-2-yl)amino]piperidin-1-yl}-N-methylacetamide C₁₉ H₂₃ N₇ O AJLILYAPRHIFAS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
JNO	BindingDB: 3CGO	IC50: 270 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.318 (Depositor), 0.300 (DCC)
R-Value Work: 0.243 (Depositor), 0.218 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.22	α = 90
b = 71.77	β = 90
c = 107.72	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-06-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-06-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description