3FAA|pdb_00003faa

Crystal structure of TGFbRI complexed with a 2-aminoimidazole inhibitor

PDB DOI: https://doi.org/10.2210/pdb3FAA/pdb

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

Deposited: 2008-11-16 Released: 2009-01-27
Deposition Author(s): Boriack-Sjodin, P.A.,Fitch, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free:
0.271 (Depositor), 0.250 (DCC)
R-Value Work:
0.228 (Depositor), 0.210 (DCC)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

2-Aminoimidazoles inhibitors of TGF-beta receptor 1.

Bonafoux, D., Chuaqui, C., Boriack-Sjodin, P.A., Fitch, C., Hankins, G., Josiah, S., Black, C., Hetu, G., Ling, L., Lee, W.C.

(2009) Bioorg Med Chem Lett 19: 912-916

PubMed: 19135364 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2008.11.119
Primary Citation of Related Structures:
3FAA

PubMed Abstract:
The 4-(5-fluoro-6-methyl-pyridin-2-yl)-5-quinoxalin-6-yl-1H-imidazol-2-ylamine 3 is a potent and selective inhibitor of TGF-betaR1. Substitution of the amino group of 3 typically led to a slight decrease in the affinity for the receptor and in TGF-beta-inducted PAI-luciferase reporter activity. However, 2-acetamidoimidazoles were identified as attractive candidates for further optimization as a result of their significant activity combined to their superior pharmacokinetic profile.

Organizational Affiliation

Abbot Laboratories, 381 Plantation Street, Worcester, MA 01605-2323, USA. dominique.bonafoux@abbott.com

Macromolecule Content

Total Structure Weight: 197.65 kDa
Atom Count: 13,294
Modelled Residue Count: 1,642
Deposited Residue Count: 1,710
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TGF-beta receptor type-1	A,B,C,D,E	342	Homo sapiens	Mutation(s): 0 Gene Names: TGFBR1 EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for P36897 (Homo sapiens) Explore P36897 Go to UniProtKB: P36897
PHAROS: P36897 GTEx: ENSG00000106799
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P36897
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
55F Query on 55F Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain T [auth E] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain T [auth E] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain T [auth E] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth D]	F [auth A], J [auth B], N [auth C], P [auth D], T [auth E]	N-[4-(5-fluoro-6-methylpyridin-2-yl)-5-quinoxalin-6-yl-1H-imidazol-2-yl]acetamide C₁₉ H₁₅ F N₆ O TYPILNNEZPSNTI-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain T [auth E] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain T [auth E]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain V [auth E] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth D] SDF format, chain U [auth E] SDF format, chain W [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain V [auth E] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth E]	G [auth A] H [auth A] I [auth A] K [auth B] L [auth B] G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], O [auth C], Q [auth D], R [auth D], S [auth D], U [auth E], V [auth E], W [auth E]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E]

Binding Affinity Annotations
ID	Source	Binding Affinity
55F	BindingDB: 3FAA	Ki: 7.1 (nM) from 1 assay(s)
55F	BindingDB: 3FAA	EC50: min: 180, max: 1.48e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free: 0.271 (Depositor), 0.250 (DCC)
R-Value Work: 0.228 (Depositor), 0.210 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.861	α = 90
b = 248.852	β = 90
c = 138.628	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-01-27

Deposition Author(s):

Boriack-Sjodin, P.A.

Fitch, C.

Revision History (Full details and data files)

Version 1.0: 2009-01-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations

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3FAA|pdb_00003faa

Crystal structure of TGFbRI complexed with a 2-aminoimidazole inhibitor

2-Aminoimidazoles inhibitors of TGF-beta receptor 1.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)