3KCF | pdb_00003kcf

Crystal structure of TGFbRI complexed with a pyrazolone inhibitor

PDB DOI: https://doi.org/10.2210/pdb3KCF/pdb

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

Deposited: 2009-10-21 Released: 2009-12-22
Deposition Author(s): Boriack-Sjodin, P.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.278 (Depositor), 0.273 (DCC)
R-Value Work:
0.235 (Depositor), 0.232 (DCC)
R-Value Observed:
0.237 (Depositor)

Starting Model: experimental
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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

Pyrazolone based TGFbetaR1 kinase inhibitors.

Guckian, K., Carter, M.B., Lin, E.Y., Choi, M., Sun, L., Boriack-Sjodin, P.A., Chuaqui, C., Lane, B., Cheung, K., Ling, L., Lee, W.C.

(2010) Bioorg Med Chem Lett 20: 326-329

PubMed: 19914068 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2009.10.108
Primary Citation Related Structures:
3KCF

PubMed Abstract:
Interruption of TGFbeta signaling through inhibition of the TGFbetaR1 kinase domain may prove to have beneficial effect in both fibrotic and oncological diseases. Herein we describe the SAR of a novel series of TGFbetaR1 kinase inhibitors containing a pyrazolone core. Most TGFbetaR1 kinase inhibitors described to date contain a core five-membered ring bearing N as H-bond acceptor. Described herein is a novel strategy to replace the core structure with pyrazolone ring, in which the carbonyl group is designed as an H-bond acceptor to interact with catalytic Lys 232.

Organizational Affiliation

Biogen Idec Inc., 14 Cambridge Center, Cambridge, MA 02142, USA. kevin.guckian@biogenidec.com

Macromolecule Content

Total Structure Weight: 197.64 kDa
Atom Count: 13,297
Modeled Residue Count: 1,642
Deposited Residue Count: 1,710
Unique protein chains: 1

Macromolecules

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| 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, TGFBRI 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36897
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JZO Query on JZO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain T [auth E] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain T [auth E] MOL2 format, chain P [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain T [auth E] mmCIF format, chain P [auth D]	F [auth A], J [auth B], N [auth C], P [auth D], T [auth E]	4-[3-(methoxymethyl)phenyl]-1,2-dimethyl-5-quinoxalin-6-yl-1,2-dihydro-3H-pyrazol-3-one C₂₁ H₂₀ N₄ O₂ OWJLLMXRMBEWIM-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 H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth D] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain W [auth E] SDF format, chain V [auth E] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth E] MOL2 format, chain V [auth E] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth E] mmCIF format, chain V [auth E] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	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
JZO	BindingDB: 3KCF	Ki: 35 (nM) from 1 assay(s)
JZO	BindingDB: 3KCF	IC50: 3690 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.278 (Depositor), 0.273 (DCC)
R-Value Work: 0.235 (Depositor), 0.232 (DCC)
R-Value Observed: 0.237 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.025	α = 90
b = 249.076	β = 90
c = 138.011	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
CNX	refinement
HKL-2000	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: 2009-12-22

Deposition Author(s):

Boriack-Sjodin, P.A.

Revision History (Full details and data files)

Version 1.0: 2009-12-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2024-04-03
Changes: Refinement description

3KCF | pdb_00003kcf

Crystal structure of TGFbRI complexed with a pyrazolone inhibitor

Literature

Pyrazolone based TGFbetaR1 kinase inhibitors.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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