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- PDB-9suv: Structure of an inhibitor of Human TGF-beta Type I Receptor -

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Basic information

Entry
Database: PDB / ID: 9suv
TitleStructure of an inhibitor of Human TGF-beta Type I Receptor
ComponentsTGF-beta receptor type-1
KeywordsTRANSFERASE / Human TGF-beta Type I Receptor / TGFbetaR1 / cytokine / inhibitor / kinase
Function / homology
Function and homology information


extracellular structure organization / epicardium morphogenesis / vascular endothelial cell proliferation / parathyroid gland development / regulation of cardiac muscle cell proliferation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / myofibroblast differentiation / transforming growth factor beta receptor activity / TGFBR2 Kinase Domain Mutants in Cancer / trophoblast cell migration ...extracellular structure organization / epicardium morphogenesis / vascular endothelial cell proliferation / parathyroid gland development / regulation of cardiac muscle cell proliferation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / myofibroblast differentiation / transforming growth factor beta receptor activity / TGFBR2 Kinase Domain Mutants in Cancer / trophoblast cell migration / pharyngeal system development / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / angiogenesis involved in coronary vascular morphogenesis / positive regulation of mesenchymal stem cell proliferation / ventricular compact myocardium morphogenesis / positive regulation of tight junction disassembly / positive regulation of extracellular matrix assembly / cardiac epithelial to mesenchymal transition / neuron fate commitment / mesenchymal cell differentiation / transforming growth factor beta receptor activity, type I / TGFBR3 regulates TGF-beta signaling / positive regulation of vasculature development / activin receptor activity, type I / activin receptor complex / primordial germ cell migration / regulation of epithelial to mesenchymal transition / anterior/posterior pattern specification / receptor protein serine/threonine kinase / type II transforming growth factor beta receptor binding / activin binding / embryonic cranial skeleton morphogenesis / transmembrane receptor protein serine/threonine kinase activity / TGFBR1 LBD Mutants in Cancer / ventricular trabecula myocardium morphogenesis / coronary artery morphogenesis / activin receptor signaling pathway / collagen fibril organization / artery morphogenesis / skeletal system morphogenesis / negative regulation of chondrocyte differentiation / response to cholesterol / transforming growth factor beta binding / I-SMAD binding / endothelial cell activation / roof of mouth development / ventricular septum morphogenesis / thymus development / SMAD binding / TGF-beta receptor signaling activates SMADs / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / regulation of protein ubiquitination / skeletal system development / cellular response to transforming growth factor beta stimulus / bicellular tight junction / transforming growth factor beta receptor signaling pathway / positive regulation of stress fiber assembly / positive regulation of epithelial to mesenchymal transition / kidney development / positive regulation of endothelial cell proliferation / in utero embryonic development / positive regulation of apoptotic signaling pathway / negative regulation of cell migration / negative regulation of extrinsic apoptotic signaling pathway / cell motility / wound healing / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / peptidyl-serine phosphorylation / cellular response to growth factor stimulus / heart development / regulation of gene expression / UCH proteinases / positive regulation of cell growth / nervous system development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cell cycle / protein kinase activity / signaling receptor complex / endosome / intracellular signal transduction / Ub-specific processing proteases / positive regulation of cell migration / membrane raft / ubiquitin protein ligase binding / protein serine/threonine kinase activity / apoptotic process / positive regulation of gene expression / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / cell surface / signal transduction / ATP binding / membrane / metal ion binding / nucleus / plasma membrane
Similarity search - Function
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / TGF-beta receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCaria, S. / Hole, A.J.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2026
Title: Discovery of a Novel Lung-Restricted ALK5 Inhibitor for the Treatment of Idiopathic Pulmonary Fibrosis.
Authors: Ronchi, P. / Pizzirani, D. / Pala, D. / Capelli, A.M. / Rescigno, D. / Bertani, B. / Trist, I.M.L. / Milioli, M. / Cesari, N. / Federico, G. / Pappani, A. / Venturi, L. / Pecorari, D. / ...Authors: Ronchi, P. / Pizzirani, D. / Pala, D. / Capelli, A.M. / Rescigno, D. / Bertani, B. / Trist, I.M.L. / Milioli, M. / Cesari, N. / Federico, G. / Pappani, A. / Venturi, L. / Pecorari, D. / Guariento, S. / Marchini, G. / Stellari, F.F. / Xanxo Fernandez, S. / Biagetti, M. / Civelli, M. / Bianchi, F. / Remelli, R. / Barilli, A. / Pompilio, D. / Hole, A.J. / Caria, S. / Armani, E.
History
DepositionSep 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2026Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 24, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TGF-beta receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5773
Polymers34,9391
Non-polymers6382
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-1 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.16, 61.69, 91.6
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TGF-beta receptor type-1 / TGFR-1 / Activin A receptor type II-like protein kinase of 53kD / Activin receptor-like kinase 5 / ...TGFR-1 / Activin A receptor type II-like protein kinase of 53kD / Activin receptor-like kinase 5 / ALK-5 / ALK5 / Serine/threonine-protein kinase receptor R4 / SKR4 / TGF-beta type I receptor / Transforming growth factor-beta receptor type I / TGF-beta receptor type I / TbetaR-I


Mass: 34939.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR1, ALK5, SKR4 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P36897, receptor protein serine/threonine kinase
#2: Chemical ChemComp-A1JQO / ~{N}-[4-[[6-(5-chloranyl-2-fluoranyl-phenyl)-3-(2-hydroxyethylsulfanyl)pyridazin-4-yl]amino]pyridin-2-yl]-3-(4-methylpiperazin-1-yl)propanamide


Mass: 546.060 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H29ClFN7O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium thiocyanate 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2021 / Details: Vertical CRL / Horizontal CRL
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.469→45.8 Å / Num. obs: 44637 / % possible obs: 92.4 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.029 / Rrim(I) all: 0.072 / Net I/σ(I): 14.1
Reflection shellResolution: 1.469→1.519 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.199 / Num. unique obs: 2233 / CC1/2: 0.519 / R split: 1.5 / Rpim(I) all: 0.53 / Rrim(I) all: 1.313 / % possible all: 49.1

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→45.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.081 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.087 / SU Rfree Blow DPI: 0.084 / SU Rfree Cruickshank DPI: 0.081 / Details: Gelly refinement carried out.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2112 5.42 %RANDOM
Rwork0.1835 ---
obs0.1848 43339 95.5 %-
Displacement parametersBiso mean: 23.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.5594 Å20 Å20 Å2
2---0.2677 Å20 Å2
3----0.2917 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.5→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 43 290 2649
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112533HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.13438HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d952SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes444HARMONIC5
X-RAY DIFFRACTIONt_it2533HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion322SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies18HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2908SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.41
X-RAY DIFFRACTIONt_other_torsion15.11
LS refinement shellResolution: 1.5→1.52 Å
RfactorNum. reflection% reflection
Rfree0.315 47 -
Rwork0.2622 --
obs0.2649 867 57.41 %

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