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- PDB-5qil: TGF-BETA RECEPTOR TYPE 1 KINASE DOMAIN (T204D) IN COMPLEX WITH N-... -

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Basic information

Entry
Database: PDB / ID: 5qil
TitleTGF-BETA RECEPTOR TYPE 1 KINASE DOMAIN (T204D) IN COMPLEX WITH N-{4-[3-(6-METHOXYPYRIDIN-3-YL)-1H-PYRROLO[3,2-B]PYRIDIN-2-YL]PYRIDIN-2-YL}ACETAMIDE
ComponentsTGF-beta receptor type-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ALK5 / SB431542 / KINASE DOMAIN / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX / TRANSFERASE
Function / homology
Function and homology information


extracellular structure organization / epicardium morphogenesis / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of tight junction disassembly / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity ...extracellular structure organization / epicardium morphogenesis / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of tight junction disassembly / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / positive regulation of mesenchymal stem cell proliferation / ventricular compact myocardium morphogenesis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of vasculature development / regulation of epithelial to mesenchymal transition / activin receptor activity, type I / cardiac epithelial to mesenchymal transition / transforming growth factor beta receptor activity, type I / activin receptor complex / mesenchymal cell differentiation / neuron fate commitment / positive regulation of extracellular matrix assembly / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / angiogenesis involved in coronary vascular morphogenesis / receptor protein serine/threonine kinase / germ cell migration / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / coronary artery morphogenesis / activin receptor signaling pathway / ventricular trabecula myocardium morphogenesis / filopodium assembly / transforming growth factor beta binding / embryonic cranial skeleton morphogenesis / response to cholesterol / I-SMAD binding / collagen fibril organization / negative regulation of chondrocyte differentiation / endothelial cell activation / skeletal system morphogenesis / lens development in camera-type eye / endothelial cell proliferation / positive regulation of filopodium assembly / anterior/posterior pattern specification / artery morphogenesis / ventricular septum morphogenesis / roof of mouth development / SMAD binding / TGF-beta receptor signaling activates SMADs / negative regulation of endothelial cell proliferation / positive regulation of SMAD protein signal transduction / blastocyst development / regulation of protein ubiquitination / endothelial cell migration / bicellular tight junction / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / Downregulation of TGF-beta receptor signaling / negative regulation of cell migration / transforming growth factor beta receptor signaling pathway / post-embryonic development / thymus development / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / skeletal system development / kidney development / positive regulation of apoptotic signaling pathway / cell motility / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cellular response to growth factor stimulus / UCH proteinases / male gonad development / nervous system development / heart development / positive regulation of cell growth / regulation of gene expression / peptidyl-serine phosphorylation / in utero embryonic development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / Ub-specific processing proteases / regulation of cell cycle / endosome / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of gene expression / positive regulation of DNA-templated transcription
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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-J2V / TGF-beta receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsSheriff, S.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Discovery of 4-Azaindole Inhibitors of TGF beta RI as Immuno-oncology Agents.
Authors: Zhang, Y. / Zhao, Y. / Tebben, A.J. / Sheriff, S. / Ruzanov, M. / Fereshteh, M.P. / Fan, Y. / Lippy, J. / Swanson, J. / Ho, C.P. / Wautlet, B.S. / Rose, A. / Parrish, K. / Yang, Z. / ...Authors: Zhang, Y. / Zhao, Y. / Tebben, A.J. / Sheriff, S. / Ruzanov, M. / Fereshteh, M.P. / Fan, Y. / Lippy, J. / Swanson, J. / Ho, C.P. / Wautlet, B.S. / Rose, A. / Parrish, K. / Yang, Z. / Donnell, A.F. / Zhang, L. / Fink, B.E. / Vite, G.D. / Augustine-Rauch, K. / Fargnoli, J. / Borzilleri, R.M.
History
DepositionAug 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 12, 2021Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)35,5252
Polymers35,1651
Non-polymers3591
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.600, 76.980, 89.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / ALK5 / Serine/threonine-protein kinase receptor R4 / SKR4 / TGF-beta type I receptor / Transforming growth factor-beta receptor type I / TbetaR-I


Mass: 35165.473 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP RESIDUES 200-503 / Mutation: T204D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR1, ALK5, SKR4 / Plasmid: PFASTBAC1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P36897, receptor protein serine/threonine kinase
#2: Chemical ChemComp-J2V / N-{4-[3-(6-methoxypyridin-3-yl)-1H-pyrrolo[3,2-b]pyridin-2-yl]pyridin-2-yl}acetamide


Mass: 359.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17N5O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 23%(w/v) PEG3350, 3%(v/v) glcyerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→41.6 Å / Num. obs: 20725 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 24.27 Å2 / Rsym value: 0.092 / Net I/σ(I): 14.5
Reflection shellResolution: 1.98→2.29 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.365 / Rejects: 0 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
AMoREphasing
BUSTER2.11.6refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TZM

3tzm


Resolution: 1.98→20.8 Å / Cor.coef. Fo:Fc: 0.9251 / Cor.coef. Fo:Fc free: 0.9178 / SU R Cruickshank DPI: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.179 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.147
RfactorNum. reflection% reflectionSelection details
Rfree0.2098 987 4.81 %RANDOM
Rwork0.1692 ---
obs0.1713 20531 99.9 %-
Displacement parametersBiso max: 110.35 Å2 / Biso mean: 27.44 Å2 / Biso min: 9.34 Å2
Baniso -1Baniso -2Baniso -3
1-4.8662 Å20 Å20 Å2
2---13.5326 Å20 Å2
3---8.6664 Å2
Refine analyzeLuzzati coordinate error obs: 0.188 Å
Refinement stepCycle: final / Resolution: 1.98→20.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 27 156 2591
Biso mean--20.05 32.24 -
Num. residues----303
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d891SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes408HARMONIC5
X-RAY DIFFRACTIONt_it2514HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion320SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3072SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2514HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3409HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion15.61
LS refinement shellResolution: 1.98→2.09 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.247 140 4.77 %
Rwork0.1773 2794 -
all0.1807 2934 -
obs--99.9 %

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