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- PDB-6njs: Stat3 Core in complex with compound SD36 -

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Basic information

Entry
Database: PDB / ID: 6njs
TitleStat3 Core in complex with compound SD36
ComponentsSignal transducer and activator of transcription 3
Keywordstranscription/transcription inhibitor / Stat3 / Activator / TRANSCRIPTION / transcription-transcription inhibitor complex
Function / homology
Function and homology information


RNA sequestering activity / positive regulation of metalloendopeptidase activity / PTK6 Activates STAT3 / eye photoreceptor cell differentiation / radial glial cell differentiation / retinal rod cell differentiation / negative regulation of primary miRNA processing / leptin-mediated signaling pathway / T-helper 17 type immune response / Signalling to STAT3 ...RNA sequestering activity / positive regulation of metalloendopeptidase activity / PTK6 Activates STAT3 / eye photoreceptor cell differentiation / radial glial cell differentiation / retinal rod cell differentiation / negative regulation of primary miRNA processing / leptin-mediated signaling pathway / T-helper 17 type immune response / Signalling to STAT3 / negative regulation of neuron migration / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / response to leptin / negative regulation of inflammatory response to wounding / interleukin-10-mediated signaling pathway / primary miRNA binding / interleukin-11-mediated signaling pathway / cellular response to interleukin-17 / T-helper 17 cell lineage commitment / sexual reproduction / Interleukin-9 signaling / Interleukin-21 signaling / regulation of feeding behavior / Transcriptional regulation of pluripotent stem cells / interleukin-9-mediated signaling pathway / MET activates STAT3 / interleukin-2-mediated signaling pathway / interleukin-23-mediated signaling pathway / Interleukin-23 signaling / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / cellular response to leptin stimulus / interleukin-15-mediated signaling pathway / astrocyte differentiation / negative regulation of stem cell differentiation / Interleukin-27 signaling / Interleukin-35 Signalling / STAT3 nuclear events downstream of ALK signaling / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / Interleukin-37 signaling / Signaling by Leptin / positive regulation of cytokine production involved in inflammatory response / cell surface receptor signaling pathway via STAT / negative regulation of glycolytic process / positive regulation of vascular endothelial cell proliferation / Interleukin-20 family signaling / growth hormone receptor signaling pathway / Interleukin-6 signaling / Signaling by ALK / phosphorylation / temperature homeostasis / eating behavior / interleukin-6-mediated signaling pathway / lncRNA binding / positive regulation of Notch signaling pathway / Interleukin-10 signaling / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of interleukin-10 production / somatic stem cell population maintenance / growth hormone receptor signaling pathway via JAK-STAT / positive regulation of vascular endothelial growth factor production / regulation of multicellular organism growth / cell surface receptor signaling pathway via JAK-STAT / Growth hormone receptor signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Signaling by CSF3 (G-CSF) / cellular response to hormone stimulus / positive regulation of phagocytosis / Nuclear events stimulated by ALK signaling in cancer / energy homeostasis / intracellular receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / signaling adaptor activity / negative regulation of cytokine production involved in inflammatory response / Interleukin-7 signaling / Downstream signal transduction / transforming growth factor beta receptor signaling pathway / negative regulation of autophagy / protein sequestering activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of erythrocyte differentiation / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / phosphatidylinositol 3-kinase/protein kinase B signal transduction / mRNA transcription by RNA polymerase II / defense response / Signaling by SCF-KIT / cytokine-mediated signaling pathway / Inactivation of CSF3 (G-CSF) signaling / Cytoprotection by HMOX1 / PKR-mediated signaling / chromatin DNA binding / positive regulation of miRNA transcription / response to peptide hormone / positive regulation of interleukin-6 production / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / Transcriptional regulation of granulopoiesis / nuclear receptor activity
Similarity search - Function
STAT3, SH2 domain / STAT transcription factor, DNA-binding domain / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / : / STAT transcription factor, coiled-coil domain / STAT protein, DNA binding domain ...STAT3, SH2 domain / STAT transcription factor, DNA-binding domain / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / : / STAT transcription factor, coiled-coil domain / STAT protein, DNA binding domain / STAT protein, protein interaction domain / Signal transducer and activator of transcription, linker domain / STAT protein, protein interaction domain / STAT transcription factor, N-terminal domain superfamily / Transcription factor STAT / STAT transcription factor, coiled coil / SH2 domain / SHC Adaptor Protein / p53-like transcription factor, DNA-binding / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / EF-hand / Recoverin; domain 1 / SH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-KQV / Signal transducer and activator of transcription 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMeagher, J.L. / Stuckey, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Cancer Cell / Year: 2019
Title: A Potent and Selective Small-Molecule Degrader of STAT3 Achieves Complete Tumor Regression In Vivo.
Authors: Bai, L. / Zhou, H. / Xu, R. / Zhao, Y. / Chinnaswamy, K. / McEachern, D. / Chen, J. / Yang, C.Y. / Liu, Z. / Wang, M. / Liu, L. / Jiang, H. / Wen, B. / Kumar, P. / Meagher, J.L. / Sun, D. / ...Authors: Bai, L. / Zhou, H. / Xu, R. / Zhao, Y. / Chinnaswamy, K. / McEachern, D. / Chen, J. / Yang, C.Y. / Liu, Z. / Wang, M. / Liu, L. / Jiang, H. / Wen, B. / Kumar, P. / Meagher, J.L. / Sun, D. / Stuckey, J.A. / Wang, S.
History
DepositionJan 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Signal transducer and activator of transcription 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2542
Polymers64,4181
Non-polymers8361
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.000, 84.000, 206.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Signal transducer and activator of transcription 3 / Acute-phase response factor


Mass: 64417.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAT3, APRF / Production host: Escherichia coli (E. coli) / References: UniProt: P40763
#2: Chemical ChemComp-KQV / [(2-{[(5S,8S,10aR)-3-acetyl-8-({(2S)-5-amino-1-[(diphenylmethyl)amino]-1,5-dioxopentan-2-yl}carbamoyl)-6-oxodecahydropyrrolo[1,2-a][1,5]diazocin-5-yl]carbamoyl}-1H-indol-5-yl)(difluoro)methyl]phosphonic acid (non-preferred name)


Mass: 835.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H44F2N7O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 10% peg 3350, 100-150 mM ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07812 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 21068 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 57.03 Å2 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.017 / Rrim(I) all: 0.06 / Χ2: 0.926 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.758.30.48410100.9370.1750.5160.812100
2.75-2.89.90.51310430.9320.170.5420.834100
2.8-2.8511.30.43610130.9640.1340.4560.83100
2.85-2.91120.40510360.9750.1210.4230.874100
2.91-2.9712.60.32310330.9830.0940.3370.864100
2.97-3.0412.40.28310150.9830.0830.2950.886100
3.04-3.1211.80.2210560.990.0660.230.896100
3.12-3.210.50.18210190.9890.0580.1920.899100
3.2-3.311.90.14610380.9950.0440.1530.952100
3.3-3.413.70.11210370.9980.0310.1160.969100
3.4-3.5213.50.09710340.9980.0270.1011.02100
3.52-3.6613.50.0810510.9980.0220.0831.041100
3.66-3.8313.30.06310590.9980.0180.0651.006100
3.83-4.0313.30.05310380.9980.0150.0551.03299.8
4.03-4.2913.30.04210570.9970.0120.0440.97199.8
4.29-4.6213.10.03610520.9990.010.0380.953100
4.62-5.0812.70.03110810.9990.0090.0320.878100
5.08-5.8111.70.03210790.9990.010.0340.86899.9
5.81-7.3211.30.03111090.9990.0090.0320.882100
7.32-5012.10.02212080.9990.0060.0230.91899.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CWG

3cwg


Resolution: 2.7→30.37 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.874 / SU R Cruickshank DPI: 0.75 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.065 / SU Rfree Blow DPI: 0.338 / SU Rfree Cruickshank DPI: 0.326
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1026 4.96 %RANDOM
Rwork0.2 ---
obs0.203 20668 98.3 %-
Displacement parametersBiso max: 120.18 Å2 / Biso mean: 39.38 Å2 / Biso min: 8.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.188 Å20 Å20 Å2
2--0.188 Å20 Å2
3----0.376 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.7→30.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4166 0 59 340 4565
Biso mean--36.98 40.79 -
Num. residues----523
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1546SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes747HARMONIC5
X-RAY DIFFRACTIONt_it4318HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion569SEMIHARMONIC5
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_contact5041SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4318HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5852HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.22
X-RAY DIFFRACTIONt_other_torsion19.41
LS refinement shellResolution: 2.7→2.73 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2466 19 4.59 %
Rwork0.2364 395 -
all0.2369 414 -
obs--67.15 %

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