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- PDB-8s16: c-KIT kinase domain in complex with imatinib -

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Basic information

Entry
Database: PDB / ID: 8s16
Titlec-KIT kinase domain in complex with imatinib
ComponentsMast/stem cell growth factor receptor Kit
KeywordsTRANSFERASE / stem cell factor receptor / GIST / KIT / inhibitor / imatinib / resistance
Function / homology
Function and homology information


Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants / Nilotinib-resistant KIT mutants / Regorafenib-resistant KIT mutants / Signaling by kinase domain mutants of KIT / Sunitinib-resistant KIT mutants / Signaling by juxtamembrane domain KIT mutants / Sorafenib-resistant KIT mutants ...Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants / Nilotinib-resistant KIT mutants / Regorafenib-resistant KIT mutants / Signaling by kinase domain mutants of KIT / Sunitinib-resistant KIT mutants / Signaling by juxtamembrane domain KIT mutants / Sorafenib-resistant KIT mutants / Signaling by extracellular domain mutants of KIT / hematopoietic stem cell migration / melanocyte adhesion / positive regulation of pyloric antrum smooth muscle contraction / positive regulation of colon smooth muscle contraction / stem cell factor receptor activity / positive regulation of vascular associated smooth muscle cell differentiation / melanocyte migration / Kit signaling pathway / tongue development / regulation of bile acid metabolic process / positive regulation of small intestine smooth muscle contraction / positive regulation of dendritic cell cytokine production / mast cell chemotaxis / positive regulation of mast cell proliferation / mast cell differentiation / Fc receptor signaling pathway / glycosphingolipid metabolic process / mast cell proliferation / positive regulation of pseudopodium assembly / positive regulation of long-term neuronal synaptic plasticity / positive regulation of mast cell cytokine production / lymphoid progenitor cell differentiation / melanocyte differentiation / detection of mechanical stimulus involved in sensory perception of sound / immature B cell differentiation / germ cell migration / erythropoietin-mediated signaling pathway / myeloid progenitor cell differentiation / digestive tract development / negative regulation of programmed cell death / embryonic hemopoiesis / lamellipodium assembly / positive regulation of tyrosine phosphorylation of STAT protein / Regulation of KIT signaling / megakaryocyte development / growth factor binding / mast cell degranulation / stem cell population maintenance / pigmentation / positive regulation of Notch signaling pathway / cytokine binding / negative regulation of reproductive process / negative regulation of developmental process / hemopoiesis / T cell differentiation / somatic stem cell population maintenance / spermatid development / ectopic germ cell programmed cell death / response to cadmium ion / positive regulation of DNA-binding transcription factor activity / hematopoietic progenitor cell differentiation / ovarian follicle development / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / acrosomal vesicle / SH2 domain binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / B cell differentiation / epithelial cell proliferation / erythrocyte differentiation / cell chemotaxis / positive regulation of receptor signaling pathway via JAK-STAT / stem cell differentiation / Signaling by SCF-KIT / receptor protein-tyrosine kinase / visual learning / cytoplasmic side of plasma membrane / male gonad development / fibrillar center / cytokine-mediated signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / cell-cell junction / cell migration / PIP3 activates AKT signaling / regulation of cell shape / regulation of cell population proliferation / protein autophosphorylation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / actin cytoskeleton organization / protease binding / protein tyrosine kinase activity / spermatogenesis / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / intracellular signal transduction / positive regulation of cell migration
Similarity search - Function
Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-STI / Mast/stem cell growth factor receptor Kit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTeuber, A. / Mueller, M.P. / Rauh, D.
Funding support Germany, European Union, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)RA 1055/3-2 Germany
European Regional Development FundEFRE-800400European Union
German Federal Ministry for Education and Research01ZX2201B Germany
Other governmentNW21-062C
Other privateEx-2021-0033
CitationJournal: To Be Published
Title: c-KIT kinase domain in complex with imatinib
Authors: Teuber, A. / Niggenaber, J. / Kleinboelting, S.B. / Landel, I. / Warmuth, J. / Busick, D. / Bauer, S. / Rauh, D.
History
DepositionFeb 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mast/stem cell growth factor receptor Kit
B: Mast/stem cell growth factor receptor Kit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4827
Polymers74,3892
Non-polymers1,0945
Water7,566420
1
A: Mast/stem cell growth factor receptor Kit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7945
Polymers37,1941
Non-polymers6004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mast/stem cell growth factor receptor Kit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6882
Polymers37,1941
Non-polymers4941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.230, 90.140, 90.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Mast/stem cell growth factor receptor Kit / SCFR / Piebald trait protein / PBT / Proto-oncogene c-Kit / Tyrosine-protein kinase Kit / p145 c- ...SCFR / Piebald trait protein / PBT / Proto-oncogene c-Kit / Tyrosine-protein kinase Kit / p145 c-kit / v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog


Mass: 37194.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIT, SCFR / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P10721, receptor protein-tyrosine kinase
#2: Chemical ChemComp-STI / 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE / STI-571 / IMATINIB


Mass: 493.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H31N7O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: protein concentration: 6 mg/mL, 18% PEG3350, 100 mM Na3-citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00006 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00006 Å / Relative weight: 1
ReflectionResolution: 1.85→45.43 Å / Num. obs: 61778 / % possible obs: 100 % / Redundancy: 13.62 % / Biso Wilson estimate: 37.05 Å2 / CC1/2: 0.99 / Net I/σ(I): 14.3
Reflection shellResolution: 1.85→1.9 Å / Num. unique obs: 4674 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
PDB_EXTRACT1.20.1_4487data extraction
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→40.38 Å / SU ML: 0.2574 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4926
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2073 3088 5 %
Rwork0.176 58669 -
obs0.1775 61757 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.12 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4675 0 77 420 5172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00664925
X-RAY DIFFRACTIONf_angle_d0.79996677
X-RAY DIFFRACTIONf_chiral_restr0.0528710
X-RAY DIFFRACTIONf_plane_restr0.008847
X-RAY DIFFRACTIONf_dihedral_angle_d13.08511809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.4481380.40842629X-RAY DIFFRACTION99.93
1.88-1.910.34241390.33412629X-RAY DIFFRACTION99.96
1.91-1.940.32231370.27682620X-RAY DIFFRACTION100
1.94-1.980.29331390.23252630X-RAY DIFFRACTION99.96
1.98-2.020.23631390.20852638X-RAY DIFFRACTION100
2.02-2.060.26261390.20922646X-RAY DIFFRACTION99.96
2.06-2.10.25761390.21612639X-RAY DIFFRACTION99.96
2.1-2.150.22081380.21552625X-RAY DIFFRACTION100
2.15-2.20.23341410.18032666X-RAY DIFFRACTION99.96
2.2-2.260.2231370.18232618X-RAY DIFFRACTION99.93
2.26-2.330.2651420.17722680X-RAY DIFFRACTION100
2.33-2.410.21431380.1812626X-RAY DIFFRACTION100
2.41-2.490.22921400.17922655X-RAY DIFFRACTION99.96
2.49-2.590.20761400.18682662X-RAY DIFFRACTION100
2.59-2.710.2341390.19272655X-RAY DIFFRACTION100
2.71-2.850.26211410.19082681X-RAY DIFFRACTION100
2.85-3.030.23671420.19392682X-RAY DIFFRACTION100
3.03-3.260.19171400.18422674X-RAY DIFFRACTION100
3.27-3.590.18361420.16552700X-RAY DIFFRACTION100
3.59-4.110.18081430.14322714X-RAY DIFFRACTION100
4.11-5.180.16511440.13612737X-RAY DIFFRACTION100
5.18-40.380.17881510.16932863X-RAY DIFFRACTION99.74
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.501686478080.779100508747-0.9347394184992.60257246494-0.04309985715122.799592130860.091789553604-0.1642488685170.1902280891420.233536872154-0.05843943167880.185388184458-0.00464214371968-0.0482114676615-0.03898935533880.2933647160180.0380338734838-0.01999338150540.274731941988-0.009935146536940.25038816925-32.730480850616.5202955625-2.31866995195
22.378794446230.377365677541-0.01959726445193.65970541606-0.09326018808083.6873895022-0.0683615811192-0.0958310976660.0956936699820.0900911104039-0.01387947796470.256958498264-0.0574372136267-0.3825273828980.09325811946870.2312390866790.03178593858160.02407288470180.270408346344-0.01497429267020.221567217844-35.457321781812.4874982248-1.84547991416
33.54814205296-0.140942010407-1.581584911143.04423060917-0.2968313514219.134034159550.0620166328728-0.0860426662050.3707956327570.0630429976246-0.06597558265140.13984861472-0.672266218101-0.184056463434-0.02176038979570.2554011660020.0350281676102-0.0133405890910.307026478209-0.01186293218920.346869110248-36.393484778217.0313945369-7.2310215287
42.48050990808-1.32631606817-1.894452334836.496582613555.152941576447.86225732237-0.1085258114740.245575114702-0.467766858482-0.18237885404-0.3710309937020.5472735396120.58717762619-0.5602339688890.4573642016520.350283964484-0.04687550399980.01109672769460.2630641869070.01651908379650.349708661807-35.9025437643-0.564937538186-17.0287683732
50.7792724720550.8318348890251.533516440652.2790172590.9678657806653.361361385720.1055589565041.17751610618-0.3955267306460.118012796482-0.09188505307881.62132248630.989122123357-1.794221553210.187354785820.560284783246-0.141006150661-0.1019659052130.827746170034-0.182946043050.741936020021-41.4751043589-5.93378575062-32.6141537012
61.607948352560.743191602004-0.1908589493583.303379936530.7906797012533.18584828454-0.03450058550640.1660011415450.0526574101504-0.139652435878-0.05171060040180.273117554261-0.0150369953822-0.1959487386210.1082080425030.2364847229340.0422182367383-0.01232116588760.290018377521-0.00535136575930.27929943513-29.71746809059.70523347566-21.2679429333
73.21287490212-0.342128897453-2.108877704394.039108285930.1985144956263.57890987618-0.222221178159-0.517848888998-0.4785702922080.4834669347560.079798565044-0.1215618736030.4288952678840.5422667159950.1349747287360.355214734540.0734190904414-0.02523332846260.3684196447020.03158483014550.283258109259-19.20447824960.724417390968-8.39752525501
81.772908896790.48084036298-0.1289935265262.870717582460.6638962845193.25793248434-0.02500512179590.0027580872601-0.220467438874-0.1514993772380.0544227338473-0.3575435116230.2010393940110.412044724299-0.03948572044770.2585624675220.0659039790520.03001900431160.322476360672-0.004203288012520.324043582468-14.63538930882.65690362683-23.8851286965
98.860039943492.208938354243.214951618028.38755980942.584463407371.96974743293-0.2682868146680.8377373118020.366323746094-1.07664335102-0.02076946370750.677603832443-0.881822829326-0.1824459005430.2806643764370.4315123623890.0501569144247-0.02106602560360.4069190484720.04523479222330.291548626501-27.265496679312.4869265494-35.0798216906
102.491887583511.527194880191.341170078823.798120206221.145575027976.00875506585-0.24166828795-0.06029099319410.686086404183-0.700083937430.0545322794268-0.351661364948-0.964540086821-0.2145488744220.2044501520370.8223849995090.04916656310710.1300798120380.350099490107-0.008271773358190.707244462135-55.881272644319.893089662-23.1014328347
116.289838797611.571152475484.150223996672.787332196881.843141147917.69451765498-0.6458347707120.1920979312190.345864618378-0.621562426060.322217059282-0.771045774949-1.106483531820.2353237648140.3110766458640.633562378624-0.002281865090170.08389337020150.2669449398910.004024802292840.717482974173-52.83807472517.3053414806-23.0747630439
124.617508844481.44142840896-1.079314689587.28078407652-0.2618652753327.68677178389-0.2013939909570.3698596607070.723975661425-0.6396569822020.2177202105830.542700809545-0.828485084751-0.9749925778260.007318510255620.5190666625170.0832406605253-0.02964488476690.4305295346720.0130484436210.587831065226-68.788800944917.0839648671-22.8111802358
134.207992807911.9769229283-0.6383955593582.09193581626-0.5893680860183.98037698530.250711993661-0.1498735882230.4992751598510.447675878515-0.261841839904-0.430931738767-0.5280805183920.125336030746-0.02724208298050.6251840543840.05269030754-0.06554143350060.329723136716-0.05570134831920.529783128518-60.089102258415.8020083837-16.4391696277
143.40917599858-0.483274187028-0.1740927848267.91688227990.0182490531982.514843673170.0689973551581-0.178145432988-0.2205429331070.03341570880770.00799085376992-1.704485026160.05367373437550.458957146558-0.01955638047110.316035552734-0.0136522707559-0.03371121656240.3674952159150.02524792257950.653481519234-51.7443760917-4.24769320273-19.2150877565
152.619428250231.657783952550.2233663759426.436782811360.6871920674723.95305655210.0713525126345-0.002837998204340.1892617480180.110501761993-0.001847327545140.0267234983062-0.343060891421-0.187027066241-0.04693618879440.2202601304540.02981180722980.008401051213730.2152026343460.01219886116820.253788635863-66.8042839057-3.42109663697-22.1804310413
163.828306412111.127419954591.134891071728.5306608598-1.023313987269.178037018590.02887637389050.386900661640.0464831736657-0.6749301041790.03281837251040.4170479833450.510310888196-0.528664297808-0.1152253992970.262177871634-0.04264971422660.0007323144711510.286597555837-0.002785970593180.274108348436-71.9512705972-17.5149752855-26.2447232512
173.80367672554-0.1016430462980.1053166858597.249650014720.02780740464565.072669701270.08631797671-0.6489366119120.08626310916781.34793146552-0.03113228491240.131221167998-0.0711123726425-0.312585837957-0.0367565418870.476173989751-0.03427237138880.04974374352050.341784064128-0.01621416469690.244412009334-71.4122506989-11.8256432811-9.87643706285
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 566 through 600 )AA566 - 6001 - 35
22chain 'A' and (resid 601 through 647 )AA601 - 64736 - 82
33chain 'A' and (resid 648 through 666 )AA648 - 66683 - 101
44chain 'A' and (resid 667 through 688 )AA667 - 688102 - 123
55chain 'A' and (resid 689 through 765 )AA689 - 765124 - 139
66chain 'A' and (resid 766 through 808 )AA766 - 808140 - 182
77chain 'A' and (resid 809 through 837 )AA809 - 837183 - 211
88chain 'A' and (resid 838 through 916 )AA838 - 916212 - 290
99chain 'A' and (resid 917 through 932 )AA917 - 932291 - 306
1010chain 'B' and (resid 578 through 600 )BC578 - 6001 - 23
1111chain 'B' and (resid 601 through 630 )BC601 - 63024 - 53
1212chain 'B' and (resid 631 through 647 )BC631 - 64754 - 70
1313chain 'B' and (resid 648 through 666 )BC648 - 66671 - 89
1414chain 'B' and (resid 667 through 765 )BC667 - 76590 - 118
1515chain 'B' and (resid 766 through 876 )BC766 - 876119 - 229
1616chain 'B' and (resid 877 through 896 )BC877 - 896230 - 249
1717chain 'B' and (resid 897 through 931 )BC897 - 931250 - 284

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