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- PDB-7khj: Crystal structure of KIT kinase domain with a small molecule inhi... -

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Basic information

Entry
Database: PDB / ID: 7khj
TitleCrystal structure of KIT kinase domain with a small molecule inhibitor, PLX8512 in the DFG-in state
ComponentsMast/stem cell growth factor receptor Kit
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / transferase / tyrosine-protein kinase / ATP-binding / kinase-kinase inhibitor complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homologyChem-WEG
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhang, Y.
CitationJournal: Jama Oncol / Year: 2021
Title: Association of Combination of Conformation-Specific KIT Inhibitors With Clinical Benefit in Patients With Refractory Gastrointestinal Stromal Tumors: A Phase 1b/2a Nonrandomized Clinical Trial.
Authors: Wagner, A.J. / Severson, P.L. / Shields, A.F. / Patnaik, A. / Chugh, R. / Tinoco, G. / Wu, G. / Nespi, M. / Lin, J. / Zhang, Y. / Ewing, T. / Habets, G. / Burton, E.A. / Matusow, B. / Tsai, ...Authors: Wagner, A.J. / Severson, P.L. / Shields, A.F. / Patnaik, A. / Chugh, R. / Tinoco, G. / Wu, G. / Nespi, M. / Lin, J. / Zhang, Y. / Ewing, T. / Habets, G. / Burton, E.A. / Matusow, B. / Tsai, J. / Tsang, G. / Shellooe, R. / Carias, H. / Chan, K. / Rezaei, H. / Sanftner, L. / Marimuthu, A. / Spevak, W. / Ibrahim, P.N. / Inokuchi, K. / Alcantar, O. / Michelson, G. / Tsiatis, A.C. / Zhang, C. / Bollag, G. / Trent, J.C. / Tap, W.D.
History
DepositionOct 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 11, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Sep 29, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)76,5734
Polymers76,0522
Non-polymers5212
Water64936
1
A: Mast/stem cell growth factor receptor Kit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2862
Polymers38,0261
Non-polymers2601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mast/stem cell growth factor receptor Kit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2862
Polymers38,0261
Non-polymers2601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.743, 61.739, 206.909
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 571 through 596 or resid 601...
21(chain B and (resid 571 through 826 or resid 829 through 930))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEGLYGLY(chain A and (resid 571 through 596 or resid 601...AA571 - 59630 - 55
12GLYGLYLEULEU(chain A and (resid 571 through 596 or resid 601...AA601 - 68260 - 141
13ASPASPTHRTHR(chain A and (resid 571 through 596 or resid 601...AA765 - 801166 - 202
14ILEILEILEILE(chain A and (resid 571 through 596 or resid 601...AA805 - 817206 - 218
15SERSERARGARG(chain A and (resid 571 through 596 or resid 601...AA821 - 888222 - 289
16GLUGLUGLUGLU(chain A and (resid 571 through 596 or resid 601...AA893 - 930294 - 331
21ILEILELYSLYS(chain B and (resid 571 through 826 or resid 829 through 930))BB571 - 82630 - 227
22ALAALAGLUGLU(chain B and (resid 571 through 826 or resid 829 through 930))BB829 - 930230 - 331

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Components

#1: Protein Mast/stem cell growth factor receptor Kit


Mass: 38026.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-WEG / 2-phenyl-5-(1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridine


Mass: 260.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Imidazole-HCl, pH7.0, 1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.8→59.161 Å / Num. obs: 18097 / % possible obs: 95.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 76.27 Å2 / Rsym value: 0.05 / Net I/σ(I): 9.6
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 2113 / Rsym value: 0.47

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T45

1t45


Resolution: 2.8→59.161 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.286 1801 9.95 %
Rwork0.2411 16296 -
obs0.2454 18097 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.07 Å2 / Biso mean: 96.7508 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.8→59.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4368 0 40 36 4444
Biso mean--118.14 32.95 -
Num. residues----549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114497
X-RAY DIFFRACTIONf_angle_d1.3086075
X-RAY DIFFRACTIONf_chiral_restr0.063664
X-RAY DIFFRACTIONf_plane_restr0.008762
X-RAY DIFFRACTIONf_dihedral_angle_d18.8732674
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2302X-RAY DIFFRACTION11.367TORSIONAL
12B2302X-RAY DIFFRACTION11.367TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8001-2.87580.32991120.3239109885
2.8758-2.96040.34821380.2999112489
2.9604-3.05590.34291280.2874117590
3.0559-3.16520.34411310.2993122796
3.1652-3.29190.3711340.2991125096
3.2919-3.44170.3051350.2633127797
3.4417-3.62310.30461530.2451125198
3.6231-3.85010.28551430.2445131098
3.8501-4.14730.30561380.2382126999
4.1473-4.56450.23291500.1993128499
4.5645-5.22460.25161490.2293132699
5.2246-6.58110.27791410.2515132998
6.5811-59.1610.28171490.2201137696

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