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- PDB-5zxb: Crystal structure of ACK1 with compound 10d -

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Basic information

Entry
Database: PDB / ID: 5zxb
TitleCrystal structure of ACK1 with compound 10d
ComponentsActivated CDC42 kinase 1
KeywordsTRANSFERASE / inhibitor / Kinase
Function / homology
Function and homology information


regulation of clathrin-dependent endocytosis / Grb2-EGFR complex / GTPase inhibitor activity / cytoophidium / Signaling by LTK / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / WW domain binding / phosphorylation ...regulation of clathrin-dependent endocytosis / Grb2-EGFR complex / GTPase inhibitor activity / cytoophidium / Signaling by LTK / clathrin-coated vesicle / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / WW domain binding / phosphorylation / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity / non-specific protein-tyrosine kinase / adherens junction / non-membrane spanning protein tyrosine kinase activity / cytoplasmic vesicle membrane / endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / protein tyrosine kinase activity / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / endosome / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / perinuclear region of cytoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / : / SAM domain-like / Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / Variant SH3 domain ...Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / : / SAM domain-like / Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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-9KO / Activated CDC42 kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.198 Å
AuthorsHong, E.M. / Kim, H.L. / Sim, T.B.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
NRF-2016M3A9B5940991 Korea, Republic Of
CitationJournal: J. Med. Chem. / Year: 2018
Title: First SAR Study for Overriding NRAS Mutant Driven Acute Myeloid Leukemia.
Authors: Cho, H. / Shin, I. / Ju, E. / Choi, S. / Hur, W. / Kim, H. / Hong, E. / Kim, N.D. / Choi, H.G. / Gray, N.S. / Sim, T.
History
DepositionMay 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.2Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _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: Activated CDC42 kinase 1
B: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1664
Polymers62,8472
Non-polymers1,3192
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-10 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.182, 43.120, 93.891
Angle α, β, γ (deg.)90.000, 98.340, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 117 through 119 or resid 121...
21(chain B and (resid 117 through 119 or resid 121...

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
11LEULEUCYSCYS(chain A and (resid 117 through 119 or resid 121...AA117 - 1191 - 3
12ILEILEASPASP(chain A and (resid 117 through 119 or resid 121...AA121 - 1345 - 18
13VALVALLEULEU(chain A and (resid 117 through 119 or resid 121...AA139 - 22523 - 109
14GLYGLYTHRTHR(chain A and (resid 117 through 119 or resid 121...AA227 - 319111 - 203
15TRPTRPPHEPHE(chain A and (resid 117 through 119 or resid 121...AA321 - 378205 - 262
16ALAALAALAALA(chain A and (resid 117 through 119 or resid 121...AA380 - 388264 - 272
17GLNGLNGLNGLN(chain A and (resid 117 through 119 or resid 121...AA389273
18LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
19LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
110LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
111LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
112LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
113LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
114LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
115LEULEUGLNGLN(chain A and (resid 117 through 119 or resid 121...AA117 - 3891 - 273
21LEULEUCYSCYS(chain B and (resid 117 through 119 or resid 121...BB117 - 1191 - 3
22ILEILELEULEU(chain B and (resid 117 through 119 or resid 121...BB121 - 1605 - 44
23ALAALATHRTHR(chain B and (resid 117 through 119 or resid 121...BB170 - 31954 - 203
24TRPTRPPHEPHE(chain B and (resid 117 through 119 or resid 121...BB321 - 378205 - 262
25ALAALAGLNGLN(chain B and (resid 117 through 119 or resid 121...BB380 - 389264 - 273

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Components

#1: Protein Activated CDC42 kinase 1 / ACK-1 / Tyrosine kinase non-receptor protein 2


Mass: 31423.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNK2, ACK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q07912, non-specific protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-9KO / N-{3-[7-{[6-(4-acetylpiperazin-1-yl)pyridin-3-yl]amino}-1-methyl-2-oxo-1,4-dihydropyrimido[4,5-d]pyrimidin-3(2H)-yl]-4-methylphenyl}-3-(trifluoromethyl)benzamide


Mass: 659.661 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H32F3N9O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.3
Details: 0.1M Bis-Tris pH6.3 0.2M AmSO4 28% PEG3350 10mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.198→36.775 Å / Num. obs: 28669 / % possible obs: 98.1 % / Redundancy: 3.8 % / Net I/σ(I): 12.2
Reflection shellResolution: 2.198→2.277 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.198→36.775 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.32
RfactorNum. reflection% reflection
Rfree0.2566 1398 4.88 %
Rwork0.2061 --
obs0.2087 28647 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.57 Å2 / Biso mean: 50.7222 Å2 / Biso min: 26.03 Å2
Refinement stepCycle: final / Resolution: 2.198→36.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3862 0 96 93 4051
Biso mean--50.62 46.99 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094080
X-RAY DIFFRACTIONf_angle_d1.4685530
X-RAY DIFFRACTIONf_chiral_restr0.067593
X-RAY DIFFRACTIONf_plane_restr0.008696
X-RAY DIFFRACTIONf_dihedral_angle_d10.6643359
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2188X-RAY DIFFRACTION14.329TORSIONAL
12B2188X-RAY DIFFRACTION14.329TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1976-2.27620.32181210.29982456257789
2.2762-2.36730.33891360.29082661279797
2.3673-2.4750.34831430.27042707285099
2.475-2.60550.31511510.23842728287999
2.6055-2.76870.27561270.22422754288199
2.7687-2.98230.23761280.21512741286999
2.9823-3.28230.28011450.208927622907100
3.2823-3.75680.24091350.18962788292399
3.7568-4.73160.20591520.178427942946100
4.7316-36.780.25361600.19012858301899

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