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- PDB-8hmt: The complex of ACK1 with the inhibitor 2-142 -

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Basic information

Entry
Database: PDB / ID: 8hmt
TitleThe complex of ACK1 with the inhibitor 2-142
ComponentsActivated CDC42 kinase 1
KeywordsTRANSFERASE / inhibitor / complex / ack1
Function / homology
Function and homology information


regulation of clathrin-dependent endocytosis / Grb2-EGFR complex / GTPase inhibitor activity / cytoophidium / phosphorylation / Signaling by LTK / clathrin-coated vesicle / epidermal growth factor receptor binding / positive regulation of peptidyl-tyrosine phosphorylation / small GTPase-mediated signal transduction ...regulation of clathrin-dependent endocytosis / Grb2-EGFR complex / GTPase inhibitor activity / cytoophidium / phosphorylation / Signaling by LTK / clathrin-coated vesicle / epidermal growth factor receptor binding / positive regulation of peptidyl-tyrosine phosphorylation / small GTPase-mediated signal transduction / WW domain binding / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity / cytoplasmic vesicle membrane / non-membrane spanning protein tyrosine kinase activity / adherens junction / non-specific protein-tyrosine kinase / endocytosis / protein tyrosine kinase activity / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / endosome / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / ubiquitin protein ligase binding / perinuclear region of cytoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / : / : / SAM domain-like ...Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / Cdc42 binding domain-like / Mig-6 domain / : / GTPase binding / EGFR receptor inhibitor Mig-6 / : / : / SAM domain-like / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-LWX / Activated CDC42 kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsZhu, S. / Xiaoyun, X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81903539 China
CitationJournal: To Be Published
Title: The complex of ACK1 with the inhibitor 2-142
Authors: Zhu, S. / Xiaoyun, X.Y.
History
DepositionDec 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activated CDC42 kinase 1
B: Activated CDC42 kinase 1
C: Activated CDC42 kinase 1
D: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,2588
Polymers124,9004
Non-polymers2,3584
Water00
1
A: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8152
Polymers31,2251
Non-polymers5901
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8152
Polymers31,2251
Non-polymers5901
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8152
Polymers31,2251
Non-polymers5901
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8152
Polymers31,2251
Non-polymers5901
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.710, 133.010, 110.667
Angle α, β, γ (deg.)90.00, 90.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 31225.092 Da / Num. of mol.: 4
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-LWX / 6-(2-bromophenyl)-2-[[3-methyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-8-[[(2S)-oxolan-2-yl]methyl]pyrido[2,3-d]pyrimidin-7-one


Mass: 589.526 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H33BrN6O2 / Feature type: SUBJECT OF INVESTIGATION
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: 3.05 Å3/Da / Density % sol: 59.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 4000, 0.2M Bis-Tris ph 6.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 3.17→110.68 Å / Num. obs: 23600 / % possible obs: 93.2 % / Redundancy: 4.4 % / Rpim(I) all: 0.116 / Net I/σ(I): 6
Reflection shellResolution: 3.17→10.03 Å / Num. unique obs: 3695 / Rpim(I) all: 0.443

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.17→51.71 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 1149 4.87 %
Rwork0.2058 --
obs0.2088 23600 92.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.17→51.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8552 0 156 0 8708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.498
X-RAY DIFFRACTIONf_dihedral_angle_d15.6311222
X-RAY DIFFRACTIONf_chiral_restr0.0741300
X-RAY DIFFRACTIONf_plane_restr0.011541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.320.37331490.26262997X-RAY DIFFRACTION100
3.32-3.490.31411280.27082965X-RAY DIFFRACTION98
3.49-3.610.3542800.25891695X-RAY DIFFRACTION99
3.72-3.990.35251430.25952806X-RAY DIFFRACTION96
3.99-4.40.24571710.18242965X-RAY DIFFRACTION99
4.4-5.030.20371650.1763025X-RAY DIFFRACTION100
5-6.340.21411660.16052989X-RAY DIFFRACTION97
5.03-6.340.26471470.19753009X-RAY DIFFRACTION99

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