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- PDB-3eqr: Crystal Structure of Ack1 with compound T74 -

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Basic information

Entry
Database: PDB / ID: 3eqr
TitleCrystal Structure of Ack1 with compound T74
ComponentsActivated CDC42 kinase 1
KeywordsTRANSFERASE / ack1 / Alternative splicing / ATP-binding / Cell membrane / Kinase / Magnesium / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Polymorphism / SH3 domain / Tyrosine-protein kinase
Function / homology
Function and homology information


regulation of clathrin-dependent endocytosis / cytoophidium / Grb2-EGFR complex / GTPase inhibitor activity / WW domain binding / clathrin-coated vesicle / small GTPase-mediated signal transduction / epidermal growth factor receptor binding / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity ...regulation of clathrin-dependent endocytosis / cytoophidium / Grb2-EGFR complex / GTPase inhibitor activity / WW domain binding / clathrin-coated vesicle / small GTPase-mediated signal transduction / epidermal growth factor receptor binding / clathrin-coated pit / protein serine/threonine/tyrosine kinase activity / adherens junction / non-specific protein-tyrosine kinase / 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 / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / ubiquitin protein ligase binding / perinuclear region of cytoplasm / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily ...Activated CDC42 kinase 1 / Cdc42 binding domain-like superfamily / : / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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-T74 / Activated CDC42 kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsLiu, J. / Wang, Z. / Walker, N.P.C.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Identification and optimization of N3,N6-diaryl-1H-pyrazolo[3,4-d]pyrimidine-3,6-diamines as a novel class of ACK1 inhibitors.
Authors: Kopecky, D.J. / Hao, X. / Chen, Y. / Fu, J. / Jiao, X. / Jaen, J.C. / Cardozo, M.G. / Liu, J. / Wang, Z. / Walker, N.P. / Wesche, H. / Li, S. / Farrelly, E. / Xiao, S.H. / Kayser, F.
History
DepositionOct 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1425
Polymers63,0772
Non-polymers1,0653
Water5,531307
1
A: Activated CDC42 kinase 1
hetero molecules

B: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1425
Polymers63,0772
Non-polymers1,0653
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area1550 Å2
ΔGint-25 kcal/mol
Surface area24330 Å2
MethodPISA
2
A: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0893
Polymers31,5381
Non-polymers5502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Activated CDC42 kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0532
Polymers31,5381
Non-polymers5151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.785, 42.915, 92.832
Angle α, β, γ (deg.)90.000, 99.670, 90.000
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: 31538.395 Da / Num. of mol.: 2 / Fragment: UNP residues 117-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNK2, ACK1 / Production host: Insect cells
References: UniProt: Q07912, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-T74 / N~3~-(2,6-dimethylphenyl)-1-(3-methoxy-3-methylbutyl)-N~6~-(4-piperazin-1-ylphenyl)-1H-pyrazolo[3,4-d]pyrimidine-3,6-diamine


Mass: 514.665 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H38N8O
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
DetectorDetector: CCD / Date: Jan 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→91.515 Å / Num. obs: 35597 / % possible obs: 94.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 4.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.113.40.4231.81699450070.42391.9
2.11-2.243.40.3232.21602347500.32391.8
2.24-2.393.40.262.61505944760.2692.3
2.39-2.583.40.222.31402541810.2292.1
2.58-2.833.30.1773.61302339270.17793.8
2.83-3.163.30.1434.31189636240.14396.4
3.16-3.653.20.1085.31071533060.10898.9
3.65-4.473.20.0797.1909928560.07999.6
4.47-6.323.10.0647.6690321930.06498.4
6.32-91.513.30.04312.8426712770.04399.8

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Processing

Software
NameVersionClassificationNB
SCALA3.1.20data scaling
REFMAC5.5.0044refinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 2→91.29 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.681 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1783 5 %RANDOM
Rwork0.21 ---
obs0.212 35585 94.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 54.27 Å2 / Biso mean: 25.44 Å2 / Biso min: 10.98 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20.18 Å2
2--1.49 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 77 307 4724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224528
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9866132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0025537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55922.899207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67315781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5261541
X-RAY DIFFRACTIONr_chiral_restr0.0830.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213419
X-RAY DIFFRACTIONr_mcbond_it0.6481.52694
X-RAY DIFFRACTIONr_mcangle_it1.23524340
X-RAY DIFFRACTIONr_scbond_it1.82631834
X-RAY DIFFRACTIONr_scangle_it3.0824.51792
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 148 -
Rwork0.263 2412 -
all-2560 -
obs--92.32 %

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