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- PDB-3hmi: The crystal structure of human ABL2 in complex with 5-AMINO-3-{[4... -

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Basic information

Entry
Database: PDB / ID: 3hmi
TitleThe crystal structure of human ABL2 in complex with 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE
ComponentsTyrosine-protein kinase ABL2
KeywordsTRANSFERASE / Tyrosine kinase / ABL / ABL2 / Abelson murine leukemia viral oncogene / ATP-binding / Cell adhesion / Cytoskeleton / Kinase / Lipoprotein / Magnesium / Manganese / Metal-binding / Myristate / Nucleotide-binding / Phosphoprotein / SH2 domain / SH3 domain / Tyrosine-protein kinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of cell motility / exploration behavior / negative regulation of Rho protein signal transduction / regulation of endocytosis / actin monomer binding / positive regulation of T cell migration / RAC3 GTPase cycle / regulation of cell adhesion ...positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of cell motility / exploration behavior / negative regulation of Rho protein signal transduction / regulation of endocytosis / actin monomer binding / positive regulation of T cell migration / RAC3 GTPase cycle / regulation of cell adhesion / cellular response to retinoic acid / Negative regulation of FLT3 / positive regulation of establishment of T cell polarity / phosphotyrosine residue binding / RAC1 GTPase cycle / regulation of autophagy / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / protein modification process / epidermal growth factor receptor signaling pathway / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / actin filament binding / actin cytoskeleton / manganese ion binding / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / protein tyrosine kinase activity / cell adhesion / protein kinase activity / magnesium ion binding / signal transduction / ATP binding / plasma membrane / cytosol
Similarity search - Function
F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / 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-DKI / Tyrosine-protein kinase ABL2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsUgochukwu, E. / Salah, E. / Barr, A. / Mahajan, P. / Shrestha, B. / Savitsky, P. / Chaikuad, A. / Allerston, C. / von Delft, F. / Bountra, C. ...Ugochukwu, E. / Salah, E. / Barr, A. / Mahajan, P. / Shrestha, B. / Savitsky, P. / Chaikuad, A. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of human ABL2 in complex with 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE
Authors: Ugochukwu, E. / Salah, E. / Barr, A. / Mahajan, P. / Shrestha, B. / Savitsky, P. / Chaikuad, A. / Allerston, C. / von Delft, F. / Knapp, S.
History
DepositionMay 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase ABL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9692
Polymers33,5431
Non-polymers4251
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)165.920, 39.800, 43.130
Angle α, β, γ (deg.)90.00, 95.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tyrosine-protein kinase ABL2 / Abelson murine leukemia viral oncogene homolog 2 / Abelson-related gene protein / Tyrosine kinase ARG


Mass: 33543.359 Da / Num. of mol.: 1 / Fragment: Protein kinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABL2 / Plasmid: pFB-LIC-Bse / Cell line (production host): High 5 insect cells / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P42684, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-DKI / 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE / CDK 1/2 INHIBITOR


Mass: 425.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13F2N7O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M lithium sulfate, 0.05M di-sodium hydrogen phosphate, 0.05M citric acid, 19%(w/v) PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: MAR225 / Detector: CCD / Date: Apr 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.65→39.72 Å / Num. obs: 28844 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 11.8
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 2.2 / Num. unique all: 13096 / Rsym value: 0.802 / % possible all: 85.4

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GVU

3gvu


Resolution: 1.65→39.72 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.828 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.124 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23394 1462 5.1 %RANDOM
Rwork0.18778 ---
all0.19015 27347 --
obs0.19015 27347 84.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 46.23 Å2 / Biso mean: 8.952 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20.4 Å2
2--1.62 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 1.65→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 28 235 2389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222260
X-RAY DIFFRACTIONr_bond_other_d0.0010.021495
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9733089
X-RAY DIFFRACTIONr_angle_other_deg0.8893.0013648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2225282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5624.06396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65515374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.297159
X-RAY DIFFRACTIONr_chiral_restr0.110.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02461
X-RAY DIFFRACTIONr_mcbond_it0.811.51361
X-RAY DIFFRACTIONr_mcbond_other0.2371.5546
X-RAY DIFFRACTIONr_mcangle_it1.35322202
X-RAY DIFFRACTIONr_scbond_it1.8773899
X-RAY DIFFRACTIONr_scangle_it2.8524.5879
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 111 -
Rwork0.282 2216 -
obs--94.82 %
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)
13.4018-0.2087-0.8861.95230.30923.2343-0.07030.0183-0.12890.0704-0.0720.13490.2139-0.57820.14230.1134-0.02230.01010.18060.00410.1409-41.26596.8628-3.7654
24.5322-1.3105-1.44424.10560.96163.8801-0.06890.1917-0.28120.1112-0.21360.12820.1782-0.24850.28250.0786-0.04230.00430.0393-0.02680.072-38.15675.9182-9.6184
31.33380.2853-0.88830.5448-0.02662.5086-0.0017-0.00390.0009-0.02770.00340.0281-0.13260.1225-0.00170.0651-0.014-0.01890.04980.00430.0574-26.309914.2316-10.0469
42.6207-0.57440.03542.00460.69983.4381-0.0202-0.2045-0.13460.06230.0389-0.05170.24840.3457-0.01860.0399-0.02960.00960.21690.0160.0664-10.29028.3094-13.8369
53.5303-1.68620.49274.93750.26753.65240.09860.06630.0079-0.2297-0.11970.1396-0.14520.48890.02110.0288-0.06120.00760.3698-0.00710.0392-2.487811.2027-19.191
62.1655-0.53690.60223.1901-0.21782.3575-0.0674-0.16850.3618-0.08740.0849-0.1494-0.27710.3794-0.01750.0862-0.10160.0070.3021-0.01690.081-7.809721.3946-11.6138
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A279 - 294
2X-RAY DIFFRACTION2A295 - 319
3X-RAY DIFFRACTION3A326 - 432
4X-RAY DIFFRACTION4A433 - 490
5X-RAY DIFFRACTION5A491 - 517
6X-RAY DIFFRACTION6A518 - 544

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