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- PDB-2xyn: HUMAN ABL2 IN COMPLEX WITH AURORA KINASE INHIBITOR VX-680 -

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Basic information

Entry
Database: PDB / ID: 2xyn
TitleHUMAN ABL2 IN COMPLEX WITH AURORA KINASE INHIBITOR VX-680
ComponentsTYROSINE-PROTEIN KINASE ABL2
KeywordsTRANSFERASE / CELL ADHESION / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


Role of ABL in ROBO-SLIT signaling / regulation of cell motility / positive regulation of establishment of T cell polarity / negative regulation of Rho protein signal transduction / exploration behavior / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / Negative regulation of FLT3 ...Role of ABL in ROBO-SLIT signaling / regulation of cell motility / positive regulation of establishment of T cell polarity / negative regulation of Rho protein signal transduction / exploration behavior / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / Negative regulation of FLT3 / regulation of cell adhesion / cellular response to retinoic acid / phosphotyrosine residue binding / RAC1 GTPase cycle / peptidyl-tyrosine phosphorylation / regulation of actin cytoskeleton organization / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / enzyme activator activity / positive regulation of neuron projection development / protein modification process / epidermal growth factor receptor signaling pathway / actin filament binding / actin cytoskeleton / manganese ion binding / positive regulation of cytosolic calcium ion concentration / cellular response to oxidative stress / protein tyrosine kinase activity / phospholipase C-activating G protein-coupled receptor signaling pathway / protein kinase activity / cell adhesion / regulation of autophagy / enzyme binding / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-VX6 / Tyrosine-protein kinase ABL2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsSalah, E. / Ugochukwu, E. / Elkins, J.M. / Barr, A.J. / Shrestha, B. / Savitsky, P. / Mahajan, P. / Muniz, J.R.C. / Yue, W.W. / Chaikuad, A. ...Salah, E. / Ugochukwu, E. / Elkins, J.M. / Barr, A.J. / Shrestha, B. / Savitsky, P. / Mahajan, P. / Muniz, J.R.C. / Yue, W.W. / Chaikuad, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2011
Title: Crystal Structures of Abl-Related Gene (Abl2) in Complex with Imatinib, Tozasertib (Vx-680), and a Type I Inhibitor of the Triazole Carbothioamide Class.
Authors: Salah, E. / Ugochukwu, E. / Barr, A.J. / von Delft, F. / Knapp, S. / Elkins, J.M.
History
DepositionNov 18, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionDec 1, 2010ID: 3NSV
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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 / _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
B: TYROSINE-PROTEIN KINASE ABL2
C: TYROSINE-PROTEIN KINASE ABL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,96413
Polymers100,6303
Non-polymers3,33410
Water23413
1
A: TYROSINE-PROTEIN KINASE ABL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0895
Polymers33,5431
Non-polymers5464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TYROSINE-PROTEIN KINASE ABL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9374
Polymers33,5431
Non-polymers1,3943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TYROSINE-PROTEIN KINASE ABL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9374
Polymers33,5431
Non-polymers1,3943
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)170.500, 170.500, 100.651
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23B
33C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYVALVAL2AA367 - 425113 - 171
211GLYGLYVALVAL2BB367 - 425113 - 171
311GLYGLYVALVAL2CC367 - 425113 - 171
121THRTHRPHEPHE2AA438 - 543184 - 289
221THRTHRPHEPHE2BB438 - 543184 - 289
321THRTHRPHEPHE2CC438 - 543184 - 289
112TRPTRPTYRTYR6AA281 - 36627 - 112
212TRPTRPTYRTYR6BB281 - 36627 - 112
312TRPTRPTYRTYR6CC281 - 36627 - 112
113VX6VX6VX6VX64AE547
213VX6VX6VX6VX64BH547
313VX6VX6VX6VX64CK547

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.44543, -0.89376, -0.05282), (-0.89516, -0.44569, -0.00738), (-0.01694, 0.05057, -0.99858)-17.04952, -20.43198, -30.23569
2given(0.23663, 0.85911, 0.4538), (-0.21144, 0.5014, -0.83898), (-0.94832, 0.10258, 0.30029)-86.93401, -29.52684, -86.71567

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Components

#1: Protein TYROSINE-PROTEIN KINASE ABL2 / ABELSON MURINE LEUKEMIA VIRAL ONCOGENE HOMOLOG 2 / ABELSON-RELATED GENE PROTEIN / TYROSINE-PROTEIN ...ABELSON MURINE LEUKEMIA VIRAL ONCOGENE HOMOLOG 2 / ABELSON-RELATED GENE PROTEIN / TYROSINE-PROTEIN KINASE ARG / ABL2


Mass: 33543.359 Da / Num. of mol.: 3 / Fragment: RESIDUES 243-510
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper)
References: UniProt: P42684, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-VX6 / CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE


Mass: 464.586 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C23H28N8OS / Comment: inhibitor*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCYCLOPROPANECARBOXYLIC ACID

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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: 4.2 Å3/Da / Density % sol: 70.69 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.8M SODIUM SUCCINATE, PH 7, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9782
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 2.81→41.14 Å / Num. obs: 41549 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.8
Reflection shellResolution: 2.81→2.96 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HMI

3hmi


Resolution: 2.81→147.66 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.886 / SU B: 27.882 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.28425 2086 5 %RANDOM
Rwork0.24587 ---
obs0.24782 39462 99.9 %-
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 mean: 94.264 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20.96 Å20 Å2
2--1.93 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.81→147.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5838 0 234 13 6085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216260
X-RAY DIFFRACTIONr_bond_other_d0.0020.023950
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9878569
X-RAY DIFFRACTIONr_angle_other_deg0.9663.0069428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3015786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71623.363223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89115824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3231523
X-RAY DIFFRACTIONr_chiral_restr0.070.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217099
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021277
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.391.53940
X-RAY DIFFRACTIONr_mcbond_other0.1051.51588
X-RAY DIFFRACTIONr_mcangle_it0.72726222
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.16332320
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9544.52326
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A967tight positional0.050.05
12B967tight positional0.040.05
13C967tight positional0.040.05
11A895medium positional0.050.5
12B895medium positional0.040.5
13C895medium positional0.060.5
31A56medium positional0.160.5
32B56medium positional0.290.5
33C56medium positional0.30.5
21A813loose positional0.435
22B813loose positional0.555
23C813loose positional0.525
11A967tight thermal0.080.5
12B967tight thermal0.080.5
13C967tight thermal0.090.5
11A895medium thermal0.12
12B895medium thermal0.082
13C895medium thermal0.082
31A56medium thermal0.722
32B56medium thermal1.742
33C56medium thermal2.252
21A813loose thermal1.1210
22B813loose thermal1.6110
23C813loose thermal1.5110
LS refinement shellResolution: 2.805→2.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 152 -
Rwork0.411 2888 -
obs--99.97 %
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)
17.22970.10070.0544.8368-0.70033.9751-0.5311.47270.4108-0.51020.3472-1.0781-0.62351.33340.18390.8533-0.6463-0.16741.0845-0.06480.5553-50.127757.9243-10.7312
26.12430.08021.19772.77840.29743.408-0.45530.04210.07310.51710.2196-0.176-0.58070.05020.23580.6386-0.1984-0.03010.216-0.04090.0363-73.078750.2875-5.2077
33.7581-0.191-1.6719.83041.11133.51310.1697-0.7612-0.39371.983-0.72410.35490.8373-0.1470.55441.1388-0.41770.02360.3677-0.03080.372-90.1252-1.9395-15.7052
41.9274-0.9516-0.44149.69963.75482.69050.42910.01310.08990.1401-1.02451.03210.0837-0.84170.59530.4551-0.11340.06690.3667-0.17190.401-94.038822.6984-21.3663
54.5108-1.1070.44125.5396-0.34645.3592-0.09070.48250.7228-0.55620.217-1.8051-0.51230.8308-0.12640.7719-0.20550.21470.41670.04531.9446-54.633718.447-36.6739
62.7856-1.3003-0.12243.4231.12853.8626-0.0155-0.36250.51871.04150.1311-1.89110.1470.4661-0.11570.9051-0.1079-0.52390.2141-0.02391.3947-63.870515.2661-14.0184
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A280 - 366
2X-RAY DIFFRACTION2A367 - 543
3X-RAY DIFFRACTION3B280 - 366
4X-RAY DIFFRACTION4B367 - 543
5X-RAY DIFFRACTION5C273 - 366
6X-RAY DIFFRACTION6C367 - 545

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