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- PDB-3uqg: c-SRC kinase domain in complex with bumpless BKI analog UW1243 -

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Basic information

Entry
Database: PDB / ID: 3uqg
Titlec-SRC kinase domain in complex with bumpless BKI analog UW1243
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / tyrosine protein kinase / ATP-binding / kinase domain / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / RAF activation / PIP3 activates AKT signaling / EPH-ephrin mediated repulsion of cells / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Activated NTRK3 signals through PI3K / Downstream signal transduction / Downregulation of ERBB4 signaling / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / DCC mediated attractive signaling / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / negative regulation of intrinsic apoptotic signaling pathway / progesterone receptor signaling pathway / immune system process / negative regulation of extrinsic apoptotic signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / epidermal growth factor receptor signaling pathway / cell-cell junction / cell junction / protein tyrosine kinase activity / protein phosphatase binding / cell differentiation / cytoskeleton / mitochondrial inner membrane / regulation of cell cycle / cell adhesion / endosome membrane / signaling receptor binding / focal adhesion / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
: / 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 / 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-B5A / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMerritt, E.A. / Larson, E.T.
Citation
Journal: J.Med.Chem. / Year: 2012
Title: Multiple Determinants for Selective Inhibition of Apicomplexan Calcium-Dependent Protein Kinase CDPK1.
Authors: Larson, E.T. / Ojo, K.K. / Murphy, R.C. / Johnson, S.M. / Zhang, Z. / Kim, J.E. / Leibly, D.J. / Fox, A.M. / Reid, M.C. / Dale, E.J. / Perera, B.G. / Kim, J. / Hewitt, S.N. / Hol, W.G. / ...Authors: Larson, E.T. / Ojo, K.K. / Murphy, R.C. / Johnson, S.M. / Zhang, Z. / Kim, J.E. / Leibly, D.J. / Fox, A.M. / Reid, M.C. / Dale, E.J. / Perera, B.G. / Kim, J. / Hewitt, S.N. / Hol, W.G. / Verlinde, C.L. / Fan, E. / Van Voorhis, W.C. / Maly, D.J. / Merritt, E.A.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Toxoplasma gondii calcium-dependent protein kinase 1 is a target for selective kinase inhibitors
Authors: Ojo, K.K. / Larson, E.T. / Keyloun, K.R. / Castaneda, L.J. / Derocher, A.E. / Inampudi, K.K. / Kim, J.E. / Arakaki, T.L. / Murphy, R.C. / Zhang, L. / Napuli, A.J. / Maly, D.J. / Verlinde, C. ...Authors: Ojo, K.K. / Larson, E.T. / Keyloun, K.R. / Castaneda, L.J. / Derocher, A.E. / Inampudi, K.K. / Kim, J.E. / Arakaki, T.L. / Murphy, R.C. / Zhang, L. / Napuli, A.J. / Maly, D.J. / Verlinde, C.L.M.J. / Buckner, F.S. / Parsons, M. / Hol, W.G.J. / Merritt, E.A. / Van Voorhis, W.C.
#2: Journal: ACS Med.Chem.Lett. / Year: 2010
Title: Discovery of potent and selective inhibitors of Calcium-Dependent Protein Kinase 1 (CDPK1) from C. parvum and T. gondii
Authors: Murphy, R.C. / Ojo, K.K. / Larson, E.T. / Castellanos-Gonzalez, A. / Perera, B.G.K. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N. / Verlinde, C.L.M.J. / Nakazawa, S.H. / Hol, W.G. ...Authors: Murphy, R.C. / Ojo, K.K. / Larson, E.T. / Castellanos-Gonzalez, A. / Perera, B.G.K. / Keyloun, K.R. / Kim, J.E. / Bhandari, J.G. / Muller, N. / Verlinde, C.L.M.J. / Nakazawa, S.H. / Hol, W.G.J. / Buckner, F.S. / Napuli, A.J. / White, C.A. / Merritt, E.A. / Van Voorhis, W.C. / Maly, D.J.
History
DepositionNov 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Proto-oncogene tyrosine-protein kinase Src
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9184
Polymers65,4532
Non-polymers4652
Water50428
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9592
Polymers32,7271
Non-polymers2321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9592
Polymers32,7271
Non-polymers2321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.540, 63.720, 74.980
Angle α, β, γ (deg.)78.170, 89.340, 90.080
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase Src / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 32726.645 Da / Num. of mol.: 2 / Fragment: kinase domain (UNP residues 251-533)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Production host: Escherichia coli (E. coli)
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-B5A / 1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine


Mass: 232.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 9% PEG 2000, 100 mM MES pH 7, 2.0 mM UW1243 in 10% DMSO, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 16, 2011
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.2→62.37 Å / Num. all: 38121 / Num. obs: 38121 / % possible obs: 97.3 % / Redundancy: 4 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 7.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 1.3 / Num. unique all: 5485 / % possible all: 96.7

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→53.21 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.2591 / WRfactor Rwork: 0.2287 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8153 / SU B: 14.511 / SU ML: 0.166 / SU R Cruickshank DPI: 0.2397 / SU Rfree: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 1905 5 %RANDOM
Rwork0.2287 ---
obs0.2302 38120 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 138.99 Å2 / Biso mean: 65.9137 Å2 / Biso min: 32.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20.21 Å2-0.1 Å2
2---0.13 Å20.29 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→53.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 34 28 4186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024269
X-RAY DIFFRACTIONr_bond_other_d0.0020.022945
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9845792
X-RAY DIFFRACTIONr_angle_other_deg0.9523.0037127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.655516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32823.71186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19615723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0991529
X-RAY DIFFRACTIONr_chiral_restr0.0640.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214674
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02869
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 131 -
Rwork0.35 2658 -
all-2789 -
obs--96.51 %
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)
11.5733-0.33230.15712.5922-0.71542.04550.0417-0.1341-0.18380.407-0.1306-0.0544-0.03360.29080.08890.0858-0.0617-0.02490.19680.06490.1355-2.719-30.918-1.898
21.20440.06530.36322.8774-0.60992.05890.0230.0456-0.012-0.3952-0.03530.03810.1903-0.26780.01220.08570.0488-0.01990.21640.02350.1294-10.558-62.228-22.341
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A258 - 533
2X-RAY DIFFRACTION2B256 - 533

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