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- PDB-5j5s: Src kinase in complex with a sulfonamide inhibitor -

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Basic information

Entry
Database: PDB / ID: 5j5s
TitleSrc kinase in complex with a sulfonamide inhibitor
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTransferase/Transferase Inhibitor / Protein kinase / inactive kinase / sulfonamide inhibitor / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / CD28 co-stimulation / CTLA4 inhibitory signaling / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Recycling pathway of L1 / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RAF activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / Downregulation of ERBB4 signaling / EPH-ephrin mediated repulsion of cells / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / Activated NTRK3 signals through PI3K / Downstream signal transduction / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell junction / protein phosphatase binding / protein tyrosine kinase activity / mitochondrial inner membrane / cell differentiation / cytoskeleton / endosome membrane / regulation of cell cycle / cell adhesion / cell cycle / phosphorylation / signaling receptor binding / focal adhesion / innate immune response / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / nucleus / 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 ...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 / 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-6G3 / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.153 Å
AuthorsLebedev, I. / Feldman, H.C. / Georghiou, G. / Maly, D.J. / Seeliger, M.
CitationJournal: To Be Published
Title: Structural and Functional Analysis of the Allosteric Modulation of IRE1a with ATP-Competitive Kinase Inhibitors
Authors: Feldman, H.C. / Tong, M. / Wang, L. / Meza-Acevedo, R. / Gobillot, T.A. / Gliedt, M.J. / Hari, S.B. / Mitra, A.K. / Backes, B.J. / Papa, F.R. / Seeliger, M.A. / Maly, D.J.
History
DepositionApr 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)66,4624
Polymers65,4532
Non-polymers1,0092
Water5,314295
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2312
Polymers32,7271
Non-polymers5051
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)33,2312
Polymers32,7271
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.210, 63.551, 73.664
Angle α, β, γ (deg.)100.60, 90.61, 90.96
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-6G3 / N-{4-[8-amino-3-(propan-2-yl)imidazo[1,5-a]pyrazin-1-yl]naphthalen-1-yl}-N'-[3-(trifluoromethyl)phenyl]urea


Mass: 504.506 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H23F3N6O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.97 Å3/Da / Density % sol: 62.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 7% PEG 5000MME, 100mM Bis-Tris pH 6, 1.5% Tacsimate pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.153→36.24 Å / Num. obs: 38412 / % possible obs: 94.2 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.06834 / Net I/σ(I): 14.19
Reflection shellResolution: 2.153→2.23 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.2434 / Mean I/σ(I) obs: 6.43 / Num. measured obs: 15762 / Num. unique all: 3992 / % possible all: 87.83

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.6phasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OIQ

2oiq


Resolution: 2.153→36.239 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 22.98
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 1999 5.2 %0.2156
Rwork0.1669 ---
obs0.1695 38408 94.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.153→36.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4130 0 74 295 4499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084312
X-RAY DIFFRACTIONf_angle_d1.1255854
X-RAY DIFFRACTIONf_dihedral_angle_d13.911623
X-RAY DIFFRACTIONf_chiral_restr0.044619
X-RAY DIFFRACTIONf_plane_restr0.005743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1528-2.20660.27721320.20322372X-RAY DIFFRACTION85
2.2066-2.26620.24921390.19982575X-RAY DIFFRACTION94
2.2662-2.33290.23391470.18612667X-RAY DIFFRACTION96
2.3329-2.40820.2281480.17022657X-RAY DIFFRACTION97
2.4082-2.49420.22721420.16522712X-RAY DIFFRACTION97
2.4942-2.59410.21061470.16542676X-RAY DIFFRACTION98
2.5941-2.71210.20711520.17172688X-RAY DIFFRACTION98
2.7121-2.8550.21161470.17242720X-RAY DIFFRACTION98
2.855-3.03380.23711520.17682725X-RAY DIFFRACTION98
3.0338-3.26790.21651430.17612665X-RAY DIFFRACTION97
3.2679-3.59650.20511400.16172630X-RAY DIFFRACTION96
3.5965-4.11630.18661430.15312489X-RAY DIFFRACTION91
4.1163-5.18370.2231330.15072409X-RAY DIFFRACTION87
5.1837-36.24430.21361340.16892424X-RAY DIFFRACTION88
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)
13.07730.0378-1.66764.0244-0.07717.56430.0785-0.36290.06330.58740.0796-0.2093-0.16650.2479-0.07330.715-0.0521-0.02750.4413-0.00130.267210.051739.366822.3269
25.1619-0.2162-2.79562.066-2.36695.2776-0.07330.48410.1597-1.07520.46630.6139-0.0154-0.7349-0.23560.7582-0.0981-0.16020.53890.04640.42518.267542.931912.2735
37.2918-1.0852-0.14566.7973-1.52275.1166-0.1868-0.10170.57260.19070.21940.2087-0.8394-0.5293-0.03270.6940.1023-0.05970.4731-0.06960.29366.448341.0817.3849
45.501-1.1459-1.0034.73023.53886.1681-0.3946-0.54170.1696-0.259-0.26840.6185-0.1406-1.14240.52481.0124-0.26060.00320.9858-0.03860.6012-4.174731.890917.9933
51.7239-0.21060.22542.65491.78194.20470.0264-0.21810.08850.4793-0.0063-0.09290.2040.0684-0.01890.29230.0142-0.03730.25490.00780.3037.191831.28913.0182
63.67-0.924-0.7134.46540.3442.7732-0.00550.21450.0669-0.0864-0.12060.43930.0058-0.38130.0830.223-0.0208-0.03940.2558-0.01540.2991-2.160328.6545-12.1355
73.5370.9001-1.11583.60921.39892.88530.1080.52740.733-1.13350.19450.5838-1.6062-0.1379-0.25951.29230.1344-0.05050.57560.01880.54512.492471.6385-41.645
85.79342.17640.55019.7901-0.62125.92680.41650.29590.7922-0.4349-0.2906-0.7423-1.51650.9104-0.14731.1047-0.19510.10390.5333-0.03060.50127.815173.0517-38.3195
96.01111.0187-1.48035.5626-2.00775.95350.4238-0.00010.8447-0.1727-0.5594-1.0061-1.65631.04880.12371.0118-0.19590.01290.8076-0.01270.629217.707963.8162-39.4335
104.6548-1.8063-0.06236.6957-3.72732.45020.00510.49050.3661-1.2096-0.0098-0.3483-0.52250.3002-0.06820.9123-0.0834-0.00390.5088-0.07450.39388.003864.1307-37.9777
111.06020.3229-0.41652.76881.40374.2994-0.00680.07040.2319-0.2392-0.08250.372-0.3493-0.29590.05770.27390.029-0.05610.25050.01210.34084.039962.3771-20.68
122.93241.4087-0.52233.66050.24641.7377-0.0282-0.14430.06670.1127-0.0151-0.1434-0.07130.13360.02640.21890.0501-0.04230.24040.0260.259614.150360.9247-9.8217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 258 through 272 )
2X-RAY DIFFRACTION2chain 'A' and (resid 273 through 286 )
3X-RAY DIFFRACTION3chain 'A' and (resid 287 through 303 )
4X-RAY DIFFRACTION4chain 'A' and (resid 304 through 316 )
5X-RAY DIFFRACTION5chain 'A' and (resid 317 through 402 )
6X-RAY DIFFRACTION6chain 'A' and (resid 403 through 533 )
7X-RAY DIFFRACTION7chain 'B' and (resid 258 through 289 )
8X-RAY DIFFRACTION8chain 'B' and (resid 290 through 302 )
9X-RAY DIFFRACTION9chain 'B' and (resid 303 through 316 )
10X-RAY DIFFRACTION10chain 'B' and (resid 317 through 338 )
11X-RAY DIFFRACTION11chain 'B' and (resid 339 through 402 )
12X-RAY DIFFRACTION12chain 'B' and (resid 403 through 533 )

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