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- PDB-5e1e: Human JAK1 kinase in complex with compound 30 at 2.30 Angstroms r... -

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Basic information

Entry
Database: PDB / ID: 5e1e
TitleHuman JAK1 kinase in complex with compound 30 at 2.30 Angstroms resolution
ComponentsTyrosine-protein kinase JAK1
KeywordsTRANSFERASE / Kinase
Function / homology
Function and homology information


protein localization to cell-cell junction / interleukin-11-mediated signaling pathway / positive regulation of homotypic cell-cell adhesion / CCR5 chemokine receptor binding / T-helper 17 cell lineage commitment / type III interferon-mediated signaling pathway / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway ...protein localization to cell-cell junction / interleukin-11-mediated signaling pathway / positive regulation of homotypic cell-cell adhesion / CCR5 chemokine receptor binding / T-helper 17 cell lineage commitment / type III interferon-mediated signaling pathway / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / interleukin-2-mediated signaling pathway / interleukin-15-mediated signaling pathway / Interleukin-15 signaling / Interleukin-12 signaling / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-2 signaling / growth hormone receptor binding / Other interleukin signaling / IFNG signaling activates MAPKs / Interleukin-20 family signaling / Interleukin-6 signaling / type I interferon-mediated signaling pathway / interleukin-6-mediated signaling pathway / positive regulation of sprouting angiogenesis / MAPK3 (ERK1) activation / Interleukin-10 signaling / MAPK1 (ERK2) activation / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / Signaling by CSF3 (G-CSF) / extrinsic component of cytoplasmic side of plasma membrane / Interleukin-7 signaling / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Inactivation of CSF3 (G-CSF) signaling / cytoplasmic side of plasma membrane / ISG15 antiviral mechanism / cellular response to virus / cytokine-mediated signaling pathway / positive regulation of protein localization to nucleus / Interferon gamma signaling / Interferon alpha/beta signaling / RAF/MAP kinase cascade / protein phosphatase binding / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / Potential therapeutics for SARS / cell differentiation / cytoskeleton / endosome / intracellular signal transduction / response to antibiotic / protein phosphorylation / focal adhesion / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine-protein kinase, non-receptor Jak1 / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain / FERM central domain / FERM superfamily, second domain ...Tyrosine-protein kinase, non-receptor Jak1 / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 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-5JG / DI(HYDROXYETHYL)ETHER / Tyrosine-protein kinase JAK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsFerguson, A.D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Identification of azabenzimidazoles as potent JAK1 selective inhibitors.
Authors: Vasbinder, M.M. / Alimzhanov, M. / Augustin, M. / Bebernitz, G. / Bell, K. / Chuaqui, C. / Deegan, T. / Ferguson, A.D. / Goodwin, K. / Huszar, D. / Kawatkar, A. / Kawatkar, S. / Read, J. / ...Authors: Vasbinder, M.M. / Alimzhanov, M. / Augustin, M. / Bebernitz, G. / Bell, K. / Chuaqui, C. / Deegan, T. / Ferguson, A.D. / Goodwin, K. / Huszar, D. / Kawatkar, A. / Kawatkar, S. / Read, J. / Shi, J. / Steinbacher, S. / Steuber, H. / Su, Q. / Toader, D. / Wang, H. / Woessner, R. / Wu, A. / Ye, M. / Zinda, M.
History
DepositionSep 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Dec 30, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase JAK1
B: Tyrosine-protein kinase JAK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9245
Polymers66,9782
Non-polymers9463
Water4,089227
1
A: Tyrosine-protein kinase JAK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0153
Polymers33,4891
Non-polymers5262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein kinase JAK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9092
Polymers33,4891
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.095, 88.708, 174.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosine-protein kinase JAK1 / Janus kinase 1 / JAK-1


Mass: 33489.207 Da / Num. of mol.: 2 / Fragment: Protein kinase 2 domain residues 865-1154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JAK1, JAK1A, JAK1B / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P23458, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-5JG / 6-chloro-2-(2-fluoro-4,5-dimethoxyphenyl)-N-(piperidin-4-ylmethyl)-3H-imidazo[4,5-b]pyridin-7-amine


Mass: 419.880 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23ClFN5O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 27% (m/v) PEG6000, 0.1 M MES/NaOH pH 6.0 and 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.3→87.46 Å / Num. obs: 30744 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 44.93 Å2 / Rmerge(I) obs: 0.11
Reflection shellResolution: 2.3→2.45 Å / Redundancy: 6 % / Rmerge(I) obs: 0.678 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: OTHER / Resolution: 2.3→48.73 Å / Cor.coef. Fo:Fc: 0.9373 / Cor.coef. Fo:Fc free: 0.9172 / SU R Cruickshank DPI: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.37 / SU Rfree Blow DPI: 0.25 / SU Rfree Cruickshank DPI: 0.247
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 1312 4.27 %RANDOM
Rwork0.2247 ---
obs0.2265 30693 99.84 %-
Displacement parametersBiso mean: 43.37 Å2
Baniso -1Baniso -2Baniso -3
1-2.9927 Å20 Å20 Å2
2---0.3151 Å20 Å2
3----2.6776 Å2
Refine analyzeLuzzati coordinate error obs: 0.325 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4587 0 65 227 4879
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014827HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.066513HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1745SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes123HARMONIC2
X-RAY DIFFRACTIONt_gen_planes728HARMONIC5
X-RAY DIFFRACTIONt_it4827HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion17.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion587SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5524SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3053 127 4.31 %
Rwork0.2355 2823 -
all0.2384 2950 -
obs--99.23 %
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)
12.74560.9631-0.60173.8336-0.81771.28510.0861-0.34580.13090.2585-0.1475-0.0875-0.2010.1450.0614-0.0313-0.017-0.02880.0868-0.0201-0.0313-5.974-19.41415.057
23.38340.09790.63990.7403-0.31851.51770.0772-0.5779-0.40770.0837-0.0755-0.02740.1179-0.1654-0.00160.0013-0.0212-0.02650.14950.06810.0134-22.24-37.79623.488
31.71620.4941-0.71923.1789-0.71381.09960.0581-0.18110.14680.1491-0.057-0.1515-0.25190.2717-0.0011-0.0168-0.0157-0.02540.1036-0.0096-0.0437-9.41224.57815.232
43.12540.07920.46270.8529-0.18171.1440.0319-0.4217-0.23040.0684-0.083-0.01980.1499-0.16080.05110.0403-0.0092-0.02490.1110.026-0.0122-25.9236.30923.377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|867 - A|959 }
2X-RAY DIFFRACTION2{ A|961 - A|1154 }
3X-RAY DIFFRACTION3{ B|867 - B|959 }
4X-RAY DIFFRACTION4{ B|961 - B|1154 }

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