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- PDB-8g8x: X-ray co-crystal structure of compound 27 in with complex JAK2 -

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Basic information

Entry
Database: PDB / ID: 8g8x
TitleX-ray co-crystal structure of compound 27 in with complex JAK2
ComponentsTyrosine-protein kinase JAK2
KeywordsTRANSFERASE/Inhibitor / inhibitor / JAK2 / kinase / TRANSFERASE / TRANSFERASE-Inhibitor complex
Function / homology
Function and homology information


interleukin-35-mediated signaling pathway / intracellular mineralocorticoid receptor signaling pathway / histone H3Y41 kinase activity / activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / symbiont-induced defense-related programmed cell death / mammary gland epithelium development / regulation of postsynapse to nucleus signaling pathway / positive regulation of growth hormone receptor signaling pathway / Signaling by Erythropoietin ...interleukin-35-mediated signaling pathway / intracellular mineralocorticoid receptor signaling pathway / histone H3Y41 kinase activity / activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / symbiont-induced defense-related programmed cell death / mammary gland epithelium development / regulation of postsynapse to nucleus signaling pathway / positive regulation of growth hormone receptor signaling pathway / Signaling by Erythropoietin / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-12 receptor binding / post-embryonic hemopoiesis / collagen-activated signaling pathway / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / interleukin-5-mediated signaling pathway / response to interleukin-12 / positive regulation of leukocyte proliferation / interleukin-12 receptor complex / activation of Janus kinase activity / interleukin-23 receptor complex / positive regulation of platelet aggregation / tyrosine phosphorylation of STAT protein / Interleukin-23 signaling / positive regulation of MHC class II biosynthetic process / positive regulation of T-helper 17 type immune response / positive regulation of platelet activation / type 1 angiotensin receptor binding / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / interleukin-3-mediated signaling pathway / regulation of nitric oxide biosynthetic process / acetylcholine receptor binding / cellular response to interleukin-3 / Signaling by Leptin / Interleukin-12 signaling / positive regulation of signaling receptor activity / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / positive regulation of cell-substrate adhesion / positive regulation of epithelial cell apoptotic process / response to hydroperoxide / regulation of receptor signaling pathway via JAK-STAT / growth hormone receptor binding / positive regulation of natural killer cell proliferation / axon regeneration / growth hormone receptor signaling pathway / peptide hormone receptor binding / negative regulation of cardiac muscle cell apoptotic process / intrinsic apoptotic signaling pathway in response to oxidative stress / extrinsic component of plasma membrane / IFNG signaling activates MAPKs / Interleukin-20 family signaling / interleukin-6-mediated signaling pathway / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / negative regulation of cell-cell adhesion / Interleukin-6 signaling / enzyme-linked receptor protein signaling pathway / Prolactin receptor signaling / positive regulation of interleukin-17 production / MAPK3 (ERK1) activation / negative regulation of DNA binding / response to amine / positive regulation of nitric-oxide synthase biosynthetic process / MAPK1 (ERK2) activation / mesoderm development / positive regulation of SMAD protein signal transduction / cell surface receptor signaling pathway via JAK-STAT / platelet-derived growth factor receptor signaling pathway / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / growth hormone receptor signaling pathway via JAK-STAT / response to tumor necrosis factor / Interleukin receptor SHC signaling / phosphatidylinositol 3-kinase binding / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / Erythropoietin activates RAS / Growth hormone receptor signaling / extrinsic apoptotic signaling pathway / positive regulation of T cell proliferation / Signaling by CSF3 (G-CSF) / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of vascular associated smooth muscle cell proliferation / tumor necrosis factor-mediated signaling pathway / actin filament polymerization / SH2 domain binding / erythrocyte differentiation / cellular response to dexamethasone stimulus / post-translational protein modification / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of interleukin-1 beta production / caveola / positive regulation of apoptotic signaling pathway / endosome lumen / positive regulation of cell differentiation
Similarity search - Function
Tyrosine-protein kinase, non-receptor Jak2 / Janus kinase 2, pseudokinase domain / Janus kinase 2, catalytic domain / Tyrosine-protein kinase JAK2, SH2 domain / JAK2, FERM domain C-lobe / 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 ...Tyrosine-protein kinase, non-receptor Jak2 / Janus kinase 2, pseudokinase domain / Janus kinase 2, catalytic domain / Tyrosine-protein kinase JAK2, SH2 domain / JAK2, FERM domain C-lobe / 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 / SH2 domain / 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. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-YT8 / Tyrosine-protein kinase JAK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMiller, S.T. / Ellis, D.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Eyes on Topical Ocular Disposition: The Considered Design of a Lead Janus Kinase (JAK) Inhibitor That Utilizes a Unique Azetidin-3-Amino Bridging Scaffold to Attenuate Off-Target Kinase ...Title: Eyes on Topical Ocular Disposition: The Considered Design of a Lead Janus Kinase (JAK) Inhibitor That Utilizes a Unique Azetidin-3-Amino Bridging Scaffold to Attenuate Off-Target Kinase Activity, While Driving Potency and Aqueous Solubility.
Authors: Gordhan, H.M. / Miller, S.T. / Clancy, D.C. / Ina, M. / McDougal, A.V. / Cutno, D.K. / Brown, R.V. / Lichorowic, C.L. / Sturdivant, J.M. / Vick, K.A. / Williams, S.S. / deLong, M.A. / White, ...Authors: Gordhan, H.M. / Miller, S.T. / Clancy, D.C. / Ina, M. / McDougal, A.V. / Cutno, D.K. / Brown, R.V. / Lichorowic, C.L. / Sturdivant, J.M. / Vick, K.A. / Williams, S.S. / deLong, M.A. / White, J.C. / Kopczynski, C.C. / Ellis, D.A.
History
DepositionFeb 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase JAK2
B: Tyrosine-protein kinase JAK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5524
Polymers74,9172
Non-polymers6352
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.650, 172.560, 52.480
Angle α, β, γ (deg.)90.00, 110.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine-protein kinase JAK2 / Janus kinase 2 / JAK-2


Mass: 37458.535 Da / Num. of mol.: 2 / Mutation: M1073S, F1076T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JAK2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O60674, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-YT8 / 3-cyclopropyl-1-{5-methyl-2-[(3-methyl-1,2-thiazol-5-yl)amino]pyrimidin-4-yl}azetidin-3-ol


Mass: 317.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H19N5OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, ammonium acetate, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.97→43.14 Å / Num. obs: 42978 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.049 / Net I/σ(I): 12.2
Reflection shellResolution: 1.97→2.02 Å / Rmerge(I) obs: 1.167 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3082 / Rpim(I) all: 0.465

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Processing

Software
NameVersionClassification
REFMAC5refinement
xia2data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IOK

3iok


Resolution: 1.97→42.73 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.314 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23569 2158 5 %RANDOM
Rwork0.19457 ---
obs0.19655 40778 99.95 %-
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 mean: 37.676 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0.57 Å2
2--1.43 Å20 Å2
3----0.78 Å2
Refinement stepCycle: 1 / Resolution: 1.97→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4636 0 44 210 4890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134787
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174545
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.6566462
X-RAY DIFFRACTIONr_angle_other_deg1.4351.58610475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7695557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05122.259270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60415882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6891534
X-RAY DIFFRACTIONr_chiral_restr0.0960.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021109
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_it2.0882.5852243
X-RAY DIFFRACTIONr_mcbond_other2.0832.5852242
X-RAY DIFFRACTIONr_mcangle_it3.2073.8562792
X-RAY DIFFRACTIONr_mcangle_other3.2073.8572793
X-RAY DIFFRACTIONr_scbond_it2.7152.9942544
X-RAY DIFFRACTIONr_scbond_other2.7152.9942544
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3284.3523660
X-RAY DIFFRACTIONr_long_range_B_refined6.949.44320135
X-RAY DIFFRACTIONr_long_range_B_other6.8649.33220003
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9316 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 176 -
Rwork0.268 3025 -
obs--99.75 %
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)
13.25150.4877-1.4770.8075-0.76314.7658-0.0465-0.2255-0.0282-0.0065-0.0448-0.0726-0.0756-0.01770.09130.08580.0627-0.05360.0624-0.02530.061817.54930.07138.545
210.29-0.02870.25327.82220.3020.41790.15680.34630.2404-0.1522-0.0917-0.6602-0.07030.0186-0.06510.1097-0.02210.00760.02310.00550.153721.03338.73121.042
31.0734-0.29230.31641.47380.05661.6623-0.1204-0.18280.20640.13870.0724-0.0093-0.1224-0.03590.0480.05630.0323-0.04440.112-0.03030.08979.77632.63229.611
40.8147-0.34130.13093.97040.67260.2299-0.0070.0534-0.0170.30260.02170.00030.0991-0.0442-0.01470.0804-0.012-0.00270.07540.02160.06237.7249.34624.405
51.2582-0.61040.23160.8134-0.60431.7454-0.0434-0.0030.01990.0096-0.0072-0.04560.0262-0.13370.05050.0701-0.0075-0.03040.0368-0.00960.09936.16524.31318.939
61.31670.24070.19811.3634-0.96082.1084-0.0171-0.06930.17510.0818-0.04740.0127-0.30770.13760.06450.0931-0.0019-0.00970.0362-0.01070.118710.56532.54312.743
70.2603-0.15940.09190.8513-0.23370.52830.0078-0.0125-0.0116-0.0299-0.026-0.0481-0.03890.0070.01820.0696-0.0146-0.01110.07520.00570.121516.08317.0279.338
85.68591.06912.735712.7780.14092.2641-0.04910.08860.0199-0.037-0.1665-0.471-0.06550.1780.21570.039-0.00850.03070.15690.03670.098328.74818.3620.995
90.7616-0.2151-0.20650.6424-0.47951.05310.03060.0881-0.0552-0.0798-0.02330.07360.00930.0348-0.00730.0633-0.0121-0.02830.0737-0.00630.09649.70913.3542.563
103.72372.04150.49155.0555-3.72724.1230.0562-0.3135-0.0624-0.04540.1720.18040.0844-0.389-0.22810.0029-0.0129-0.01260.1530.01330.1222-4.34714.29712.363
113.2505-0.10941.70662.80360.46983.92740.04040.1417-0.0257-0.03870.0504-0.0916-0.01920.1771-0.09070.097-0.01460.05690.0303-0.00750.045118.103-29.84-7.568
122.5613-1.96275.25881.717-4.178710.92870.09760.23050.097-0.0763-0.2406-0.06890.19570.51340.1430.1078-0.00020.03380.09380.01570.106516.672-29.234-7.58
131.299-2.2916-3.05594.9447.631112.7604-0.1542-0.1376-0.40050.20870.30270.27050.17260.446-0.14850.19730.13460.14990.22020.10570.376924.725-39.8558.968
143.5696-1.30180.51961.3247-0.28222.66150.01470.0687-0.16140.1287-0.14020.05810.40160.02770.12550.1236-0.01240.04420.03170.00860.08538.841-34.67.177
150.315-0.5422-0.43513.68171.68051.5162-0.04190.0123-0.0008-0.03860.1384-0.18720.05130.0812-0.09650.0772-0.00230.0430.0655-0.00360.085912.876-24.120.422
160.38951.36370.11827.8459-0.91350.631-0.05750.01330.0125-0.06630.05980.0582-0.054-0.0342-0.00230.051-0.00030.01680.10230.01570.10041.838-14.97710.812
170.3102-0.00320.36572.1243-1.35952.69630.0490.0559-0.0566-0.01020.0485-0.00110.07750.0364-0.09750.05650.01720.02890.03680.00520.10668.848-27.81714.261
180.5960.41320.0981.4007-0.68051.30620.00070.0046-0.02990.0445-0.04-0.12040.00460.08650.03930.04650.01910.01560.07140.00960.112716.342-16.7321.88
1915.24244.1069-9.600713.8636-0.65746.3428-0.3022-0.0775-0.3781-0.25340.04130.00130.17670.07570.26080.07750.02330.00520.13070.03070.060728.033-19.71928.882
200.8802-0.0014-0.09840.3758-0.37321.21620.0335-0.00510.04860.10960.03410.0559-0.0807-0.0873-0.06750.06040.01930.02170.08280.00270.10935.698-13.37625.364
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A842 - 884
2X-RAY DIFFRACTION2A885 - 898
3X-RAY DIFFRACTION3A899 - 933
4X-RAY DIFFRACTION4A934 - 959
5X-RAY DIFFRACTION5A960 - 988
6X-RAY DIFFRACTION6A989 - 1012
7X-RAY DIFFRACTION7A1013 - 1065
8X-RAY DIFFRACTION8A1066 - 1077
9X-RAY DIFFRACTION9A1078 - 1114
10X-RAY DIFFRACTION10A1115 - 1130
11X-RAY DIFFRACTION11B842 - 871
12X-RAY DIFFRACTION12B872 - 885
13X-RAY DIFFRACTION13B886 - 893
14X-RAY DIFFRACTION14B894 - 909
15X-RAY DIFFRACTION15B910 - 946
16X-RAY DIFFRACTION16B947 - 969
17X-RAY DIFFRACTION17B970 - 1009
18X-RAY DIFFRACTION18B1010 - 1071
19X-RAY DIFFRACTION19B1072 - 1076
20X-RAY DIFFRACTION20B1077 - 1130

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