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- PDB-6i5k: Crystal structure of CLK1 in complexed with furo[3,2-b]pyridine c... -

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Basic information

Entry
Database: PDB / ID: 6i5k
TitleCrystal structure of CLK1 in complexed with furo[3,2-b]pyridine compound VN345 (derivative of compound 12h)
ComponentsDual specificity protein kinase CLK1
KeywordsTRANSFERASE / splicing kinase / furopyridine / inhibitor / CLK / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


dual-specificity kinase / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / non-membrane spanning protein tyrosine kinase activity / protein tyrosine kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus
Similarity search - Function
: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-H3H / PHOSPHATE ION / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChaikuad, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Paruch, K. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2019
Title: Furo[3,2-b]pyridine: A Privileged Scaffold for Highly Selective Kinase Inhibitors and Effective Modulators of the Hedgehog Pathway.
Authors: Nemec, V. / Hylsova, M. / Maier, L. / Flegel, J. / Sievers, S. / Ziegler, S. / Schroder, M. / Berger, B.T. / Chaikuad, A. / Valcikova, B. / Uldrijan, S. / Drapela, S. / Soucek, K. / ...Authors: Nemec, V. / Hylsova, M. / Maier, L. / Flegel, J. / Sievers, S. / Ziegler, S. / Schroder, M. / Berger, B.T. / Chaikuad, A. / Valcikova, B. / Uldrijan, S. / Drapela, S. / Soucek, K. / Waldmann, H. / Knapp, S. / Paruch, K.
History
DepositionNov 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dual specificity protein kinase CLK1
B: Dual specificity protein kinase CLK1
C: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,48414
Polymers118,7453
Non-polymers1,74011
Water3,999222
1
A: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0994
Polymers39,5821
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1915
Polymers39,5821
Non-polymers6104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1945
Polymers39,5821
Non-polymers6134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.089, 117.790, 92.420
Angle α, β, γ (deg.)90.00, 99.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA-1 - 4801 - 335
21LEULEUBB-1 - 4801 - 335
12LYSLYSAA-1 - 4811 - 336
22LYSLYSCC-1 - 4811 - 336
13LEULEUBB-1 - 4801 - 335
23LEULEUCC-1 - 4801 - 335

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Dual specificity protein kinase CLK1 / CDC-like kinase 1


Mass: 39581.512 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1, CLK / Plasmid: pLIC-SGC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: P49759, dual-specificity kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-H3H / 5-(1-methylpyrazol-4-yl)-3-(3-propan-2-yloxyphenyl)furo[3,2-b]pyridine


Mass: 333.384 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H19N3O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 24-28% 1,2-propanediol, 5% glycerol, 0.1M sodium/potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.3→58.9 Å / Num. obs: 52468 / % possible obs: 98 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 2 / Num. unique obs: 7690 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G33

6g33


Resolution: 2.3→58.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 17.021 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.347 / ESU R Free: 0.22 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22405 2648 5 %RANDOM
Rwork0.19517 ---
obs0.19662 49800 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.003 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.44 Å2
2---0.09 Å20 Å2
3---0.25 Å2
Refinement stepCycle: 1 / Resolution: 2.3→58.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8276 0 122 222 8620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198655
X-RAY DIFFRACTIONr_bond_other_d0.0060.028178
X-RAY DIFFRACTIONr_angle_refined_deg1.451.94811703
X-RAY DIFFRACTIONr_angle_other_deg1.216318814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13851018
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49423.153425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.907151512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.811562
X-RAY DIFFRACTIONr_chiral_restr0.0930.21260
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029976
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022100
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_it1.2842.2844051
X-RAY DIFFRACTIONr_mcbond_other1.2842.2854052
X-RAY DIFFRACTIONr_mcangle_it2.2383.4225064
X-RAY DIFFRACTIONr_mcangle_other2.2363.4225062
X-RAY DIFFRACTIONr_scbond_it1.412.5254604
X-RAY DIFFRACTIONr_scbond_other1.412.5254605
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4373.7036635
X-RAY DIFFRACTIONr_long_range_B_refined5.42218.1739377
X-RAY DIFFRACTIONr_long_range_B_other5.42118.1769378
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A408880.08
12B408880.08
21A409340.07
22C409340.07
31B413680.06
32C413680.06
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 183 -
Rwork0.299 3726 -
obs--99.04 %
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)
11.8113-0.6553-0.020.71450.43330.7428-0.05570.0558-0.08280.0160.04720.0498-0.01610.03980.00850.0052-0.0290.01720.40440.01540.232213.182-2.35635.405
20.9623-0.743-0.14091.6825-0.09591.2545-0.1123-0.11210.08010.17770.10530.0561-0.2772-0.08150.0070.08510.02470.00020.4409-0.00290.2867-3.95514.51242.705
31.2392-0.37570.00550.51850.20980.78290.0131-0.02140.23320.0169-0.0236-0.01140.0512-0.05930.01050.0073-0.02660.03030.4459-0.0380.28656.71146.65421.881
41.51560.7663-0.83082.7344-0.8741.8412-0.15210.10580.0073-0.04710.1984-0.1690.40560.2501-0.04630.10120.0454-0.01430.4922-0.04120.212324.67629.92520.298
51.5777-0.0823-0.74640.17530.16770.76410.0860.0308-0.06750.0126-0.06590.01350.0541-0.0914-0.02010.0277-0.0089-0.01670.46560.02070.245312.04328.43878.907
61.13070.4454-0.10432.62330.74952.4481-0.00940.1182-0.1178-0.5672-0.0049-0.1858-0.04380.06630.01430.1430.0590.02430.4492-0.02180.197229.79327.962.021
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 337
2X-RAY DIFFRACTION2A338 - 483
3X-RAY DIFFRACTION3B-1 - 376
4X-RAY DIFFRACTION4B377 - 483
5X-RAY DIFFRACTION5C-1 - 376
6X-RAY DIFFRACTION6C377 - 483

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