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- PDB-5j1v: Crystal structure of human CLK1 in complex with pyrido[3,4-g]quin... -

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Basic information

Entry
Database: PDB / ID: 5j1v
TitleCrystal structure of human CLK1 in complex with pyrido[3,4-g]quinazoline derivative ZW29 (compound 13)
ComponentsDual specificity protein kinase CLK1
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / TYROSINE-PROTEIN KINASE / NUCLEUS / inhibitor / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 ...: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
pyrido[3,4-g]quinazoline-2,10-diamine / Dual specificity protein kinase CLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsChaikuad, A. / Esvan, Y.J. / Zeinyeh, W. / Boibessot, T. / Nauton, L. / Thery, V. / Loaec, N. / Meijer, L. / Giraud, F. / Moreau, P. ...Chaikuad, A. / Esvan, Y.J. / Zeinyeh, W. / Boibessot, T. / Nauton, L. / Thery, V. / Loaec, N. / Meijer, L. / Giraud, F. / Moreau, P. / Anizon, F. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Eur.J.Med.Chem. / Year: 2016
Title: Discovery of pyrido[3,4-g]quinazoline derivatives as CMGC family protein kinase inhibitors: Design, synthesis, inhibitory potency and X-ray co-crystal structure.
Authors: Esvan, Y.J. / Zeinyeh, W. / Boibessot, T. / Nauton, L. / Thery, V. / Knapp, S. / Chaikuad, A. / Loaec, N. / Meijer, L. / Anizon, F. / Giraud, F. / Moreau, P.
History
DepositionMar 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Jan 10, 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)119,5628
Polymers118,7453
Non-polymers8185
Water1,71195
1
A: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8853
Polymers39,5821
Non-polymers3032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7932
Polymers39,5821
Non-polymers2111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dual specificity protein kinase CLK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8853
Polymers39,5821
Non-polymers3032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.471, 116.021, 90.108
Angle α, β, γ (deg.)90.00, 99.28, 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
11LYSLYSAA-1 - 4811 - 336
21LYSLYSBB-1 - 4811 - 336
12SERSERAA-1 - 4831 - 338
22SERSERCC-1 - 4831 - 338
13LYSLYSBB-1 - 4821 - 337
23LYSLYSCC-1 - 4821 - 337

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 / Fragment: UNP residues 148-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK1, CLK / Plasmid: pLIC-SGC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2 / References: UniProt: P49759, dual-specificity kinase
#2: Chemical ChemComp-6FD / pyrido[3,4-g]quinazoline-2,10-diamine


Mass: 211.223 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H9N5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 30% 1,2-propanediol, 10% glycerol and 50 mM Na/K phosphate pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.52→35.47 Å / Num. obs: 38700 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 51.9 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 7.6
Reflection shellResolution: 2.52→2.66 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z57

1z57


Resolution: 2.52→35.47 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 24.407 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.691 / ESU R Free: 0.293 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24366 1897 4.9 %RANDOM
Rwork0.1991 ---
obs0.20134 36746 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 71.461 Å2
Baniso -1Baniso -2Baniso -3
1--2.59 Å2-0 Å20.32 Å2
2--3.76 Å20 Å2
3----1.21 Å2
Refinement stepCycle: 1 / Resolution: 2.52→35.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7927 0 60 95 8082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198192
X-RAY DIFFRACTIONr_bond_other_d0.0050.027651
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.94311099
X-RAY DIFFRACTIONr_angle_other_deg0.848317590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84323.646384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.879151387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1271544
X-RAY DIFFRACTIONr_chiral_restr0.070.21220
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029422
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021950
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_it2.6383.9493951
X-RAY DIFFRACTIONr_mcbond_other2.6373.9493952
X-RAY DIFFRACTIONr_mcangle_it4.1095.9184933
X-RAY DIFFRACTIONr_mcangle_other4.1075.9184931
X-RAY DIFFRACTIONr_scbond_it3.1864.2514241
X-RAY DIFFRACTIONr_scbond_other3.1854.2514241
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9926.2566167
X-RAY DIFFRACTIONr_long_range_B_refined6.97331.5269227
X-RAY DIFFRACTIONr_long_range_B_other6.97431.539228
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)
11A211130.05
12B211130.05
21A190260.06
22C190260.06
31B190250.06
32C190250.06
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 151 -
Rwork0.303 2705 -
obs--99.24 %
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)
14.8993-0.0948-1.66721.06960.30252.30290.0187-0.0803-0.4516-0.0546-0.0310.23020.2894-0.25320.01230.0609-0.0401-0.04890.19340.04370.1117-5.423825.4932-9.2294
24.13650.3984-0.27243.6681-0.07624.94260.0730.3536-0.1371-0.6075-0.04280.04390.13520.1343-0.03020.10970.0277-0.0190.0994-0.00020.081912.162826.5795-23.8865
35.06781.4579-0.46261.543-0.38272.5738-0.04150.27750.5804-0.1699-0.0182-0.1933-0.12660.45790.05980.06910.01230.01490.30370.12230.334824.8636-10.5737-22.5455
43.7670.1847-1.02543.9006-0.68393.6125-0.09470.09390.05920.06940.06020.13060.5509-0.00150.03450.09790.02220.00050.31080.0770.09657.2777-25.3842-20.0487
57.2789-1.43430.84343.04250.48721.8935-0.0039-0.22360.27250.0459-0.01990.0665-0.0184-0.04990.02380.0182-0.02290.03130.0884-0.01790.0837-0.9017-3.764-54.3475
65.0081-0.72161.90254.94010.99957.7301-0.206-0.55441.13010.07320.02380.1062-1.0591-0.11120.18220.16790.02030.04280.3803-0.1790.4537-19.47019.9371-49.4685
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 297
2X-RAY DIFFRACTION2A298 - 483
3X-RAY DIFFRACTION3B-1 - 297
4X-RAY DIFFRACTION4B298 - 482
5X-RAY DIFFRACTION5C-1 - 338
6X-RAY DIFFRACTION6C339 - 483

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