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

+
Open data


ID or keywords:

Loading...

-
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 / histone H2AXY142 kinase activity / histone H3Y41 kinase activity / protein tyrosine kinase activity / protein serine/threonine kinase activity / protein serine kinase activity / ATP binding / nucleus
Similarity search - Function
: / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more