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

+
Open data


ID or keywords:

Loading...

-
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 / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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. ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 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

-
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)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: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 0

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

-
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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.45 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

-
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

-
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

+
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