[English] 日本語
Yorodumi
- PDB-8s3x: LIM Domain Kinase 2 (LIMK2) bound to compound 52 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8s3x
TitleLIM Domain Kinase 2 (LIMK2) bound to compound 52
ComponentsLIM domain kinase 2
KeywordsTRANSFERASE / Kinase / Inhibitor / Actin cytoskeleton
Function / homology
Function and homology information


cornea development in camera-type eye / establishment of vesicle localization / head development / astral microtubule organization / negative regulation of cilium assembly / cis-Golgi network / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / EPHB-mediated forward signaling / positive regulation of protein localization to nucleus ...cornea development in camera-type eye / establishment of vesicle localization / head development / astral microtubule organization / negative regulation of cilium assembly / cis-Golgi network / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / EPHB-mediated forward signaling / positive regulation of protein localization to nucleus / mitotic spindle / actin cytoskeleton organization / spermatogenesis / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...: / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
: / LIM domain kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsMathea, S. / Chatterjee, D. / Preuss, F. / Ple, K. / Knapp, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Tetrahydropyridine LIMK inhibitors: Structure activity studies and biological characterization.
Authors: Champire, A. / Berabez, R. / Braka, A. / Cosson, A. / Corret, J. / Girardin, C. / Serrano, A. / Aci-Seche, S. / Bonnet, P. / Josselin, B. / Brindeau, P. / Ruchaud, S. / Leguevel, R. / ...Authors: Champire, A. / Berabez, R. / Braka, A. / Cosson, A. / Corret, J. / Girardin, C. / Serrano, A. / Aci-Seche, S. / Bonnet, P. / Josselin, B. / Brindeau, P. / Ruchaud, S. / Leguevel, R. / Chatterjee, D. / Mathea, S. / Knapp, S. / Brion, R. / Verrecchia, F. / Vallee, B. / Ple, K. / Benedetti, H. / Routier, S.
History
DepositionFeb 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LIM domain kinase 2
B: LIM domain kinase 2
C: LIM domain kinase 2
D: LIM domain kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,0618
Polymers139,1994
Non-polymers1,8624
Water23413
1
A: LIM domain kinase 2
C: LIM domain kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5314
Polymers69,5992
Non-polymers9312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-13 kcal/mol
Surface area22500 Å2
2
B: LIM domain kinase 2
D: LIM domain kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5314
Polymers69,5992
Non-polymers9312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area22680 Å2
Unit cell
Length a, b, c (Å)86.911, 86.921, 103.297
Angle α, β, γ (deg.)90.000, 94.380, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
LIM domain kinase 2 / LIMK-2


Mass: 34799.707 Da / Num. of mol.: 4 / Fragment: UNP residues 330-632
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMK2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P53671, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-A1H41 / 4-(5-cyclopropyl-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)-~{N}-[3-(3-methoxyphenyl)phenyl]-3,6-dihydro-2~{H}-pyridine-1-carboxamide


Mass: 465.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H27N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 16% PEG8000 0.04M potassium phosphate dibasic 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.59→45.83 Å / Num. obs: 47823 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 42.58 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.25
Reflection shellResolution: 2.59→2.68 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.556 / Num. unique obs: 4734

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Coot0.9.8.1model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→45.83 Å / SU ML: 0.394 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.1049
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2875 2380 4.99 %
Rwork0.2388 45337 -
obs0.2413 47717 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.77 Å2
Refinement stepCycle: LAST / Resolution: 2.59→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8006 0 140 13 8159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00578357
X-RAY DIFFRACTIONf_angle_d0.820811406
X-RAY DIFFRACTIONf_chiral_restr0.04971309
X-RAY DIFFRACTIONf_plane_restr0.00681565
X-RAY DIFFRACTIONf_dihedral_angle_d5.55911265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.640.42411630.34142651X-RAY DIFFRACTION99.5
2.64-2.70.38061430.31982656X-RAY DIFFRACTION99.64
2.7-2.760.35781500.32082594X-RAY DIFFRACTION99.71
2.76-2.830.32351360.31032672X-RAY DIFFRACTION99.79
2.83-2.910.42091300.3062659X-RAY DIFFRACTION99.64
2.91-2.990.37981510.29342680X-RAY DIFFRACTION99.61
2.99-3.090.34181190.27212647X-RAY DIFFRACTION99.57
3.09-3.20.28061420.25692673X-RAY DIFFRACTION99.68
3.2-3.330.31741340.27192680X-RAY DIFFRACTION99.79
3.33-3.480.30031170.25272676X-RAY DIFFRACTION99.64
3.48-3.660.311150.22552683X-RAY DIFFRACTION99.57
3.66-3.890.24331540.2232639X-RAY DIFFRACTION99.54
3.89-4.190.25211350.20642679X-RAY DIFFRACTION99.65
4.19-4.620.24111630.19822655X-RAY DIFFRACTION99.44
4.62-5.280.24481490.19582657X-RAY DIFFRACTION99.64
5.28-6.650.25281690.23372686X-RAY DIFFRACTION99.51
6.65-45.830.26471100.20382750X-RAY DIFFRACTION98.11
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)
11.249273901670.7635361251540.1576818418791.753069590731.681997364831.96891834740.3180047968710.0226133694435-0.01790340552940.273269085687-0.0214501231538-0.195784189601-0.4227925300090.0679440738324-0.243575193791.18716928111-0.1472381418060.1498831185220.367201888876-0.07863329264720.34294010320446.323444858847.656335695831.091249963
20.2194326841510.1632756045490.2403580350370.225742850647-0.02148459001970.632361054461-0.2963250433440.1796556845180.065838332723-0.03825718480310.254954200709-0.0296767811412-0.8509243209860.0468128140036-0.01738058607651.79521772174-0.1683135213950.2178164079450.470630185556-0.0434268166720.47557314562745.093682822362.802144124737.0048010835
32.68422762747-2.634237999320.1407068052333.44792780848-1.998223654264.77009917805-0.1910416415180.2395675488130.335523270193-0.2835870538680.2333762010240.166495940473-0.56087975952-0.0304852977905-0.03856792609750.678710085472-0.04591380536690.05857170431450.383191765238-0.004138299914680.302102539805-8.2764184437922.43540226526.4728658248
40.810836325635-0.00765336365389-0.8103413062750.635720700434-1.051681501812.558376141430.006234759609810.2240568308760.0356160391195-0.6080176444640.05438324022710.1593085225070.00601733102063-0.1797318676790.01378401883120.879471108807-0.005590141445210.01656648225390.3333087599140.02053438030110.279994080284-4.3546115649913.4509157492.58581464614
51.06860726986-0.363298497501-0.2780475588962.011743669850.5603584849692.98877196658-0.0263638877452-0.05165004140630.0469130670523-0.09975180973280.1030267685510.06965732989240.2632817347570.0185779378059-0.1108753678110.655924982871-0.006467263664950.0650921827220.318799846348-0.040512053920.2147275469642.523602241354.4897347755416.3077823863
60.917673360138-1.134351872220.09534032129622.06513370639-0.9762678870721.11615628616-0.244084184042-0.125815495525-0.2062679313020.02891524169210.190101077629-0.09198798946140.488820949934-0.108672342051-0.0454867245971.202265142120.06602188050760.0383675621580.3182903551080.03153940677290.2845809299283.54908431307-13.856945118514.7315537066
72.408353480850.7949554599452.364912058542.185645984811.153239711096.658633233530.04369289326490.4433058252380.503606764999-0.5519916774630.05595793795560.551251180176-0.7286897142270.02148127188070.05931787080880.3176889529670.2393942004110.005866669173740.3656765531150.1312155460980.4172722130232.295729080941.8836585242.12436676455
83.22820314225-0.859436081992-0.9883992996143.89966409168-2.573311056723.296656131490.117719231041-0.006981519783440.264728495361-0.40033417966-0.327039540263-0.22221151747-0.3497323062520.3272059453220.1764314012020.4647208131110.0972310087850.08225330386760.216115167015-0.002436390204730.23759025020444.370188499335.3890992867-2.31480212488
91.45016025316-0.7186361121910.1214044962934.56590472495-0.689305052084.03501390083-0.000853527532395-0.0599801535533-0.02124185429540.458166643077-0.03706885335970.0118018126724-0.0610220091411-0.09791477804540.001944459511380.276609300701-0.03161887133580.0595775305420.203010949331-0.02988519634520.22704427886542.241885878326.393406469314.7025303613
102.20464099855-1.15356032499-1.110150066364.973784269620.6310494381370.564930694737-0.152691846243-0.0801627021582-0.574166441315-0.159447057665.12170373544E-5-0.2969588253830.837275916445-0.07509508373340.01945989061810.8580942227280.0033367609315-0.00238195708750.2864991724780.02943447748420.41201600273248.124931811510.120039413315.9757782886
111.444758348430.0222927269812-1.210456939980.1344879688440.1285140061822.8475801105-0.141708877994-0.0324511671951-0.2291544567380.1410006791170.2132564271620.2243866988110.53998397229-0.3773113365270.09459985971771.07324329318-0.06082022200690.2818458204860.3636545867440.09162996451960.414949049838-14.52751399696.7436553837546.9595700358
120.1638576981140.121816164246-0.06718157808890.278505049027-0.5945115474151.525048098990.0119624494401-0.123980966432-0.01083489736110.4502443464840.1158587278180.07348062374260.0377606505226-0.123533242424-0.1364347017461.0499730351-0.04031724252440.150398167130.2923396292230.06375608012650.264831973714-7.8823536548315.295188236347.8350119109
130.2853803598790.173349527181-0.0238779896960.3694181631180.2210017808331.158587750280.05726448708160.1405237886740.01255487253050.2698894810430.223469673710.0809041757361-0.416584785264-0.03489905635860.2360958334921.13958457443-0.009092145889490.1894307040440.324938344876-0.06539276873370.09584376443330.064052206566726.974999772736.4918334889
141.497470237880.1574343649130.6845839338752.594829943082.0124412051.77414631274-0.2587188149870.180135407116-0.08180614338030.3739980398590.257251760211-0.228327637737-0.5690199333990.184312971494-0.0112765339171.21463357435-0.253591702130.07617323477580.402679807494-0.01218014919480.5913630732957.8408473805442.944179211631.3651096848
153.55949542668-2.18320079525-2.894530328623.149328497791.531071484856.35323755175-0.165276437361-0.39473517643-0.2525570398410.723530819128-0.01905586508070.7617335772390.447057457057-0.5564484308790.1894650462130.844270333036-0.1451771165910.3061101649950.456829162861-0.1441991456250.48235463213329.485713632527.214008436144.6122961137
160.3912709665590.340929133795-0.3210464798031.38122955160.3975209116260.671268975580.267563786655-0.09648318011460.07428076057591.00536488969-0.216021835673-0.00551151426734-0.239726812952-0.150338008306-0.100453421061.40056328548-0.06165317418420.2164304873150.43418581334-0.01776685824460.49079843147334.604100812636.345604879847.5571241421
170.292348706566-0.1751909757640.08893065665330.6127334142850.2404122620351.759206190270.198121288453-0.03161149940790.09196658689110.337442700155-0.11922249532-0.00239224909333-0.289860984977-0.08352489581670.1064313022751.36849728433-0.08828611207270.2503715828540.365059207392-0.04535745524130.31926535079639.395082364142.294902704941.0349475489
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 513 through 593 )DD513 - 593147 - 227
22chain 'D' and (resid 594 through 631 )DD594 - 631228 - 263
33chain 'A' and (resid 334 through 366 )AA334 - 3661 - 27
44chain 'A' and (resid 367 through 424 )AA367 - 42428 - 82
55chain 'A' and (resid 425 through 593 )AA425 - 59383 - 230
66chain 'A' and (resid 594 through 631 )AA594 - 631231 - 268
77chain 'B' and (resid 330 through 366 )BB330 - 3661 - 37
88chain 'B' and (resid 367 through 397 )BB367 - 39738 - 68
99chain 'B' and (resid 398 through 575 )BB398 - 57569 - 220
1010chain 'B' and (resid 576 through 631 )BB576 - 631221 - 275
1111chain 'C' and (resid 330 through 366 )CC330 - 3661 - 37
1212chain 'C' and (resid 367 through 424 )CC367 - 42438 - 93
1313chain 'C' and (resid 425 through 616 )CC425 - 61694 - 258
1414chain 'C' and (resid 617 through 631 )CC617 - 631259 - 273
1515chain 'D' and (resid 331 through 366 )DD331 - 3661 - 28
1616chain 'D' and (resid 367 through 424 )DD367 - 42429 - 84
1717chain 'D' and (resid 425 through 512 )DD425 - 51285 - 146

+
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