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- PDB-7qhg: LIM domain kinase 2 (LIMK2) in complex with TH-470 -

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Basic information

Entry
Database: PDB / ID: 7qhg
TitleLIM domain kinase 2 (LIMK2) in complex with TH-470
ComponentsLIM domain kinase 2
KeywordsTRANSFERASE / Kinase / Type-2 inhibitor / Actin dynamics / CFL-1
Function / homology
Function and homology information


cornea development in camera-type eye / head development / establishment of vesicle localization / 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 / mitotic spindle ...cornea development in camera-type eye / head development / establishment of vesicle localization / 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 / mitotic spindle / positive regulation of protein localization to nucleus / actin cytoskeleton organization / spermatogenesis / non-specific serine/threonine protein kinase / positive regulation of protein phosphorylation / phosphorylation / 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 / PDZ superfamily ...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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, 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
Similarity search - Domain/homology
Chem-T3B / LIM domain kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMathea, S. / Salah, E. / Hanke, T. / Knapp, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Development and Characterization of Type I, Type II, and Type III LIM-Kinase Chemical Probes.
Authors: Hanke, T. / Mathea, S. / Woortman, J. / Salah, E. / Berger, B.T. / Tumber, A. / Kashima, R. / Hata, A. / Kuster, B. / Muller, S. / Knapp, S.
History
DepositionDec 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,1219
Polymers69,5992
Non-polymers1,5227
Water6,828379
1
A: LIM domain kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5925
Polymers34,8001
Non-polymers7924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIM domain kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5304
Polymers34,8001
Non-polymers7303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.000, 66.692, 82.925
Angle α, β, γ (deg.)90.000, 97.961, 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

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Components

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


Mass: 34799.707 Da / Num. of mol.: 2 / 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-T3B / 2-(2-methylpropanoylamino)-~{N}-[2-[(phenylmethyl)-[4-(phenylsulfamoyl)phenyl]carbonyl-amino]ethyl]-1,3-thiazole-5-carboxamide


Mass: 605.728 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H31N5O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M bis-tris-propane pH 7.5, 0.2 M Na2SO4, 10% ethylene glycol, 17% PEG3.35K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→62.39 Å / Num. obs: 118826 / % possible obs: 98.86 % / Redundancy: 3.4 % / Biso Wilson estimate: 15.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Net I/σ(I): 9.5
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5820 / CC1/2: 0.743

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5nxd

5nxd


Resolution: 1.45→45.56 Å / SU ML: 0.1308 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.9756
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.177 5879 4.95 %
Rwork0.1652 112939 -
obs0.1658 118818 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.83 Å2
Refinement stepCycle: LAST / Resolution: 1.45→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4393 0 104 379 4876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624653
X-RAY DIFFRACTIONf_angle_d0.84786314
X-RAY DIFFRACTIONf_chiral_restr0.084709
X-RAY DIFFRACTIONf_plane_restr0.0079855
X-RAY DIFFRACTIONf_dihedral_angle_d6.1363702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.26151910.23533735X-RAY DIFFRACTION98.42
1.47-1.480.24432320.2123681X-RAY DIFFRACTION97.73
1.48-1.50.23361950.20093731X-RAY DIFFRACTION98.52
1.5-1.520.2262090.19213650X-RAY DIFFRACTION97.7
1.52-1.540.19441960.17913752X-RAY DIFFRACTION98.36
1.54-1.560.19521690.17613744X-RAY DIFFRACTION98.42
1.56-1.590.21272210.17223726X-RAY DIFFRACTION98.11
1.59-1.610.19271880.173731X-RAY DIFFRACTION98.99
1.61-1.630.18781900.16433730X-RAY DIFFRACTION98.29
1.63-1.660.21072060.16383724X-RAY DIFFRACTION98.55
1.66-1.690.18131750.16863755X-RAY DIFFRACTION98.74
1.69-1.720.17631680.16843756X-RAY DIFFRACTION98.2
1.72-1.750.19271840.17843760X-RAY DIFFRACTION98.11
1.75-1.790.19851870.17063741X-RAY DIFFRACTION99.34
1.79-1.830.18362110.16583762X-RAY DIFFRACTION98.83
1.83-1.870.18671820.16323768X-RAY DIFFRACTION98.87
1.87-1.920.17941790.16153790X-RAY DIFFRACTION99
1.92-1.970.18711950.16233797X-RAY DIFFRACTION99.13
1.97-2.030.17541890.16063742X-RAY DIFFRACTION99.24
2.03-2.090.16422090.16043772X-RAY DIFFRACTION99.3
2.09-2.170.1881930.15883783X-RAY DIFFRACTION99.15
2.17-2.250.18012180.16073748X-RAY DIFFRACTION99.22
2.25-2.360.16062060.16173803X-RAY DIFFRACTION99.58
2.36-2.480.19271800.16383793X-RAY DIFFRACTION99.5
2.48-2.640.18031840.1753814X-RAY DIFFRACTION99.68
2.64-2.840.1892120.16853795X-RAY DIFFRACTION99.6
2.84-3.130.19221880.18073832X-RAY DIFFRACTION99.6
3.13-3.580.19521950.17443818X-RAY DIFFRACTION99.33
3.58-4.510.13572220.14273810X-RAY DIFFRACTION99.36
4.51-45.560.1472050.15163896X-RAY DIFFRACTION99.01
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)
11.371105119160.3092564428940.09127748210281.472554104250.05732884870561.4513426582-0.05082456775250.00172937292413-0.05413374829030.0290291983897-0.0118041331708-0.267413577997-0.1534654187730.2335927931330.06031787180960.151031383797-0.0252651777976-0.0197946584640.1763618632820.02422465881950.16062572850943.5378959835-3.11798465451105.699532933
22.423152582310.414949664414-0.168167854910.759968446213-0.3596082213911.03839019714-0.06962398553930.184627269728-0.302909784167-0.04929533036390.0129773532906-0.08653603950180.08716437181960.0928230634730.1073797888560.1609806553110.004185216798630.02623221994170.158327190815-0.009761318095180.19537392065237.6687443696-15.5342905488101.224347514
31.90064760148-0.225615199122-0.1593062901230.649751039951-0.4611838167410.658288354744-0.02497349752670.182372245317-0.0787895359804-0.0464544552508-0.01622631030730.0741111091141-0.0284158359663-0.01240510159870.04243619109060.127582068196-0.0181516662055-0.01024813337930.1514355858350.01331303083860.1210421028330.6273694452-1.871672934397.7568026309
41.926646585260.0238637888171-0.2497134204981.12213068256-0.5102023474261.044885757970.008709585526640.2516063917740.2391264457250.0205404282821-0.00795425819096-0.0238795204264-0.129184812614-0.02971123750190.01317471617080.16043485706-0.0190983941038-0.01533562262940.2036550730480.05344065668870.13426283494532.67229585588.5415412816293.0968055311
51.388856145850.493275835793-0.3917270047071.17298301787-0.221361433461.016944949180.03964212512960.252354647260.39003596488-0.0831652843455-0.136404347063-0.250757011622-0.2605523507430.2391399025870.0007113553356420.194557836407-0.0679623116862-0.02745956856340.2853005905450.1181717625550.28508108433547.886840865412.6533481493.3309350975
62.34941095823-0.0265734147533-0.2883319878180.990252679391-0.2628272582981.735541475550.04996920828740.397073190010.0819446516149-0.103140981424-0.140736122368-0.1818171494570.004487947381360.03119758899470.001674951082050.230502497837-0.00510222730408-0.01408978490180.282133097160.1117662922460.15873914044234.562959758313.474617442384.8866470929
72.708483295410.7885113704960.5945838445350.3779033571450.1554940841920.431883720555-0.1455522029560.4969220775390.218814708928-0.08529929675110.07277003469820.102223094987-0.0111906593170.0151732602474-0.003157146553510.142516933026-0.0176410319732-0.01860312511790.2318061397950.03485358940190.17186323744310.1542915917-1.6319998496494.6858741394
80.7286530905410.229326997625-0.04728113167331.62492515068-0.3212238048831.06520196676-0.09575284328160.35498591902-0.138330188583-0.1073562606420.122970859051-0.09249881337190.1822313661220.0335839476769-0.0005142023622050.166666955125-0.0249480737118-0.0137475688580.254941847685-0.05506486748070.14306175778411.1441949256-16.672330758992.0837224988
90.8823063228640.157944831382-0.3610437412860.7366261618520.3120018308371.79889687665-0.08981124299890.265089712287-0.0752729986828-0.2067535441720.0431627076382-0.01053151179260.101806033132-0.0359021603103-0.01152137697340.143814721163-0.023470589362-0.007205125137660.199645713463-0.03380852843740.1314049272027.99694360725-14.046470968594.9272974553
100.6462069518530.108254032543-0.1244289214140.770040001439-0.1216810121690.5326592718420.009774788759240.02171683590390.04222604625320.03677234445890.02056255614780.0961707936383-0.0569477095599-0.100398365524-0.0157308005190.1276893042320.004325120622420.003211861502270.09965948396440.002553533608560.12251436199810.7186526582-9.0935427172115.867011388
111.08124964036-0.129414496062-0.1926871789220.801921682543-0.1562080870350.955319718936-0.04177403984470.0747821441535-0.0974492937993-0.03966697453590.00334737895171-0.05628463013320.04892402721040.04633004979860.04307077262310.117177153181-0.009124012406740.01086051232980.0893602419712-0.004994556403710.11825448688822.5496998867-16.0992318042111.634934252
122.097078372880.317446777908-0.4519737666380.51094569513-0.5035206701960.992295919336-0.0355678952722-0.267075833571-0.06168934238180.119906468823-0.03980724752840.002519304972670.03603606421650.1393882874720.02306331213550.128004970088-0.00404805727047-0.01159537841230.1085519426330.01359810285710.12964630402422.2546486343-16.5617454883126.788249049
131.71406100526-0.0500677294953-1.084229152230.939241221725-0.03591153097272.0180062994-0.03837592938620.05000671503060.03559751447030.09841487126620.05777602034490.08167312887460.0519990123196-0.2700737672630.01697989483580.1384166511780.006337874358690.01037085346590.1236571569160.01968387003880.1524554224376.03723467648-18.328562587127.940454164
143.281445192610.7324236676660.4569944374921.43507915569-0.0420910359021.359979485750.135461488437-0.525921821709-0.3248330151960.411144803307-0.313274950987-0.376985390452-0.05953512218960.2380970785730.04086855497310.229951667089-0.0182165775151-0.06203472883770.2026689584550.06769068952250.20132996780520.1124871707-21.1647984354135.396460741
154.17541200489-0.5017545478840.8871374020090.753622509343-0.3949991682060.810466445549-0.0842075986528-0.0352015598696-0.03248999672960.110136636769-0.0419987171162-0.1186063138650.04991381296720.1736065428930.1100665561040.149021403596-0.00137812029325-0.02961580142860.2142949475910.04589323657020.17487057805446.0260864907-12.3337691227121.898824108
162.24039586538-0.4628006062940.4707506348420.549993862999-0.6468057051541.572451942750.0211421038247-0.0605073884016-0.4042440055710.0334808653757-0.0944543895122-0.385115825850.16233492207-0.04714771890620.03298951891070.1561512249520.010875313864-0.0180563758720.2194071264180.07834748656710.28788381617248.7779865762-17.274141588115.882647635
171.262981611320.0127613667212-0.1249879753381.04752730636-0.2528631345451.37574003172-0.07371691139060.083702217404-0.300455298918-0.0633477838123-0.0353689011294-0.196990905670.2505837607710.07714905190770.1471553741780.1586232715140.006350707326010.01578553852020.1910873394160.01791409518090.22455520996851.1491577404-17.554848517105.937796829
181.24235906324-0.4058735609930.2786396576771.60879426871-0.1905067703231.23786585394-0.143525880731-0.179224205351-0.05443181190310.25660023730.07677314792230.0419917930912-0.110110071197-0.01541466496840.0686003602110.157328266724-0.0184126824398-0.01142456832530.1856277039290.021323770590.12951405334942.7132197221-2.70377074097113.965873933
191.41134577459-0.624444154153-0.3118525108441.604398166060.1009683306380.803252770411-0.05053955736780.09452050373480.1303076990310.105748651687-0.00188361034998-0.255732195779-0.08307465269980.1612204010750.03993878651070.133665706992-0.0282663729396-0.02702932200330.2001191248440.03682102175410.15409751525646.43389415633.3633912518399.8178672435
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 446 through 467 )BB446 - 467119 - 140
22chain 'B' and (resid 468 through 509 )BB468 - 509141 - 160
33chain 'B' and (resid 510 through 559 )BB510 - 559161 - 210
44chain 'B' and (resid 560 through 593 )BB560 - 593211 - 244
55chain 'B' and (resid 594 through 616 )BB594 - 616245 - 267
66chain 'B' and (resid 617 through 632 )BB617 - 632268 - 283
77chain 'A' and (resid 330 through 350 )AA330 - 3502 - 22
88chain 'A' and (resid 351 through 382 )AA351 - 38223 - 54
99chain 'A' and (resid 383 through 406 )AA383 - 40655 - 78
1010chain 'A' and (resid 407 through 445 )AA407 - 44579 - 117
1111chain 'A' and (resid 446 through 559 )AA446 - 559118 - 210
1212chain 'A' and (resid 560 through 593 )AA560 - 593211 - 244
1313chain 'A' and (resid 594 through 616 )AA594 - 616245 - 267
1414chain 'A' and (resid 617 through 632 )AA617 - 632268 - 283
1515chain 'B' and (resid 330 through 350 )BB330 - 3503 - 23
1616chain 'B' and (resid 351 through 366 )BB351 - 36624 - 39
1717chain 'B' and (resid 367 through 397 )BB367 - 39740 - 70
1818chain 'B' and (resid 398 through 424 )BB398 - 42471 - 97
1919chain 'B' and (resid 425 through 445 )BB425 - 44598 - 118

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  • 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

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