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

ID or keywords:

Entry

Database: PDB / ID: 7qhg

Title

LIM domain kinase 2 (LIMK2) in complex with TH-470

Components

LIM domain kinase 2

Keywords

TRANSFERASE / Kinase / Type-2 inhibitor / Actin dynamics / CFL-1

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Mathea, S. / Salah, E. / Hanke, T. / Knapp, S.

Funding support

1items

Citation

Journal: 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

Deposition	Dec 12, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 22, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 11, 2023	Group: 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 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7qhg.cif.gz	304 KB	Display	PDBx/mmCIF format
PDB format	pdb7qhg.ent.gz	204 KB	Display	PDB format
PDBx/mmJSON format	7qhg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qh/7qhg ftp://data.pdbj.org/pub/pdb/validation_reports/qh/7qhg	HTTPS FTP

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Related structure data

Related structure data	8aauC 5nxdS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2ydk-d 5n9s-d 2yex-d 3dbc-d 1v0b-1 5a4c-2 2gqg-2 5jzn-1 5n7q-2 7lm7-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#126 - Jun 2010 Epidermal Growth Factor similarity (1) #148 - Apr 2012 Ras Protein similarity (1) #245 - May 2020 Spliceosomes similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: LIM domain kinase 2

B: LIM domain kinase 2

hetero molecules

71.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: LIM domain kinase 2

hetero molecules

defined by author
Evidence: gel filtration
35.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: LIM domain kinase 2

hetero molecules

defined by author
35.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#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 Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.38 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 21, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.45→62.39 Å / Num. obs: 118826 / % possible obs: 98.86 % / Redundancy: 3.4 % / B_iso Wilson estimate: 15.21 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.054 / Net I/σ(I): 9.5
Reflection shell	Resolution: 1.45→1.48 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.613 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5820 / CC_1/2: 0.743

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.177	5879	4.95 %
R_work	0.1652	112939	-
obs	0.1658	118818	98.86 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 20.83 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→45.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4393	0	104	379	4876

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0062	4653
X-RAY DIFFRACTION	f_angle_d	0.8478	6314
X-RAY DIFFRACTION	f_chiral_restr	0.084	709
X-RAY DIFFRACTION	f_plane_restr	0.0079	855
X-RAY DIFFRACTION	f_dihedral_angle_d	6.1363	702

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.45-1.47	0.2615	191	0.2353	3735	X-RAY DIFFRACTION	98.42
1.47-1.48	0.2443	232	0.212	3681	X-RAY DIFFRACTION	97.73
1.48-1.5	0.2336	195	0.2009	3731	X-RAY DIFFRACTION	98.52
1.5-1.52	0.226	209	0.1921	3650	X-RAY DIFFRACTION	97.7
1.52-1.54	0.1944	196	0.1791	3752	X-RAY DIFFRACTION	98.36
1.54-1.56	0.1952	169	0.1761	3744	X-RAY DIFFRACTION	98.42
1.56-1.59	0.2127	221	0.1722	3726	X-RAY DIFFRACTION	98.11
1.59-1.61	0.1927	188	0.17	3731	X-RAY DIFFRACTION	98.99
1.61-1.63	0.1878	190	0.1643	3730	X-RAY DIFFRACTION	98.29
1.63-1.66	0.2107	206	0.1638	3724	X-RAY DIFFRACTION	98.55
1.66-1.69	0.1813	175	0.1686	3755	X-RAY DIFFRACTION	98.74
1.69-1.72	0.1763	168	0.1684	3756	X-RAY DIFFRACTION	98.2
1.72-1.75	0.1927	184	0.1784	3760	X-RAY DIFFRACTION	98.11
1.75-1.79	0.1985	187	0.1706	3741	X-RAY DIFFRACTION	99.34
1.79-1.83	0.1836	211	0.1658	3762	X-RAY DIFFRACTION	98.83
1.83-1.87	0.1867	182	0.1632	3768	X-RAY DIFFRACTION	98.87
1.87-1.92	0.1794	179	0.1615	3790	X-RAY DIFFRACTION	99
1.92-1.97	0.1871	195	0.1623	3797	X-RAY DIFFRACTION	99.13
1.97-2.03	0.1754	189	0.1606	3742	X-RAY DIFFRACTION	99.24
2.03-2.09	0.1642	209	0.1604	3772	X-RAY DIFFRACTION	99.3
2.09-2.17	0.188	193	0.1588	3783	X-RAY DIFFRACTION	99.15
2.17-2.25	0.1801	218	0.1607	3748	X-RAY DIFFRACTION	99.22
2.25-2.36	0.1606	206	0.1617	3803	X-RAY DIFFRACTION	99.58
2.36-2.48	0.1927	180	0.1638	3793	X-RAY DIFFRACTION	99.5
2.48-2.64	0.1803	184	0.175	3814	X-RAY DIFFRACTION	99.68
2.64-2.84	0.189	212	0.1685	3795	X-RAY DIFFRACTION	99.6
2.84-3.13	0.1922	188	0.1807	3832	X-RAY DIFFRACTION	99.6
3.13-3.58	0.1952	195	0.1744	3818	X-RAY DIFFRACTION	99.33
3.58-4.51	0.1357	222	0.1427	3810	X-RAY DIFFRACTION	99.36
4.51-45.56	0.147	205	0.1516	3896	X-RAY DIFFRACTION	99.01

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.37110511916	0.309256442894	0.0912774821028	1.47255410425	0.0573288487056	1.4513426582	-0.0508245677525	0.00172937292413	-0.0541337482903	0.0290291983897	-0.0118041331708	-0.267413577997	-0.153465418773	0.233592793133	0.0603178718096	0.151031383797	-0.0252651777976	-0.019794658464	0.176361863282	0.0242246588195	0.160625728509	43.5378959835	-3.11798465451	105.699532933
2	2.42315258231	0.414949664414	-0.16816785491	0.759968446213	-0.359608221391	1.03839019714	-0.0696239855393	0.184627269728	-0.302909784167	-0.0492953303639	0.0129773532906	-0.0865360395018	0.0871643718196	0.092823063473	0.107379788856	0.160980655311	0.00418521679863	0.0262322199417	0.158327190815	-0.00976131809518	0.195373920652	37.6687443696	-15.5342905488	101.224347514
3	1.90064760148	-0.225615199122	-0.159306290123	0.649751039951	-0.461183816741	0.658288354744	-0.0249734975267	0.182372245317	-0.0787895359804	-0.0464544552508	-0.0162263103073	0.0741111091141	-0.0284158359663	-0.0124051015987	0.0424361910906	0.127582068196	-0.0181516662055	-0.0102481333793	0.151435585835	0.0133130308386	0.12104210283	30.6273694452	-1.8716729343	97.7568026309
4	1.92664658526	0.0238637888171	-0.249713420498	1.12213068256	-0.510202347426	1.04488575797	0.00870958552664	0.251606391774	0.239126445725	0.0205404282821	-0.00795425819096	-0.0238795204264	-0.129184812614	-0.0297112375019	0.0131747161708	0.16043485706	-0.0190983941038	-0.0153356226294	0.203655073048	0.0534406566887	0.134262834945	32.6722958558	8.54154128162	93.0968055311
5	1.38885614585	0.493275835793	-0.391727004707	1.17298301787	-0.22136143346	1.01694494918	0.0396421251296	0.25235464726	0.39003596488	-0.0831652843455	-0.136404347063	-0.250757011622	-0.260552350743	0.239139902587	0.000711355335642	0.194557836407	-0.0679623116862	-0.0274595685634	0.285300590545	0.118171762555	0.285081084335	47.8868408654	12.65334814	93.3309350975
6	2.34941095823	-0.0265734147533	-0.288331987818	0.990252679391	-0.262827258298	1.73554147555	0.0499692082874	0.39707319001	0.0819446516149	-0.103140981424	-0.140736122368	-0.181817149457	0.00448794738136	0.0311975889947	0.00167495108205	0.230502497837	-0.00510222730408	-0.0140897849018	0.28213309716	0.111766292246	0.158739140442	34.5629597583	13.4746174423	84.8866470929
7	2.70848329541	0.788511370496	0.594583844535	0.377903357145	0.155494084192	0.431883720555	-0.145552202956	0.496922077539	0.218814708928	-0.0852992967511	0.0727700346982	0.102223094987	-0.011190659317	0.0151732602474	-0.00315714655351	0.142516933026	-0.0176410319732	-0.0186031251179	0.231806139795	0.0348535894019	0.171863237443	10.1542915917	-1.63199984964	94.6858741394
8	0.728653090541	0.229326997625	-0.0472811316733	1.62492515068	-0.321223804883	1.06520196676	-0.0957528432816	0.35498591902	-0.138330188583	-0.107356260642	0.122970859051	-0.0924988133719	0.182231366122	0.0335839476769	-0.000514202362205	0.166666955125	-0.0249480737118	-0.013747568858	0.254941847685	-0.0550648674807	0.143061757784	11.1441949256	-16.6723307589	92.0837224988
9	0.882306322864	0.157944831382	-0.361043741286	0.736626161852	0.312001830837	1.79889687665	-0.0898112429989	0.265089712287	-0.0752729986828	-0.206753544172	0.0431627076382	-0.0105315117926	0.101806033132	-0.0359021603103	-0.0115213769734	0.143814721163	-0.023470589362	-0.00720512513766	0.199645713463	-0.0338085284374	0.131404927202	7.99694360725	-14.0464709685	94.9272974553
10	0.646206951853	0.108254032543	-0.124428921414	0.770040001439	-0.121681012169	0.532659271842	0.00977478875924	0.0217168359039	0.0422260462532	0.0367723444589	0.0205625561478	0.0961707936383	-0.0569477095599	-0.100398365524	-0.015730800519	0.127689304232	0.00432512062242	0.00321186150227	0.0996594839644	0.00255353360856	0.122514361998	10.7186526582	-9.0935427172	115.867011388
11	1.08124964036	-0.129414496062	-0.192687178922	0.801921682543	-0.156208087035	0.955319718936	-0.0417740398447	0.0747821441535	-0.0974492937993	-0.0396669745359	0.00334737895171	-0.0562846301332	0.0489240272104	0.0463300497986	0.0430707726231	0.117177153181	-0.00912401240674	0.0108605123298	0.0893602419712	-0.00499455640371	0.118254486888	22.5496998867	-16.0992318042	111.634934252
12	2.09707837288	0.317446777908	-0.451973766638	0.51094569513	-0.503520670196	0.992295919336	-0.0355678952722	-0.267075833571	-0.0616893423818	0.119906468823	-0.0398072475284	0.00251930497267	0.0360360642165	0.139388287472	0.0230633121355	0.128004970088	-0.00404805727047	-0.0115953784123	0.108551942633	0.0135981028571	0.129646304024	22.2546486343	-16.5617454883	126.788249049
13	1.71406100526	-0.0500677294953	-1.08422915223	0.939241221725	-0.0359115309727	2.0180062994	-0.0383759293862	0.0500067150306	0.0355975144703	0.0984148712662	0.0577760203449	0.0816731288746	0.0519990123196	-0.270073767263	0.0169798948358	0.138416651178	0.00633787435869	0.0103708534659	0.123657156916	0.0196838700388	0.152455422437	6.03723467648	-18.328562587	127.940454164
14	3.28144519261	0.732423667666	0.456994437492	1.43507915569	-0.042091035902	1.35997948575	0.135461488437	-0.525921821709	-0.324833015196	0.411144803307	-0.313274950987	-0.376985390452	-0.0595351221896	0.238097078573	0.0408685549731	0.229951667089	-0.0182165775151	-0.0620347288377	0.202668958455	0.0676906895225	0.201329967805	20.1124871707	-21.1647984354	135.396460741
15	4.17541200489	-0.501754547884	0.887137402009	0.753622509343	-0.394999168206	0.810466445549	-0.0842075986528	-0.0352015598696	-0.0324899967296	0.110136636769	-0.0419987171162	-0.118606313865	0.0499138129672	0.173606542893	0.110066556104	0.149021403596	-0.00137812029325	-0.0296158014286	0.214294947591	0.0458932365702	0.174870578054	46.0260864907	-12.3337691227	121.898824108
16	2.24039586538	-0.462800606294	0.470750634842	0.549993862999	-0.646805705154	1.57245194275	0.0211421038247	-0.0605073884016	-0.404244005571	0.0334808653757	-0.0944543895122	-0.38511582585	0.16233492207	-0.0471477189062	0.0329895189107	0.156151224952	0.010875313864	-0.018056375872	0.219407126418	0.0783474865671	0.287883816172	48.7779865762	-17.274141588	115.882647635
17	1.26298161132	0.0127613667212	-0.124987975338	1.04752730636	-0.252863134545	1.37574003172	-0.0737169113906	0.083702217404	-0.300455298918	-0.0633477838123	-0.0353689011294	-0.19699090567	0.250583760771	0.0771490519077	0.147155374178	0.158623271514	0.00635070732601	0.0157855385202	0.191087339416	0.0179140951809	0.224555209968	51.1491577404	-17.554848517	105.937796829
18	1.24235906324	-0.405873560993	0.278639657677	1.60879426871	-0.190506770323	1.23786585394	-0.143525880731	-0.179224205351	-0.0544318119031	0.2566002373	0.0767731479223	0.0419917930912	-0.110110071197	-0.0154146649684	0.068600360211	0.157328266724	-0.0184126824398	-0.0114245683253	0.185627703929	0.02132377059	0.129514053349	42.7132197221	-2.70377074097	113.965873933
19	1.41134577459	-0.624444154153	-0.311852510844	1.60439816606	0.100968330638	0.803252770411	-0.0505395573678	0.0945205037348	0.130307699031	0.105748651687	-0.00188361034998	-0.255732195779	-0.0830746526998	0.161220401075	0.0399387865107	0.133665706992	-0.0282663729396	-0.0270293220033	0.200119124844	0.0368210217541	0.154097515256	46.4338941563	3.36339125183	99.8178672435

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'B' and (resid 446 through 467 )	B	B	446 - 467	119 - 140
2	2	chain 'B' and (resid 468 through 509 )	B	B	468 - 509	141 - 160
3	3	chain 'B' and (resid 510 through 559 )	B	B	510 - 559	161 - 210
4	4	chain 'B' and (resid 560 through 593 )	B	B	560 - 593	211 - 244
5	5	chain 'B' and (resid 594 through 616 )	B	B	594 - 616	245 - 267
6	6	chain 'B' and (resid 617 through 632 )	B	B	617 - 632	268 - 283
7	7	chain 'A' and (resid 330 through 350 )	A	A	330 - 350	2 - 22
8	8	chain 'A' and (resid 351 through 382 )	A	A	351 - 382	23 - 54
9	9	chain 'A' and (resid 383 through 406 )	A	A	383 - 406	55 - 78
10	10	chain 'A' and (resid 407 through 445 )	A	A	407 - 445	79 - 117
11	11	chain 'A' and (resid 446 through 559 )	A	A	446 - 559	118 - 210
12	12	chain 'A' and (resid 560 through 593 )	A	A	560 - 593	211 - 244
13	13	chain 'A' and (resid 594 through 616 )	A	A	594 - 616	245 - 267
14	14	chain 'A' and (resid 617 through 632 )	A	A	617 - 632	268 - 283
15	15	chain 'B' and (resid 330 through 350 )	B	B	330 - 350	3 - 23
16	16	chain 'B' and (resid 351 through 366 )	B	B	351 - 366	24 - 39
17	17	chain 'B' and (resid 367 through 397 )	B	B	367 - 397	40 - 70
18	18	chain 'B' and (resid 398 through 424 )	B	B	398 - 424	71 - 97
19	19	chain 'B' and (resid 425 through 445 )	B	B	425 - 445	98 - 118

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