PDB-9zkg: VRK1 in complex with the inhibitor MP-60

ID or keywords:

Entry

Database: PDB / ID: 9zkg

Title

VRK1 in complex with the inhibitor MP-60

Components

Serine/threonine-protein kinase VRK1

Keywords

TRANSFERASE/TRANSFERASE INHIBITOR / PROTEIN KINASE / INHIBITOR / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex

Function / homology

Function and homology information

histone H2AX kinase activity / Golgi disassembly / Cajal body organization / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / histone H3S10 kinase activity / regulation of neuron migration / Golgi stack ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.06 Å

Authors

Aroucha, J.P. / Crowley-Dolen, E.K. / Mitchison, T.J. / Massirer, K.B. / Borges, R.J.

Funding support

Brazil, 2items

Citation

Journal: J.Biol.Chem. / Year: 2026
Title: Structure-based discovery of selective vaccinia-related kinase 1 inhibitors and fluorogenic active-site probes.
Authors: Crowley-Dolen, E.K. / Borges, R.J. / Charifson, P.S. / Payne, N.C. / de Oliveira, R.G. / Cunha, M.R. / Mazitschek, R. / Massirer, K.B. / Mitchison, T.J.

History

Deposition	Dec 6, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 29, 2026	Provider: repository / Type: Initial release
Revision 1.1	May 13, 2026	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9zkg.cif.gz	628.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9zkg.ent.gz		Display	PDB format
PDBx/mmJSON format	9zkg.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/zk/9zkg ftp://data.pdbj.org/pub/pdb/validation_reports/zk/9zkg	HTTPS FTP

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Related structure data

Similar structure data	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	#213 - Sep 2017 Sirtuins similarity (1) #85 - Jan 2007 Importins similarity (1)

Deposited unit

A: Serine/threonine-protein kinase VRK1

B: Serine/threonine-protein kinase VRK1

C: Serine/threonine-protein kinase VRK1

D: Serine/threonine-protein kinase VRK1

hetero molecules

168 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Serine/threonine-protein kinase VRK1

hetero molecules

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

2

B: Serine/threonine-protein kinase VRK1

hetero molecules

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

3

C: Serine/threonine-protein kinase VRK1

hetero molecules

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

4

D: Serine/threonine-protein kinase VRK1

hetero molecules

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

Unit cell

Length a, b, c (Å)	91.460, 95.930, 191.830
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Serine/threonine-protein kinase VRK1 / Vaccinia-related kinase 1 Mass: 41138.125 Da / Num. of mol.: 4 Mutation: M1A, M2P, K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VRK1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q99986, non-specific serine/threonine protein kinase

#1: Protein

Serine/threonine-protein kinase VRK1 / Vaccinia-related kinase 1

Mass: 41138.125 Da / Num. of mol.: 4
Mutation: M1A, M2P, K34A, K35A, E36A, E212A, K214A, E215A, E292A, K293A, K295A, K359A, K360A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: VRK1 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q99986, non-specific serine/threonine protein kinase

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Non-polymers , 9 types, 572 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-ACN / ACETONE Mass: 58.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₆O
#7: Chemical	ChemComp-GG0 / 2-(2-azanylethanoylamino)ethanoic acid Mass: 132.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₈N₂O₃
#8: Chemical	ChemComp-A1C2O / (5Z)-3-butyl-5-[(3,5-dichloro-4-hydroxyphenyl)methylidene]-1,3-thiazolidine-2,4-dione Mass: 346.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₁₃Cl₂NO₃S / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 539 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.56 Å³/Da / Density % sol: 51.9 %
Crystal grow	Temperature: 303 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30,25% PEG3350, 0.2 M LiSO4, 0.1M SBG pH 6,5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 18, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97718 Å / Relative weight: 1
Reflection	Resolution: 2.05→47.97 Å / Num. obs: 106167 / % possible obs: 99.8 % / Redundancy: 13.2 % / B_iso Wilson estimate: 33.06 Å² / CC_1/2: 0.996 / R_rim(I) all: 0.264 / Net I/σ(I): 9.9
Reflection shell	Resolution: 2.05→2.18 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 1.14 / Num. unique obs: 16844 / CC_1/2: 0.479 / R_rim(I) all: 2.346 / % possible all: 98.8

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
XDS		data reduction
XDS		data scaling
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.06→47.97 Å / SU ML: 0.2583 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9066
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2159	5245	5 %
R_work	0.1807	99632	-
obs	0.1825	104877	99.98 %

Solvent computation

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

Displacement parameters

B_iso mean: 41.78 Å²

Refinement step

Cycle: LAST / Resolution: 2.06→47.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9950	0	175	539	10664

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0042	10414
X-RAY DIFFRACTION	f_angle_d	0.6425	14087
X-RAY DIFFRACTION	f_chiral_restr	0.0421	1482
X-RAY DIFFRACTION	f_plane_restr	0.0062	1816
X-RAY DIFFRACTION	f_dihedral_angle_d	17.1821	3855

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 (%)
2.06-2.08	0.3618	177	0.3112	3315	X-RAY DIFFRACTION	99.97
2.08-2.11	0.3489	170	0.3008	3251	X-RAY DIFFRACTION	100
2.11-2.13	0.3397	175	0.2915	3303	X-RAY DIFFRACTION	99.97
2.13-2.16	0.3027	170	0.2675	3239	X-RAY DIFFRACTION	100
2.16-2.19	0.3134	173	0.2661	3300	X-RAY DIFFRACTION	99.97
2.19-2.22	0.3166	174	0.2543	3286	X-RAY DIFFRACTION	100
2.22-2.25	0.2491	172	0.2488	3262	X-RAY DIFFRACTION	99.97
2.25-2.28	0.2886	176	0.2342	3335	X-RAY DIFFRACTION	99.97
2.28-2.32	0.2774	171	0.2325	3260	X-RAY DIFFRACTION	100
2.32-2.36	0.2668	174	0.2215	3303	X-RAY DIFFRACTION	100
2.36-2.4	0.3107	173	0.2219	3289	X-RAY DIFFRACTION	100
2.4-2.44	0.2223	172	0.2084	3275	X-RAY DIFFRACTION	100
2.44-2.49	0.2797	173	0.1973	3303	X-RAY DIFFRACTION	99.97
2.49-2.54	0.2612	174	0.198	3314	X-RAY DIFFRACTION	100
2.54-2.6	0.2277	175	0.1923	3320	X-RAY DIFFRACTION	100
2.6-2.66	0.2498	172	0.1964	3274	X-RAY DIFFRACTION	100
2.66-2.72	0.2732	174	0.1959	3304	X-RAY DIFFRACTION	100
2.72-2.8	0.2281	175	0.1946	3315	X-RAY DIFFRACTION	100
2.8-2.88	0.2506	174	0.1848	3305	X-RAY DIFFRACTION	100
2.88-2.97	0.2305	173	0.1793	3292	X-RAY DIFFRACTION	100
2.97-3.08	0.2107	176	0.1782	3336	X-RAY DIFFRACTION	100
3.08-3.2	0.2083	175	0.1756	3332	X-RAY DIFFRACTION	99.97
3.2-3.35	0.1892	175	0.1667	3318	X-RAY DIFFRACTION	99.97
3.35-3.52	0.2029	176	0.1652	3353	X-RAY DIFFRACTION	100
3.52-3.74	0.195	175	0.1471	3317	X-RAY DIFFRACTION	100
3.74-4.03	0.1684	178	0.1409	3389	X-RAY DIFFRACTION	100
4.03-4.44	0.1601	176	0.1364	3343	X-RAY DIFFRACTION	100
4.44-5.08	0.1583	178	0.1366	3406	X-RAY DIFFRACTION	100
5.08-6.39	0.1822	180	0.1738	3421	X-RAY DIFFRACTION	99.97
6.4-47.97	0.189	189	0.1767	3572	X-RAY DIFFRACTION	99.79

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	0.62426350437	-0.361598599875	0.0574473525425	0.250524079574	-0.0282283204863	0.400333506302	0.00415685222033	-0.00869966973434	-0.103513749932	0.174486632062	0.107498083429	0.0773400511791	0.0438144743463	0.0692159514627	-6.54972883672E-5	0.291528628351	0.00866978017966	-0.0273951565751	0.276833285826	0.0123920484243	0.254402812622	-35.1911776841	1.51960274221	3.91358900985
2	0.0547740631758	-0.134248362132	0.679287418462	1.25493094334	-0.789975947558	1.27606593315	0.0715295971249	0.15750837847	-0.0106314266759	-0.123396845886	-0.109612958385	0.0748365412516	0.153451485747	0.13509115626	5.47209080591E-5	0.266022702339	0.0386950400136	-0.0228318569666	0.275949738187	0.00398268310482	0.232970723852	-20.5836195748	-0.676380557462	15.0824960527
3	0.0214509296828	-0.0328166742132	0.0396055065237	0.128490313078	0.041822924674	0.0850411120564	-0.036814069613	0.0727685555477	0.204229803724	0.0237807028668	0.175190677582	0.334174122015	-0.389956064753	-0.537734320622	0.000251218103998	0.485761008466	-0.0248048398147	-0.0996715907416	0.462332025178	0.109176551677	0.392673625351	-15.4256211783	12.8500805365	28.7663252897
4	0.135816894516	-0.243809560541	0.564417557587	0.969072754796	-0.396202251064	1.21711905946	0.0260733526107	0.0591069312892	0.0121989494414	0.225044744938	-0.101644607856	-0.0611060811519	0.0896389100685	0.202119294225	0.000432165844675	0.336869196997	0.0530967686089	-0.0482226700822	0.260229611554	0.0434212495256	0.236749927124	-12.0321397081	-7.70737843702	32.6821217249
5	0.0331543927495	-0.010763153354	-0.0520389548435	0.105282453378	-0.151470108569	0.168596645433	-0.159505552585	-0.0239818987252	0.154398355413	-0.0501851579745	0.149356861485	-0.0734791173005	-0.134379627727	0.0998155911013	0.000513648536999	0.527490106719	0.0875531984202	-0.0178399878618	0.264199798984	0.0417684836173	0.3003402607	-18.0590327282	14.1939848	51.4814647014
6	0.836801801263	-0.0759241241004	-0.866315295762	0.584642544568	-0.236676792321	1.36451699625	0.0305771345985	0.111103815443	0.05817471889	-0.186228309468	-0.063356145495	0.087973489757	-0.192611995159	-0.26338122449	-0.000604148769135	0.303348716795	0.0659991746258	-0.0516110780601	0.27574941494	-0.0104362348224	0.272731129953	-23.6035366553	0.271694335011	61.9500484177
7	0.115797105855	0.0711724076509	0.0152755329497	0.0628467943996	-0.0604927526336	0.0591180034937	0.0206716125743	-0.00491897319466	0.452386490747	-0.254574199865	-0.0281014817464	-0.075251282688	-0.197668242361	0.62751732935	0.000309017272391	0.31629207302	0.0233668708663	0.0562906432855	0.406763513935	0.0393062060659	0.400267656986	-10.1912680172	-7.14910147257	76.838105357
8	0.785423329177	0.460701129455	-0.191257539402	0.319638890988	-0.307373622973	1.35710542468	-0.0763282591135	-0.141368451913	0.0308485313062	0.0499614669187	-0.0943227239216	0.159779577199	0.0337038546142	-0.243467672177	-0.000121014475684	0.18707024007	0.0212060553627	0.0248432256154	0.311637764789	-0.0299814249897	0.292262374865	-31.3497301022	-9.28460900906	80.1807472698
9	0.676665207524	-0.549346708938	-0.154914171454	1.60053057171	-0.696180194467	0.320524615954	-0.198530531274	-0.0836435116216	-0.236193881657	0.155763977801	0.395960607783	0.684115535744	0.0712055809487	-0.222901198656	0.00802254099938	0.390129236322	-0.0425779248211	0.0708619021285	0.436389441453	0.0857413415996	0.552942671316	-26.0245462196	34.8336803834	53.0923945438
10	0.768987041484	-0.235445935579	0.292265031721	1.18722455862	0.0235488777479	1.41563343666	-0.0461077101043	0.031357178992	0.0517691776602	0.0452660329943	-0.00832321267077	0.0796563992561	-0.0658411790351	-0.16531429933	-1.86840273083E-5	0.275568794888	0.00391102425251	-0.00505238986681	0.236471277413	-0.00606440957094	0.245129927637	-10.8440239068	49.8350154008	39.2345527909
11	0.387153204985	-0.0581888147411	0.464697089408	0.0950605922953	-0.0395032491587	0.715664825233	0.518223030211	0.379781305043	0.864283883815	0.0101327827352	-0.253938702721	0.292034452317	-0.286656707732	0.27505445064	0.114316972685	0.490727351761	-0.0636828414962	0.157563225686	0.262366868539	0.0966112239461	0.82395631117	-7.98443442064	57.982187422	-6.09891825949
12	0.228826745976	0.0364719155051	-0.277489474292	0.182767694199	0.0533736296204	0.219822076238	0.512629686069	0.0720953294706	0.712403058194	0.359456492097	-0.401400763739	0.33482568879	-0.0985334836439	0.375125687124	-0.000277846663312	0.397092805863	0.00317588560839	-0.0120419376224	0.444945035846	0.0734728354766	0.659727170289	-10.533752867	55.7852858197	-4.85039468185
13	0.162381043265	-0.103905340102	0.00112499816879	0.190319438251	-0.10082833573	0.0175999297108	-0.0850715081893	0.11985640317	0.347863521844	-0.207282000119	0.0111708196117	0.0640097434351	-0.121883369221	0.0466376617433	1.44102750495E-5	0.293902659502	-0.0467025012819	-0.0306123411437	0.35519374624	0.0303966098978	0.280449629989	-9.80527413338	37.021267164	-7.28727530982
14	0.644151418184	0.223238889197	-0.187979405162	0.0740480734431	-0.510993873423	1.07425185688	-0.0784495645381	0.228612306702	0.206318089478	-0.233824580686	0.147665620521	0.192608327817	-0.0659425613998	-0.0796696317702	0.00689155208071	0.209447774594	-0.0202128072143	-0.0540313617947	0.229283258614	0.0377240888649	0.354286299472	-20.1049179048	41.9728038637	-2.16745866436
15	0.962233667562	0.348708047228	-0.27454462689	0.494531246016	0.186425406722	0.689926826315	-0.0918088471368	-0.0307308957692	0.232091174952	-0.0403601931021	0.105827757474	0.0250812948638	0.0217292942813	0.119373123151	1.69076393216E-7	0.193239414938	-0.00948828737444	-0.0269654869097	0.270109670247	-0.000312772262828	0.280474245285	-17.5465237913	34.8711020104	7.2019952455
16	0.221238857927	0.120865029564	0.0481378878658	0.0975654313327	-0.135992683495	0.200606717086	-0.106307116399	-0.533922992814	-0.00279031897134	0.486600512895	-0.0159185399664	0.561320270977	0.0309382552541	-0.0222630888174	-0.00129411689838	0.274435352495	0.0172952360498	0.0343470015632	0.394146727069	-0.0661005480518	0.396165856557	-26.275014908	33.9286372631	22.2512444061
17	0.226791155345	0.29667444295	0.231091022691	0.364563263517	0.103639686034	0.548868101548	0.0149305228646	0.0863299985344	-0.00848018075446	-0.0275903331594	-0.0254872487371	0.211207671729	0.109714197605	-0.276472984125	-7.35880893004E-5	0.22935776952	-0.0365170089641	-0.00612027881525	0.292493947667	0.0165081180754	0.324155032834	-30.1837436513	24.7150117577	11.2381760475
18	0.0874759868065	0.0999963090229	-0.0562190457354	0.236435946204	-0.439340939166	0.909953435512	-0.0734799269832	0.441225316928	0.28951686473	-0.462015812022	0.129513210736	0.094134946034	0.373144640294	-0.302642317346	-0.0916733785695	0.316641321671	-0.141868543362	-0.103145552334	0.49905728957	0.0683874784805	0.392287549294	-34.2601730659	29.0325044303	-3.88464116105

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 'A' and (resid 20 through 67 )	A	A	20 - 67	1 - 48
2	2	chain 'A' and (resid 68 through 205 )	A	A	68 - 205	49 - 186
3	3	chain 'A' and (resid 206 through 223 )	A	A	206 - 223	187 - 204
4	4	chain 'A' and (resid 224 through 342 )	A	A	224 - 342	205 - 323
5	5	chain 'B' and (resid 21 through 56 )	B	D	21 - 56	1 - 31
6	6	chain 'B' and (resid 57 through 205 )	B	D	57 - 205	32 - 180
7	7	chain 'B' and (resid 206 through 223 )	B	D	206 - 223	181 - 198
8	8	chain 'B' and (resid 224 through 341 )	B	D	224 - 341	199 - 316
9	9	chain 'C' and (resid 22 through 132 )	C	K	22 - 132	1 - 106
10	10	chain 'C' and (resid 133 through 341 )	C	K	133 - 341	107 - 315
11	11	chain 'D' and (resid 22 through 56 )	D	R	22 - 56	1 - 30
12	12	chain 'D' and (resid 57 through 78 )	D	R	57 - 78	31 - 52
13	13	chain 'D' and (resid 79 through 102 )	D	R	79 - 102	53 - 76
14	14	chain 'D' and (resid 103 through 171 )	D	R	103 - 171	77 - 145
15	15	chain 'D' and (resid 172 through 256 )	D	R	172 - 256	146 - 230
16	16	chain 'D' and (resid 257 through 280 )	D	R	257 - 280	231 - 254
17	17	chain 'D' and (resid 281 through 316 )	D	R	281 - 316	255 - 290
18	18	chain 'D' and (resid 317 through 341 )	D	R	317 - 341	291 - 315

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