PDB-7vbt: Crystal structure of RIOK2 in complex with CQ211

ID or keywords:

Entry

Database: PDB / ID: 7vbt

Title

Crystal structure of RIOK2 in complex with CQ211

Components

Serine/threonine-protein kinase RIO2

Keywords

TRANSFERASE / RIOK2

Function / homology

Function and homology information

positive regulation of ribosomal small subunit export from nucleus / positive regulation of rRNA processing / regulation of mitotic metaphase/anaphase transition / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of SSU-rRNA / ribosomal small subunit biogenesis / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.54001480108 Å

Authors

Zhu, C. / Zhang, Z.M.

Funding support

1items

Citation

Journal: J.Med.Chem. / Year: 2022
Title: Discovery of 8-(6-Methoxypyridin-3-yl)-1-(4-(piperazin-1-yl)-3-(trifluoromethyl)phenyl)-1,5-dihydro- 4H -[1,2,3]triazolo[4,5- c ]quinolin-4-one (CQ211) as a Highly Potent and Selective RIOK2 Inhibitor.
Authors: Ouyang, Y. / Si, H. / Zhu, C. / Zhong, L. / Ma, H. / Li, Z. / Xiong, H. / Liu, T. / Liu, Z. / Zhang, Z. / Zhang, Z.M. / Cai, Q.

History

Deposition	Sep 1, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7vbt.cif.gz	292.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7vbt.ent.gz	197.9 KB	Display	PDB format
PDBx/mmJSON format	7vbt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7vbt_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	7vbt_full_validation.pdf.gz	1.1 MB	Display
Data in XML	7vbt_validation.xml.gz	23.2 KB	Display
Data in CIF	7vbt_validation.cif.gz	30.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vb/7vbt ftp://data.pdbj.org/pub/pdb/validation_reports/vb/7vbt	HTTPS FTP

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Related structure data

Related structure data	6hk6S S: Starting model for refinement
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	#60 - Dec 2004 Ubiquitin similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #86 - Feb 2007 Exosomes similarity (1)

Deposited unit

A: Serine/threonine-protein kinase RIO2

B: Serine/threonine-protein kinase RIO2

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	70.517, 93.605, 110.965
Angle α, β, γ (deg.)	90.0, 90.0, 90.0
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

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	VAL	VAL	SER	SER	chain 'A'	A	A	6 - 43	6 - 43
1	2	HIS	HIS	LEU	LEU	chain 'A'	A	A	46 - 127	46 - 127
1	3	HIS	HIS	ARG	ARG	chain 'A'	A	A	146 - 292	146 - 292
1	4	ASP	ASP	ASP	ASP	chain 'A'	A	A	297 - 312	297 - 312
2	5	VAL	VAL	SER	SER	chain 'B'	B	B	6 - 43	6 - 43
2	6	HIS	HIS	LEU	LEU	chain 'B'	B	B	46 - 127	46 - 127
2	7	HIS	HIS	ARG	ARG	chain 'B'	B	B	146 - 292	146 - 292
2	8	ASP	ASP	ASP	ASP	chain 'B'	B	B	297 - 312	297 - 312

#1: Protein	Serine/threonine-protein kinase RIO2 / RIO kinase 2 Mass: 37052.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RIOK2, RIO2 / Production host: Escherichia coli (E. coli) References: UniProt: Q9BVS4, non-specific serine/threonine protein kinase
#2: Chemical	ChemComp-5ZH / 8-(6-methoxypyridin-3-yl)-1-[4-piperazin-1-yl-3-(trifluoromethyl)phenyl]-5H-[1,2,3]triazolo[4,5-c]quinolin-4-one Mass: 521.494 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₆H₂₂F₃N₇O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.49 Å³/Da / Density % sol: 50.57 %
Crystal grow	Temperature: 293 K / Method: evaporation, recrystallization / Details: 50 mM MES (pH 5.5), 3% isopropanol, 10 mM MgCl2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9897 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 20, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9897 Å / Relative weight: 1
Reflection	Resolution: 2.54→50 Å / Num. obs: 26038 / % possible obs: 100 % / Redundancy: 8.3 % / CC_1/2: 0.953 / Net I/σ(I): 19.8
Reflection shell	Resolution: 2.54→2.59 Å / Num. unique obs: 2539 / CC_1/2: 0.92

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692+SVN	refinement
Coot		model building
HKL-2000		data scaling
Coot		model building
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6HK6

6hk6

Resolution: 2.54001480108→46.8025 Å / SU ML: 0.367422054854 / Cross valid method: FREE R-VALUE / σ(F): 1.37325144812 / Phase error: 29.0636468347

	R_factor	Num. reflection	% reflection
R_free	0.259163702742	1906	7.68393469059 %
R_work	0.221363193536	22899	-
obs	0.224129822459	24805	99.7105760341 %

Solvent computation

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

Displacement parameters

B_iso mean: 65.9266065378 Å²

Refinement step

Cycle: LAST / Resolution: 2.54001480108→46.8025 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4570	0	76	23	4669

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0038573906731	4755
X-RAY DIFFRACTION	f_angle_d	0.849569926783	6452
X-RAY DIFFRACTION	f_chiral_restr	0.0357514593963	705
X-RAY DIFFRACTION	f_plane_restr	0.00495789248769	817
X-RAY DIFFRACTION	f_dihedral_angle_d	16.0161347261	1727

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 (%)
2.54002-2.6035	0.360901065349	135	0.330767756147	1622	X-RAY DIFFRACTION	99.7728563316
2.6035-2.6739	0.349715381377	132	0.328687762567	1587	X-RAY DIFFRACTION	100
2.6739-2.7526	0.338535250367	135	0.30312897558	1603	X-RAY DIFFRACTION	99.8276852384
2.7526-2.8414	0.297141755192	134	0.284451295983	1621	X-RAY DIFFRACTION	99.8293515358
2.8414-2.943	0.369737780251	135	0.268019421773	1634	X-RAY DIFFRACTION	100
2.943-3.0608	0.301759253827	134	0.26778780705	1612	X-RAY DIFFRACTION	99.885583524
3.0608-3.2	0.283963371306	135	0.266122271241	1619	X-RAY DIFFRACTION	99.943019943
3.2-3.3687	0.316211016347	136	0.256601932556	1641	X-RAY DIFFRACTION	99.9437570304
3.3687-3.5797	0.244684690388	136	0.229366671967	1620	X-RAY DIFFRACTION	100
3.5797-3.856	0.223336354836	135	0.207847298784	1626	X-RAY DIFFRACTION	99.8865570051
3.856-4.2438	0.262074878426	138	0.199442953808	1656	X-RAY DIFFRACTION	99.8330550918
4.2438-4.8573	0.225795782584	138	0.189730998416	1655	X-RAY DIFFRACTION	99.9442586399
4.8573-6.1176	0.213704802637	139	0.208162863479	1665	X-RAY DIFFRACTION	99.6134732192
6.1176-46.8	0.234275757393	144	0.181232338264	1738	X-RAY DIFFRACTION	97.7662337662

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	5.61002489454	0.99103271398	-1.18812695303	5.7704512045	-1.39614899152	5.38998860235	0.263709849011	-1.20568425307	0.143439244449	0.909535810156	-0.236816210093	-0.807331538814	-0.606574754215	0.754822242882	-0.00429218418434	0.635826417009	-0.0665399972514	-0.0547766979671	0.964693541293	-0.0916805241282	0.528005829246	43.8301488992	-4.72720376174	22.284962101
2	3.52934852892	0.292667147426	-0.356082966195	6.85647945031	-1.35823094079	6.01546979446	0.389965181432	-0.978873468094	-0.333778447387	1.01172203278	0.0341777757687	-0.39109516267	0.269941206798	-0.214427768181	-0.436346094964	0.651233111063	-0.0657891245255	0.0199366965338	0.884883010039	0.0152671901286	0.458474155748	33.9525808969	-10.9082421745	26.7868759238
3	4.2541105041	0.973761382278	-1.16264773438	2.63050359186	-0.475091394643	1.61149596462	0.230872438473	-0.632943674536	0.0207956911415	0.384053448977	-0.0759932025072	-0.134948928236	0.0356019446694	-0.246742731723	-0.130257238755	0.625531163629	-0.087686973474	-0.0612560970885	0.742027885054	-0.0760811014296	0.420880398119	36.3376515819	-3.18638713137	19.6989213192
4	6.22217607097	-2.84087945805	1.3967094412	2.97815569829	-2.5369504855	3.55829575099	-0.118337655799	-0.65669469628	-0.150700912798	0.429201631681	0.0612745322026	0.119978845799	-0.336963321592	-0.31733606829	0.316238750397	0.62531282223	-0.106149949434	0.0557120669252	0.704510203487	-0.115885279872	0.517044246028	48.7560000061	7.3607114147	10.0352680713
5	1.97484913299	-0.262961252438	-0.56990833163	2.36500022161	-0.052205213805	4.44076587483	0.131572422428	-0.0937363059084	0.0265336131438	0.249342831434	-0.139305516329	-0.353729644938	-0.225238600145	0.25736999096	0.0134008802347	0.459589879689	-0.0506357131665	-0.0387521821785	0.455588988561	-0.0247474388556	0.448807421508	46.9181348805	-1.36045142052	4.10365138846
6	0.984396937257	1.23047599329	-1.35201848037	2.48514346416	-0.394317361861	2.70192533463	0.0939250053582	-0.119779405212	0.306344456334	0.167970566663	-0.0664437881823	-0.0605697331918	-0.519392188618	0.493332923293	-0.0440403881368	0.542245998589	-0.11298366888	-0.0388964667671	0.639013953677	-0.0291414126131	0.610168677084	53.2140281924	8.64732680863	0.124429086581
7	1.11713584157	-1.38628727581	-1.48507268746	3.40129723135	2.77412053814	3.93651598886	-0.232275636443	-0.0816635211738	0.465235495505	0.244701464015	0.214915256677	-0.140734815931	0.0962955337243	0.329920475296	0.0801157218278	0.500173292996	-0.0932678438779	0.00231063342536	0.719004124232	0.0127919490391	0.599869108672	49.3692188113	9.35088589359	-13.8208197895
8	2.41396849907	-0.110321101831	-0.680103728006	4.140311645	1.54618740726	3.56576735745	-0.0563503090109	0.0357749825809	0.295438651277	-0.240313898584	-0.0109583053352	-0.272872560986	-0.214831024506	0.369156646368	0.0783041359895	0.520929517091	-0.0438913088487	0.00787740044155	0.598096292802	0.0123184137579	0.595343588801	45.3958561797	10.5152955738	-12.6699870179
9	0.886164388426	-0.311267298717	-0.794080469184	8.24525429911	-0.140869779525	0.765564721705	0.126875843841	0.820410191067	0.0800639508436	1.0352725283	-0.743496657267	-1.7226696313	0.26864450298	0.252655666494	0.445823888845	1.08786877582	-0.191007679141	0.00109133462725	1.2333654984	-0.0907529952907	0.887964318602	49.3944933849	6.11431017395	-22.5832213692
10	2.47792550161	2.31137169196	-2.11134051905	5.85061038687	-3.56067004177	2.54172194566	-0.00159512786847	-0.793767636646	-0.510426131167	0.561947180304	-0.294195286654	-0.436398341527	0.61572795172	0.787567663395	0.0962883006848	0.502538365375	0.0280347228232	0.0551789926211	0.509023853115	0.0122181287352	0.574945560022	47.4841049652	-13.5406257364	2.74635112926
11	3.7375148611	-0.177015935298	0.0882507869674	6.43742116238	-1.39456737633	2.91768821468	0.0446319458651	0.234378709114	-0.336742242733	-0.0215942602022	0.165577156709	-0.257996464528	0.387143092678	-0.163896441023	-0.194651404027	0.68998623527	-0.072557368728	-0.0224463682749	0.650211682532	0.0335885062266	0.614460020219	31.3800844142	-30.7040678146	-5.27679919768
12	1.77548616382	-1.83687753489	-0.911488901386	6.03301856489	-0.863994260841	2.89956259129	0.096851014417	0.282946602019	-0.276584616948	-0.219552404473	-0.117465026757	-0.107969357841	0.425574016194	-0.112837029099	0.0636387381677	0.628692633409	-0.163302028988	-0.0345937040315	0.629722170594	-0.0827323744705	0.483899050793	29.4877692761	-21.089885745	-11.2869836987
13	3.38535467089	-2.50786881642	-0.0992773759368	4.77877174541	-0.4838101501	1.86720710277	0.0544448118844	0.0585037095784	-0.297447014213	-0.0872631169032	0.0423025955894	0.429990315586	0.125957909119	-1.05268657978	-0.108488255309	0.443990028583	-0.0698244528914	0.000621964062892	0.766209082516	-0.0635369658143	0.403411229379	21.5890611282	-8.46132197752	-8.12861040801
14	3.99482990669	0.317831204291	1.25637955864	2.42128472283	1.21523959341	3.52651751171	-0.151049678763	0.0266927587685	0.418756304998	-0.0721417805138	-0.105734456709	0.257842819327	-0.134169274372	-0.601700318962	0.221584810628	0.483905364341	0.0358975504128	-0.0169926208838	0.683200549736	-0.0026665321145	0.479226037518	24.0729963845	9.62104953226	-15.4235082571
15	2.74264941714	0.15881753241	0.399638370092	2.00252713079	0.761721617993	2.29742328518	0.230377689136	-0.43964186273	1.23586972095	0.669574950946	0.367986489319	0.316938188671	-0.497315612587	0.176045718652	-0.152713098993	1.00628623869	0.261371063701	-0.0147319762546	0.83666888731	0.0117866490904	1.01632259733	24.3532785658	20.1261675851	-10.6003445679
16	6.88847464763	-2.75116052288	3.14952390219	9.07448823081	-4.33661338728	6.64866084199	0.140331886876	-0.703582733406	-0.367405320654	0.290434291002	0.0298655042244	0.116198359623	0.000103655001793	-0.0818345107766	-0.184064151934	0.60714686908	-0.0190476749415	0.00401368755457	1.07113083413	-0.0734588213863	0.485736819775	21.1415986624	-4.79130502903	5.19712978853

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 28 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 58 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 59 through 91 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 92 through 113 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 114 through 171 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 172 through 204 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 205 through 233 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 234 through 277 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 278 through 297 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 298 through 319 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 6 through 58 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 59 through 106 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 107 through 188 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 189 through 276 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 277 through 297 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 298 through 313 )

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi