PDB-10hm: Trypanosoma brucei CLK1 kinase domain in complex with a covalent ...

ID or keywords:

Entry

Database: PDB / ID: 10hm

Title

Trypanosoma brucei CLK1 kinase domain in complex with a covalent Amidobenzimidazole (AB4) inhibitor

Components

Protein kinase, putative

Keywords

TRANSFERASE/Inhibitor / CLK1 KKT10 / TRANSFERASE / TRANSFERASE-Inhibitor complex

Function / homology

Function and homology information

Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / cell tip / regulation of RNA splicing / chromosome segregation / kinetochore / mitotic cell cycle / protein phosphorylation / protein kinase activity / protein serine/threonine kinase activity / ATP binding ...
Similarity search - Function

Biological species

Trypanosoma brucei brucei TREU927 (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Mamo, M.

Funding support

1items

Citation

Journal: To Be Published
Title: Trypanosoma brucei CLK1 kinase domain in complex with a covalent Amidobenzimidazole (AB4) inhibitor
Authors: Mamo, M.

History

Deposition	Jan 20, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 17, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	10hm.cif.gz	2.1 MB	Display	PDBx/mmCIF format
PDB format	pdb10hm.ent.gz		Display	PDB format
PDBx/mmJSON format	10hm.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/0h/10hm ftp://data.pdbj.org/pub/pdb/validation_reports/0h/10hm	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

Deposited unit

A: Protein kinase, putative

B: Protein kinase, putative

C: Protein kinase, putative

D: Protein kinase, putative

E: Protein kinase, putative

F: Protein kinase, putative

G: Protein kinase, putative

H: Protein kinase, putative

I: Protein kinase, putative

J: Protein kinase, putative

K: Protein kinase, putative

L: Protein kinase, putative

M: Protein kinase, putative

N: Protein kinase, putative

O: Protein kinase, putative

P: Protein kinase, putative

hetero molecules

699 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	147.679, 147.679, 265.554
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	Protein kinase, putative Mass: 43040.805 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote) Gene: Tb11.01.4230 / Production host: Bacterial expression vector pAIL2 (others) References: UniProt: Q382U0, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical	ChemComp-A1C5R / %{N}-(1-{(3%{R})-1-[4-(dimethylamino)butanoyl]azepan-3-yl}-4,6-difluoro-1%{H}-1,3-benzimidazol-2-yl)-5-fluoropyridine-3-carboxamide Mass: 502.532 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₂₅H₂₉F₃N₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1858 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.43 Å³/Da / Density % sol: 49.34 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 %v/v 2-PropOH, 1.8 M (NH4)2SO4, 0.1 M BIS-TRIS 6.5 pH

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Mar 28, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.4→127.89 Å / Num. obs: 253968 / % possible obs: 99.9 % / Redundancy: 5.4 % / CC_1/2: 0.363 / Net I/σ(I): 0.8
Reflection shell	Resolution: 2.4→2.53 Å / Num. unique obs: 253968 / CC_1/2: 0.363 / CC star: 0.983

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Processing

Software

Name	Version	Classification
BUSTER	2.11.8	refinement
autoPROC		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→127.89 Å / Cor.coef. F_o:F_c: 0.879 / Cor.coef. F_o:F_c free: 0.831 / SU R Cruickshank DPI: 0.569 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.546 / SU R_free Blow DPI: 0.332 / SU R_free Cruickshank DPI: 0.34

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3349	12444	-	RANDOM
R_work	0.2964	238968	-	-
obs	0.2983	251412	98.9 %	-

Displacement parameters

B_iso mean: 35.65 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.6117 Å²	0 Å²	0 Å²
2-	-	-2.6117 Å²	0 Å²
3-	-	-	5.2234 Å²

Refine analyze

Luzzati coordinate error obs: 0.452 Å

Refinement step

Cycle: LAST / Resolution: 2.4→127.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	42645	0	720	1858	45223

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.009	44587	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.04	60677	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		15065	SINUSOIDAL	2
X-RAY DIFFRACTION	t_gen_planes		7625	HARMONIC	5
X-RAY DIFFRACTION	t_it		43944	HARMONIC	10
X-RAY DIFFRACTION	t_chiral_improper_torsion		5739	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies		4	HARMONIC	1
X-RAY DIFFRACTION	t_ideal_dist_contact		36831	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_omega_torsion	3.02
X-RAY DIFFRACTION	t_other_torsion	17.16

LS refinement shell

Resolution: 2.4→2.41 Å

	R_factor	Num. reflection	% reflection
R_free	0.4155	239	-
R_work	0.3547	4790	-
obs	0.3575	5029	91.09 %

Refinement TLS params.

L33: _ / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°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	0.2604	-0.0024	0.0241	0.2794	-0.1422	-0.0757	0.0038	-0.0622	-0.0184	-0.0187	0.0157	-0.0524	0.0075	0.0944	-0.0438	-0.0271	0.0159	-0.069	-0.0098	0.0686	56.1479	-9.2746	-69.8853
2	0.4989	-0.1966	-0.0633	0.0253	0.2248	-0.0585	-0.0362	-0.0238	-0.0146	-0.0225	-0.0547	-0.024	-0.0497	0.081	-0.0819	-0.0008	0.0012	-0.0274	0.0227	0.0604	16.9373	10.7448	-26.4808
3	0.1086	0.0558	0.2716	0.6973	-0.1594	-0.0096	0.0374	-0.0695	-0.0167	-0.0952	-0.0791	-0.0801	-0.0365	0.1048	-0.0206	-0.0039	-0.0162	-0.0728	-0.0124	0.0337	21.1023	-76.7172	-69.3402
4	0.4213	-0.084	-0.0774	0.0931	0.1487	-0.0586	-0.0584	-0.0268	-0.0383	-0.0428	-0.0483	-0.0301	-0.0337	0.1013	-0.083	0.0007	0.006	-0.0405	0.0286	0.0728	53.8084	-53.2047	-26.4572
5	0.0811	0.0999	0.1059	0.6256	-0.1119	-0.0363	0.0255	-0.0513	-0.0078	-0.0755	-0.0782	-0.0686	-0.0598	0.1117	-0.0541	-0.0097	-0.0106	-0.0503	-0.0196	0.0454	-15.5991	-12.6097	-69.5432
6	0.5241	-0.2104	0.0541	0.144	0.2319	-0.0819	-0.002	-0.072	0.0508	-0.0372	0.0015	-0.0412	-0.0453	0.119	-0.0838	0.0121	-0.0271	-0.0393	0.0004	0.073	-18.1377	-56.7699	-26.8796
7	0.6272	-0.2031	-0.1186	0.1381	0.2936	-0.12	-0.0189	-0.0691	0.034	-0.0324	-0.0172	-0.0458	-0.033	0.1523	-0.075	0.009	-0.0225	-0.0309	0.0004	0.0517	-55.1171	7.1407	-26.9159
8	0.2508	0.0549	-0.1092	0.3713	0.1104	-0.0784	0.0097	0.0707	-0.0068	-0.0176	-0.0139	0.0676	-0.0143	0.096	-0.0343	-0.0193	-0.0175	-0.0791	0.0119	0.0617	-19.1437	-54.6652	-69.9032
9	0.36	-0.0203	-0.1226	0.1176	-0.1078	-0.0492	0.0599	-0.0288	0.0353	-0.0664	0.0574	-0.0357	0.0397	0.1157	-0.0919	-0.0069	-0.002	-0.022	-0.0243	0.0704	20.0216	-53.306	18.6102
10	0.4545	-0.2291	0.105	0.0538	-0.1016	-0.0397	-0.0539	0.0159	-0.0329	-0.0404	0.0659	0.0179	0.0591	0.0801	-0.0882	-0.0019	0.0034	-0.0268	-0.0136	0.0683	-16.9267	-10.7501	-26.5095
11	0.3547	0.0129	0.0756	0.1561	-0.1125	-0.0203	-0.0661	0.0502	-0.0525	-0.0878	0.0685	0.0469	0.042	0.108	-0.0885	0.0011	0.001	-0.0216	-0.0321	0.0621	20.0047	-74.6457	-26.4627
12	0.6502	-0.2096	-0.0269	0.1989	-0.2795	-0.0586	0.0057	0.1111	0.0626	-0.0677	0.0565	0.0886	0.0977	0.1263	-0.0704	-0.0018	0.0287	-0.0364	0.0118	0.0461	-55.6863	-71.135	-26.9033
13	0.5576	-0.235	0.0689	0.1773	-0.2805	-0.0319	0.0008	0.0906	0.0396	-0.0697	0.0324	0.0599	0.0584	0.1016	-0.0719	-0.0156	0.0195	-0.0346	0.0045	0.0494	55.1824	-7.1558	-26.891
14	0.2502	-0.0567	-0.311	0.684	0.1481	-0.0282	0.0404	0.0323	-0.0439	-0.1043	0.0904	0.0924	0.0166	0.1325	-0.0289	-0.0092	0.0146	-0.0795	0.0166	0.0603	52.7191	-51.1726	-69.4176
15	0.1623	0.0758	-0.1663	0.6072	0.2305	-0.0587	0.025	0.0528	-0.0305	-0.0678	0.0654	0.0533	0.0387	0.1265	-0.0535	-0.0288	0.0071	-0.0603	0.0198	0.0594	15.5707	12.6042	-69.559
16	0.08	0.0409	0.127	0.5269	-0.1417	-0.0683	-0.0013	-0.0638	-0.0206	-0.0047	0.0157	-0.0524	0.01	0.073	-0.0431	-0.0211	0.0201	-0.0687	-0.0158	0.0569	-54.7013	-73.2379	-69.9099

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ N\|* }	N	127 - 465
2	X-RAY DIFFRACTION	1	{ N\|* }	N	501
3	X-RAY DIFFRACTION	2	{ A\|* }	A	127 - 465
4	X-RAY DIFFRACTION	2	{ A\|* }	A	501
5	X-RAY DIFFRACTION	3	{ O\|* }	O	127 - 465
6	X-RAY DIFFRACTION	3	{ O\|* }	O	501
7	X-RAY DIFFRACTION	4	{ B\|* }	B	127 - 465
8	X-RAY DIFFRACTION	4	{ B\|* }	B	501
9	X-RAY DIFFRACTION	5	{ P\|* }	P	127 - 465
10	X-RAY DIFFRACTION	5	{ P\|* }	P	501
11	X-RAY DIFFRACTION	6	{ C\|* }	C	127 - 465
12	X-RAY DIFFRACTION	6	{ C\|* }	C	501
13	X-RAY DIFFRACTION	7	{ D\|* }	D	127 - 465
14	X-RAY DIFFRACTION	7	{ D\|* }	D	501
15	X-RAY DIFFRACTION	8	{ E\|* }	E	127 - 465
16	X-RAY DIFFRACTION	8	{ E\|* }	E	501
17	X-RAY DIFFRACTION	9	{ F\|* }	F	127 - 465
18	X-RAY DIFFRACTION	9	{ F\|* }	F	501
19	X-RAY DIFFRACTION	10	{ G\|* }	G	127 - 465
20	X-RAY DIFFRACTION	10	{ G\|* }	G	501
21	X-RAY DIFFRACTION	11	{ H\|* }	H	127 - 465
22	X-RAY DIFFRACTION	11	{ H\|* }	H	501 - 502
23	X-RAY DIFFRACTION	12	{ I\|* }	I	127 - 465
24	X-RAY DIFFRACTION	12	{ I\|* }	I	501
25	X-RAY DIFFRACTION	13	{ J\|* }	J	127 - 465
26	X-RAY DIFFRACTION	13	{ J\|* }	J	501
27	X-RAY DIFFRACTION	14	{ K\|* }	K	127 - 465
28	X-RAY DIFFRACTION	14	{ K\|* }	K	501
29	X-RAY DIFFRACTION	15	{ L\|* }	L	127 - 465
30	X-RAY DIFFRACTION	15	{ L\|* }	L	501
31	X-RAY DIFFRACTION	16	{ M\|* }	M	127 - 465
32	X-RAY DIFFRACTION	16	{ M\|* }	M	501

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