PDB-13cu: Crystal structure of covalent inhibitor 2-chloro-N-(3-((pyridin-2...

ID or keywords:

Entry

Database: PDB / ID: 13cu

Title

Crystal structure of covalent inhibitor 2-chloro-N-(3-((pyridin-2-ylthio)methyl)phenyl)acetamide bound to Ubiquitin C-terminal Hydrolase-L3

Components

Ubiquitin carboxyl-terminal hydrolase isozyme L3

Keywords

HYDROLASE/HYDROLASE INHIBITOR / UCHL3 / covalent inhibitor / chloroacetamide / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

Function and homology information

deNEDDylase activity / protein deubiquitination / protein catabolic process / post-translational protein modification / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / peptidase activity / UCH proteinases / Neddylation / ubiquitin-dependent protein catabolic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Patel, R. / Pannala, N. / Flaherty, D. / Das, C.

Funding support

1items

Citation

Journal: Biorxiv / Year: 2026
Title: Identification, optimization, and structural elucidation of chloroacetamide scaffold as covalent inhibitors for Ubiquitin C-terminal Hydrolase L3
Authors: Beeralingappa, N.C. / Lu, M. / Patel, R. / Pannala, N. / Dhiman, A. / Heil, B.N. / Imhoff, R.D. / Smith, E.G. / Bahler, M.B. / Marsden, H.L. / Allen-Petersen, B.L. / Wendt, M.K. / Das, C. / Flaherty, D.P.

History

Deposition	Apr 30, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 26, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	13cu.cif.gz	274 KB	Display	PDBx/mmCIF format
PDB format	pdb13cu.ent.gz		Display	PDB format
PDBx/mmJSON format	13cu.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/3c/13cu ftp://data.pdbj.org/pub/pdb/validation_reports/3c/13cu	HTTPS FTP

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Related structure data

Related structure data	13cvC 13cwC 13dfC 35yhC 1uch C: citing same article (ref.)
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) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: Ubiquitin carboxyl-terminal hydrolase isozyme L3

B: Ubiquitin carboxyl-terminal hydrolase isozyme L3

C: Ubiquitin carboxyl-terminal hydrolase isozyme L3

hetero molecules

81.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ubiquitin carboxyl-terminal hydrolase isozyme L3

hetero molecules

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

2

B: Ubiquitin carboxyl-terminal hydrolase isozyme L3

hetero molecules

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

3

C: Ubiquitin carboxyl-terminal hydrolase isozyme L3

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

Unit cell

Length a, b, c (Å)	44.464, 81.066, 100.709
Angle α, β, γ (deg.)	90.00, 98.61, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Ubiquitin carboxyl-terminal hydrolase isozyme L3 / UCH-L3 / Ubiquitin thioesterase L3 Mass: 26998.436 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UCHL3 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15374, ubiquitinyl hydrolase 1
#2: Chemical	ChemComp-A1DFC / N-(3-{[(pyridin-2-yl)sulfanyl]methyl}phenyl)propanamide Mass: 292.784 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₁₃ClN₂OS
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.23 Å³/Da / Density % sol: 45 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 5% tacsimate 45% PEG8000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.98 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 1.95→50 Å / Num. obs: 50050 / % possible obs: 98.5 % / Redundancy: 6.2 % / CC_1/2: 0.993 / CC star: 0.998 / R_merge(I) obs: 0.149 / R_pim(I) all: 0.064 / R_rim(I) all: 0.162 / Χ²: 1.264 / Net I/σ(I): 4.7 / Num. measured all: 308677

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.95-2.02	6.2	1.854	4985	0.573	0.853	0.792	2.021	1.019	98.4
2.02-2.1	6.2	1.419	4996	0.61	0.871	0.61	1.548	1.062	98.7
2.1-2.2	6.2	1.006	4971	0.805	0.944	0.433	1.098	1.152	99
2.2-2.31	6	0.727	4995	0.881	0.968	0.317	0.795	1.289	98.2
2.31-2.46	5.9	0.536	4925	0.917	0.978	0.237	0.587	1.386	97.4
2.46-2.65	6.6	0.427	5020	0.951	0.987	0.178	0.463	1.408	99.5
2.65-2.91	6.5	0.302	5042	0.973	0.993	0.127	0.328	1.544	99.1
2.91-3.33	6.1	0.182	4989	0.984	0.996	0.08	0.199	1.332	98.2
3.33-4.2	6	0.112	4998	0.993	0.998	0.05	0.123	1.29	97.9
4.2-50	6.1	0.07	5129	0.997	0.999	0.03	0.076	1.138	98.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-3000		data scaling
HKL-3000		data reduction
PHENIX		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→43.96 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.9 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.253	2398	4.8 %
R_work	0.2058	-	-
obs	0.2081	49907	96.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.95→43.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4994	0	36	203	5233

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	5143
X-RAY DIFFRACTION	f_angle_d	1.266	6981
X-RAY DIFFRACTION	f_dihedral_angle_d	7.735	679
X-RAY DIFFRACTION	f_chiral_restr	0.073	779
X-RAY DIFFRACTION	f_plane_restr	0.012	914

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 (%)
1.95-1.99	0.3902	110	0.3609	2128	X-RAY DIFFRACTION	74
1.99-2.03	0.3731	144	0.3483	2815	X-RAY DIFFRACTION	97
2.03-2.08	0.3336	128	0.3264	2817	X-RAY DIFFRACTION	98
2.08-2.13	0.3783	141	0.302	2819	X-RAY DIFFRACTION	99
2.13-2.19	0.2917	132	0.2888	2874	X-RAY DIFFRACTION	99
2.19-2.26	0.3283	147	0.2667	2802	X-RAY DIFFRACTION	98
2.26-2.33	0.3196	158	0.248	2798	X-RAY DIFFRACTION	98
2.33-2.41	0.2989	136	0.2449	2746	X-RAY DIFFRACTION	96
2.41-2.51	0.3024	142	0.2315	2842	X-RAY DIFFRACTION	99
2.51-2.62	0.3178	142	0.2304	2906	X-RAY DIFFRACTION	99
2.62-2.76	0.3235	147	0.2333	2836	X-RAY DIFFRACTION	99
2.76-2.93	0.3181	155	0.2413	2833	X-RAY DIFFRACTION	99
2.93-3.16	0.2685	141	0.225	2854	X-RAY DIFFRACTION	99
3.16-3.48	0.2687	140	0.2059	2758	X-RAY DIFFRACTION	96
3.48-3.98	0.2129	154	0.1705	2872	X-RAY DIFFRACTION	99
3.98-5.02	0.186	148	0.1503	2878	X-RAY DIFFRACTION	99
5.02-43.96	0.1954	133	0.1708	2931	X-RAY DIFFRACTION	99

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	2.5223	-1.4791	-0.3335	1.8299	-0.5938	0.7456	-0.4583	1.1093	0.1235	-0.4452	0.2407	0.3731	0.1555	-0.5129	-0.0582	0.4328	-0.044	-0.1141	0.4546	-0.0714	0.4447	-8.1915	7.5585	3.3722
2	0.7131	-0.6924	-0.5795	3.2726	-1.2183	1.8325	-0.198	0.135	0.4457	-0.5179	0.3416	0.7451	0.4353	-0.3301	-0.1663	0.3248	-0.0404	-0.115	0.5678	-0.0163	0.4543	-10.7594	18.4335	3.7607
3	0.3433	0.2803	-0.5969	1.818	-0.9668	1.5786	-0.0118	0.0563	0.0464	-0.1567	0.1297	0.2986	-0.119	-0.3445	-0.0902	0.2617	-0.0068	-0.0877	0.4101	-0.0031	0.2926	-2.5819	23.2374	2.2149
4	5.9385	-1.3272	-3.3432	3.607	1.7011	2.1652	0.1537	-0.4293	-0.0349	0.2731	0.0302	-0.3206	-0.0248	0.5497	-0.2724	0.2892	-0.0365	-0.0342	0.4331	0.0022	0.405	16.8214	19.3508	13.7466
5	4.1505	-0.8524	0.1125	2.769	-0.6058	2.6271	-0.0759	-0.1213	0.1844	0.1422	-0.0056	0.0955	-0.2192	-0.3051	-0.1209	0.2153	0.0009	-0.0415	0.4205	0.0058	0.2188	2.7075	13.4032	19.1103
6	5.7347	-2.5449	0.2253	5.385	0.6388	3.7229	-0.1134	-0.1787	-0.1792	0.3284	0.1075	0.3801	0.0335	-0.3959	-0.0006	0.2604	-0.0659	-0.0451	0.391	0.0346	0.2796	-6.7397	14.4795	14.5634
7	5.4764	-1.1257	0.5916	3.3249	0.309	3.2322	-0.1164	-0.7785	-0.487	0.3348	0.1251	0.6862	0.4991	-1.0732	-0.0534	0.3328	-0.0195	0.0333	0.6121	0.0716	0.3893	-12.5949	9.0192	20.4496
8	4.7972	0.9079	0.6426	2.1319	1.6203	4.4963	0.1808	-1.0969	-0.807	1.0724	0.1171	-0.0503	0.4498	0.1546	-0.0932	0.3352	0.014	0.0145	0.5214	0.0864	0.3739	-0.0859	3.52	22.2899
9	3.8059	1.1963	-0.4533	3.9684	-1.9239	1.531	-0.6173	0.4926	-1.2874	-0.5729	0.3029	-0.4858	0.6611	0.0807	-0.0752	0.5395	-0.062	0.0073	0.4247	-0.1177	0.5478	-1.0412	1.2966	7.7117
10	3.0653	0.9023	1.2478	3.2884	-0.1208	4.7337	-0.0935	-0.1588	0.2696	0.0855	0.0414	0.0115	-0.3035	0.2339	0.0261	0.2598	0.0208	-0.0556	0.3413	-0.0468	0.2801	2.0233	21.8108	14.5302
11	3.3595	-2.0097	-5.272	5.03	2.2955	8.6665	0.2154	-0.4435	0.5961	-0.2421	-0.0161	-0.2667	-0.3471	0.7655	-0.15	0.3251	-0.0563	-0.094	0.4044	0.0087	0.4208	5.5272	26.1363	4.5471
12	6.4205	0.3098	-4.4687	4.5646	0.726	8.3433	-0.7021	0.6763	0.0199	-0.4866	0.1245	0.096	0.4621	0.1491	0.4219	0.3484	-0.0454	-0.0597	0.3534	0.051	0.2355	1.3728	18.9122	-0.4347
13	3.9752	1.9748	1.2614	7.1033	0.5381	2.6421	0.3443	-0.9626	-0.0082	0.9955	-0.2004	0.3443	0.36	0.0891	-0.0815	0.4191	0.0339	0.1254	0.662	0.0997	0.3118	1.2511	-16.3485	34.8076
14	1.4397	-1.4919	1.3199	2.024	-1.0115	2.1932	-0.1512	-0.2384	-0.1539	0.0224	0.2175	-0.162	0.1606	0.0082	-0.0197	0.3594	0.0372	0.0713	0.5776	0.0468	0.3079	14.1428	-20.2279	31.289
15	4.6301	1.4664	2.1366	4.6964	1.7917	5.0833	-0.2044	0.7255	0.1979	-0.2857	0.053	-0.3546	-0.3917	0.9457	-0.0018	0.2065	-0.0189	0.0347	0.4393	0.0139	0.2789	14.6667	-2.6785	12.2569
16	4.2027	-1.3294	-0.6546	1.4373	0.6451	2.8115	0.0732	-0.2237	-0.4976	0.0035	0.0113	0.2661	0.5618	-0.4952	-0.046	0.3501	-0.1319	-0.0501	0.4084	0.0913	0.3541	0.2035	-20.8816	19.746
17	4.6172	-0.5851	0.0932	5.0197	0.7828	2.2273	0.1821	-0.9182	0.2707	0.3246	-0.0357	0.4069	-0.3356	-1.2287	-0.101	0.3444	-0.1133	-0.0369	0.7174	0.0509	0.4604	-7.6343	-15.6182	24.7436
18	5.7429	0.5633	-2.8153	0.1458	0.0931	2.9816	1.1894	-1.2446	0.6703	0.9255	-0.4875	0.5472	-0.5462	0.4283	-0.5752	0.8736	-0.0537	0.0864	1.307	0.0241	0.588	4.5188	-2.2877	35.1688
19	1.2894	-1.7244	0.3205	3.0941	-1.6114	2.3094	0.0789	0.0768	0.0784	-0.2138	-0.2071	-0.0803	0.0224	-0.0398	0.1229	0.2963	-0.0051	-0.049	0.4466	0.0318	0.2769	12.4504	-16.9092	17.4301
20	2.4877	-1.1923	0.8683	7.4531	0.6847	1.7693	-0.3471	0.4743	0.2209	0.1024	0.4379	-0.1615	0.0682	0.6588	-0.111	0.337	-0.023	-0.0627	0.6404	0.0541	0.3415	21.0788	-12.6323	23.465
21	4.2899	-0.3992	1.3536	4.8521	2.3316	2.3218	0.086	-0.6132	0.0278	0.7217	-0.1605	-0.445	0.0657	0.1969	0.0338	0.2968	0.0032	-0.0592	0.5654	0.0414	0.2525	15.5987	-11.5929	31.3515
22	9.4235	4.3108	-6.515	4.3336	-4.2605	5.1885	0.5652	0.8388	0.8075	0.2067	0.6045	0.862	-1.4242	-1.7158	-1.1972	0.8482	0.2072	0.006	1.0105	0.1411	0.5573	-3.2763	33.1398	37.3294
23	2.6772	-1.9375	-0.5534	2.2245	1.2524	5.3925	0.1215	0.2834	-0.0281	-0.3231	-0.186	-0.0696	-0.2914	-0.289	0.0177	0.3086	-0.0503	-0.0373	0.5683	0.0118	0.3147	6.7507	23.9934	34.6869
24	2.158	0.7057	3.4506	5.754	-0.5081	7.5837	-0.266	-0.0568	-0.0624	0.6441	0.1456	0.87	0.2648	-0.9436	0.0321	0.5522	-0.0867	0.0827	0.5263	-0.0412	0.4666	-1.4169	10.8296	55.9358
25	3.6858	-0.0467	-0.8339	4.042	-1.7129	2.376	0.0994	-0.0589	0.6791	-0.0089	0.0912	0.0101	-0.707	-0.2071	-0.191	0.6611	-0.013	0.0525	0.5025	-0.0614	0.3321	5.4033	32.7488	50.0886
26	2.8652	0.124	-0.7212	5.0661	-1.0299	7.1616	0.0353	-0.0572	0.1154	0.0599	0.1179	0.3374	-0.3624	-0.1458	-0.1579	0.374	-0.0502	-0.0299	0.6059	-0.0261	0.289	4.8843	22.6732	48.08
27	2.7511	3.3447	-1.0295	7.6899	-0.4907	3.2348	0.4428	-0.2471	-0.4362	0.4766	0.0481	0.1797	-0.2334	-0.4386	-0.4558	0.4616	-0.0801	-0.0942	0.8915	-0.0546	0.4611	1.3481	18.7219	36.344

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 22 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 38 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 59 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 60 through 76 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 77 through 94 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 95 through 110 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 111 through 130 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 131 through 140 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 141 through 167 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 168 through 200 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 201 through 216 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 217 through 230 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 4 through 22 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 23 through 59 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 60 through 76 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 77 through 130 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 131 through 151 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 152 through 167 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 168 through 200 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 201 through 216 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 217 through 230 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 5 through 22 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 23 through 59 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 60 through 76 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 77 through 130 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 131 through 215 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 216 through 230 )

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About Yorodumi

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Yorodumi