PDB-13cv: Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(...

ID or keywords:

Entry

Database: PDB / ID: 13cv

Title

Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(pyridin-2-yl)benzamide 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: 1.94 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	13cv.cif.gz	365.4 KB	Display	PDBx/mmCIF format
PDB format	pdb13cv.ent.gz		Display	PDB format
PDBx/mmJSON format	13cv.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/13cv ftp://data.pdbj.org/pub/pdb/validation_reports/3c/13cv	HTTPS FTP

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Related structure data

Related structure data	13cuC 13cwC 13dfC 35yhC 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

D: Ubiquitin carboxyl-terminal hydrolase isozyme L3

hetero molecules

109 kDa, 4 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
27.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Ubiquitin carboxyl-terminal hydrolase isozyme L3

hetero molecules

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

4

D: Ubiquitin carboxyl-terminal hydrolase isozyme L3

hetero molecules

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

Unit cell

Length a, b, c (Å)	48.029, 85.605, 124.078
Angle α, β, γ (deg.)	90.00, 96.81, 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: 26625.031 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UCHL3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15374, ubiquitinyl hydrolase 1
#2: Chemical	ChemComp-A1DFD / 3-(2-chloroacetamido)-N-(pyridin-2-yl)benzamide Mass: 289.717 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₁₂ClN₃O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.36 Å³/Da / Density % sol: 48 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 200 mM Bis-Tris Propane 2.5 M Ammonium Sulfate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 0.98 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 13, 2024

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 1.94→50 Å / Num. obs: 71476 / % possible obs: 98.2 % / Redundancy: 5.5 % / CC_1/2: 0.995 / CC star: 0.999 / R_merge(I) obs: 0.128 / R_pim(I) all: 0.058 / R_rim(I) all: 0.141 / Χ²: 1.158 / Net I/σ(I): 8.2

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	5.3	1.213	7025	0.592	0.862	0.56	1.34	1.193	97
2.02-2.1	5.7	0.967	7226	0.747	0.925	0.423	1.058	1.194	99.7
2.1-2.2	5.7	0.67	7233	0.857	0.961	0.294	0.733	1.196	99.7
2.2-2.31	5.7	0.498	7174	0.91	0.976	0.221	0.546	1.186	99.1
2.31-2.46	5.5	0.383	7179	0.935	0.983	0.172	0.421	1.196	99.2
2.46-2.65	5.4	0.282	7182	0.959	0.989	0.129	0.311	1.154	98.6
2.65-2.91	5.2	0.209	6887	0.972	0.993	0.098	0.232	1.198	94.9
2.91-3.33	5.8	0.138	7248	0.988	0.997	0.062	0.152	1.121	99.5
3.33-4.2	5.4	0.09	7155	0.993	0.998	0.042	0.1	1.041	97.8
4.2-50	5.5	0.067	7188	0.996	0.999	0.031	0.074	1.102	96.5

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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: 1.94→42.8 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.71 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2437	3829	2.78 %
R_work	0.2036	-	-
obs	0.2047	71476	95.59 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.94→42.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6744	0	126	305	7175

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	7052
X-RAY DIFFRACTION	f_angle_d	2.038	9585
X-RAY DIFFRACTION	f_dihedral_angle_d	7.265	922
X-RAY DIFFRACTION	f_chiral_restr	0.134	1056
X-RAY DIFFRACTION	f_plane_restr	0.014	1255

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 (%)
1.94-1.97	0.3108	106	0.3718	3663	X-RAY DIFFRACTION	71
1.97-2	0.3884	145	0.3555	4979	X-RAY DIFFRACTION	95
2-2.02	0.4121	132	0.3296	5098	X-RAY DIFFRACTION	99
2.02-2.05	0.3576	143	0.3168	5120	X-RAY DIFFRACTION	99
2.05-2.08	0.3663	150	0.3156	5153	X-RAY DIFFRACTION	99
2.08-2.11	0.3202	143	0.2948	5070	X-RAY DIFFRACTION	99
2.11-2.15	0.2871	158	0.2782	5147	X-RAY DIFFRACTION	99
2.15-2.19	0.2998	128	0.2625	5191	X-RAY DIFFRACTION	98
2.19-2.23	0.3492	148	0.2488	5094	X-RAY DIFFRACTION	99
2.23-2.27	0.31	170	0.2417	5057	X-RAY DIFFRACTION	98
2.27-2.32	0.2586	144	0.2262	5116	X-RAY DIFFRACTION	98
2.32-2.37	0.2749	130	0.2266	5091	X-RAY DIFFRACTION	98
2.37-2.42	0.2372	148	0.2271	5074	X-RAY DIFFRACTION	98
2.42-2.48	0.2348	154	0.226	5081	X-RAY DIFFRACTION	98
2.48-2.55	0.2763	147	0.2238	5087	X-RAY DIFFRACTION	97
2.55-2.62	0.2313	135	0.2179	4973	X-RAY DIFFRACTION	97
2.62-2.71	0.2471	146	0.2265	4922	X-RAY DIFFRACTION	94
2.71-2.8	0.2984	147	0.2396	4630	X-RAY DIFFRACTION	89
2.8-2.92	0.2543	137	0.2179	4942	X-RAY DIFFRACTION	96
2.92-3.05	0.2305	141	0.213	5147	X-RAY DIFFRACTION	98
3.05-3.21	0.2666	147	0.2022	5079	X-RAY DIFFRACTION	97
3.21-3.41	0.2458	148	0.1949	5020	X-RAY DIFFRACTION	97
3.41-3.67	0.3026	141	0.1722	4874	X-RAY DIFFRACTION	94
3.67-4.04	0.1825	127	0.16	4863	X-RAY DIFFRACTION	93
4.04-4.63	0.1657	147	0.15	4719	X-RAY DIFFRACTION	92
4.63-5.83	0.1742	122	0.1652	4757	X-RAY DIFFRACTION	91
5.83-42.8	0.2413	145	0.1838	5131	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	0.5566	-0.3705	-1.1783	5.3908	-0.3534	4.7261	-0.1418	0.0601	-0.0997	0.0988	0.2067	0.4595	0.252	-0.5303	-0.0371	0.2638	-0.1074	0.0424	0.4487	-0.0732	0.3705	-20.3867	-0.9288	-63.7544
2	1.3778	-0.2139	-0.3642	2.8486	0.3834	1.2613	0.0074	-0.0359	-0.0175	0.0447	0.0568	-0.1161	-0.002	0.0388	-0.0522	0.1742	-0.0173	0.0197	0.3209	0.0007	0.2805	-12.2168	8.5366	-50.9696
3	0.8692	0.2037	-1.2749	5.0817	0.2252	3.9878	0.0878	0.2483	0.2387	-0.4626	0.0316	0.1694	-0.3972	-0.2353	-0.1514	0.2337	-0.0066	-0.0252	0.4012	0.0458	0.2788	-18.7256	14.9477	-65.8334
4	3.4382	0.0739	-1.1094	2.9563	0.1879	2.8269	-0.0674	-0.002	-0.2032	0.1498	0.0261	0.0557	0.2422	0.0078	0.0621	0.2098	0.0059	0.0366	0.2174	0	0.2541	-11.7251	4.1369	-52.2627
5	2.88	0.5824	0.9013	9.1314	-1.1863	0.5252	-0.3299	-0.3339	0.4395	-0.1327	-0.1694	-0.6589	0.1747	-0.3354	0.6866	0.5432	-0.0046	-0.1438	0.343	-0.0198	0.5187	-26.2587	23.898	-20.1738
6	2.3872	-1.8131	0.8434	3.8728	-0.4353	2.3382	-0.3321	-0.3414	0.2776	0.8025	0.0711	0.1305	-0.4192	-0.1158	0.2826	0.5688	-0.0148	0.0577	0.2682	-0.063	0.3807	-37.7357	27.2332	-22.0406
7	3.6085	-3.1719	3.657	3.8978	-2.6533	8.6325	0.0637	0.1631	-0.2956	0.1957	-0.0226	0.3176	0.4477	-0.1352	-0.1062	0.2859	-0.0369	0.0931	0.2149	-0.0569	0.4042	-39.5285	7.7105	-39.4717
8	1.7351	-1.1074	0.2236	3.014	-0.0133	2.3587	-0.0314	0.1404	0.7707	-0.3068	-0.1178	-0.8946	-0.4198	0.2885	0.1566	0.3584	-0.0621	0.0532	0.2726	0.067	0.5919	-28.4949	28.7491	-37.5144
9	2.2253	-0.4362	-0.7864	3.5049	-0.369	3.626	0.063	-0.0339	0.5794	-0.0332	-0.1488	-1.0312	-0.072	0.6226	0.0886	0.3056	-0.0418	0.053	0.3167	0.0006	0.5734	-24.6645	20.8438	-32.857
10	5.0811	-2.1812	-0.9633	4.5355	0.1318	3.8492	-0.0677	0.4926	0.0336	0.0397	-0.1394	0.153	-0.0111	-0.2277	-0.01	0.2609	-0.0117	0.0421	0.2178	-0.0073	0.3082	-40.494	21.557	-38.3518
11	4.3018	-3.5842	1.4067	3.2924	-2.5168	5.8712	-0.4923	-0.4744	-0.2336	0.1142	0.5185	0.3382	-0.1489	-0.4494	0.0132	0.4374	0.003	0.1543	0.3674	-0.0214	0.4344	-45.6237	21.0167	-27.7841
12	3.8409	-1.2359	0.6877	2.5853	-1.7581	5.05	-0.3064	0.0311	-0.0291	0.7105	0.2076	-0.2597	-0.1	-0.0713	0.1194	0.4516	0.0499	0.1757	0.2362	0.0086	0.3308	-37.5008	17.4722	-21.8987
13	9.8002	0.5742	-5.3882	1.5552	-0.4303	3.0619	0.6705	0.1992	0.5097	0.2361	-0.0589	0.4124	-0.9011	-0.3946	-0.2441	0.6302	0.0626	0.2242	0.3588	0.0977	0.5443	-53.3832	0.047	-6.4712
14	2.2865	-0.8042	0.9401	2.9888	1.3845	3.8563	-0.6648	-0.3629	-0.0231	0.5495	0.2987	0.0906	-0.5556	-0.0144	-0.5779	0.9636	0.1435	0.5611	0.3831	0.0074	0.5707	-47.2283	8.0068	3.9208
15	0.674	0.1133	0.1019	2.5644	-1.9515	3.1216	0.1329	-0.009	0.1354	0.0755	-0.0689	-0.3775	0.0619	0.3985	-0.0338	0.5776	-0.0476	0.1127	0.3011	-0.049	0.4363	-30.9339	-6.6743	-6.1324
16	1.4207	0.2532	0.6619	2.639	0.3188	4.2045	-0.0572	-0.287	-0.1948	0.4764	0.032	0.5726	0.4862	-0.2009	0.0212	0.7164	0.0001	0.2388	0.342	0.0614	0.4722	-48.2657	-13.6987	1.2576
17	3.2289	0.2827	1.393	3.2814	1.4753	4.725	-0.0276	-0.2061	0.0581	0.5487	-0.066	0.0112	0.1378	0.0013	0.0966	0.6812	-0.0171	0.1506	0.2849	0.0411	0.3681	-37.7162	-5.5855	0.0881
18	2.9093	-0.0401	-0.1305	4.6384	-0.9426	3.6382	0.1538	-0.2343	0.2308	0.304	-0.0131	-0.1764	-0.073	0.1041	-0.1854	0.6844	-0.0207	0.1707	0.2366	-0.005	0.4036	-36.4837	4.2614	-3.3755
19	4.2029	-0.6529	2.5245	2.9349	-3.3022	8.1894	0.2368	0.4719	0.4596	-0.1123	-0.581	-1.276	1.0433	0.8063	0.2799	0.6087	0.1284	0.039	0.4366	0.0147	0.6311	-16.6737	-21.782	-31.0432
20	1.0226	0.8182	1.614	5.2683	0.0638	2.8965	-0.0967	0.1201	-0.3858	0.5569	-0.0156	-1.3092	1.4653	0.5092	-0.1542	1.1172	0.1136	0.1706	0.3552	-0.0634	0.7258	-21.465	-31.5093	-31.9743
21	2.1098	-1.4805	-0.3646	4.2209	1.656	1.6183	0.0288	0.1383	0.0082	0.1025	-0.1428	0.4812	0.1522	-0.1967	0.0903	0.4509	-0.0703	0.1494	0.2847	0.0041	0.4012	-34.2941	-16.0519	-36.8937
22	2.98	1.2007	0.2633	3.0787	0.353	3.4444	-0.0947	-0.2573	-0.4852	0.8283	0.0827	0.2492	0.9519	-0.036	0.0188	1.0696	-0.0543	0.227	0.3163	0.0192	0.5431	-31.1087	-26.7651	-21.2204
23	1.3243	-0.8339	-0.4555	3.4656	0.4555	4.2161	-0.102	0.0121	-0.1839	0.3442	-0.0334	0.0955	0.453	-0.1092	0.0756	0.5395	-0.0649	0.2343	0.2922	-0.0329	0.4911	-31.546	-19.172	-30.9987

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 38 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 39 through 94 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 95 through 161 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 162 through 230 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 5 through 22 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 23 through 59 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 60 through 76 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 77 through 130 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 131 through 176 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 177 through 197 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 198 through 215 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 216 through 230 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 5 through 23 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 24 through 48 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 49 through 76 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 77 through 161 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 162 through 200 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 201 through 230 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 5 through 22 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 23 through 34 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 35 through 76 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 77 through 130 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 131 through 230 )

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi