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

ID or keywords:

Entry

Database: PDB / ID: 13cw

Title

Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(m-tolyl)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: 2.48 Å

Authors

Pannala, N. / Patel, R. / 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	13cw.cif.gz	352.5 KB	Display	PDBx/mmCIF format
PDB format	pdb13cw.ent.gz		Display	PDB format
PDBx/mmJSON format	13cw.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/13cw ftp://data.pdbj.org/pub/pdb/validation_reports/3c/13cw	HTTPS FTP

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Related structure data

Related structure data	13cuC 13cvC 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
27.5 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
27.4 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
27.3 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
27.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	47.814, 85.406, 124.129
Angle α, β, γ (deg.)	90.00, 97.65, 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.: 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-A1DFF / 3-(2-chloroacetamido)-N-(3-methylphenyl)benzamide Mass: 302.756 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₆H₁₅ClN₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H₂O
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: 2.35 Å³/Da / Density % sol: 47.6 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: Bis-Tris Propane 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: 2.48→50 Å / Num. obs: 67155 / % possible obs: 97.8 % / Redundancy: 6.6 % / CC_1/2: 0.993 / CC star: 0.998 / R_merge(I) obs: 0.152 / R_pim(I) all: 0.064 / R_rim(I) all: 0.165 / Χ²: 1.25 / Net I/σ(I): 8

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
2.5-2.59	6.3	1.512	3406	0.508	0.821	0.645	1.648	1.102	97.8
2.59-2.69	6.2	1.151	3470	0.689	0.903	0.495	1.256	1.167	98.1
2.69-2.82	5.7	0.928	3256	0.699	0.907	0.418	1.022	1.191	93.6
2.82-2.96	6.5	0.662	3409	0.871	0.965	0.276	0.719	1.25	97.6
2.96-3.15	7.1	0.422	3472	0.954	0.988	0.168	0.455	1.373	99.1
3.15-3.39	7.1	0.265	3482	0.978	0.995	0.106	0.286	1.44	99.3
3.39-3.73	7	0.172	3503	0.989	0.997	0.07	0.186	1.412	99.4
3.73-4.27	6.7	0.116	3499	0.992	0.998	0.049	0.126	1.243	99.5
4.27-5.38	6.2	0.085	3383	0.993	0.998	0.037	0.093	1.116	95.3
5.38-50	6.9	0.064	3545	0.998	0.999	0.026	0.069	1.132	98.6

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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: 2.48→47.39 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.271	3935	5.86 %
R_work	0.2123	-	-
obs	0.2157	67155	97.31 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.48→47.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6561	0	95	94	6750

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	6803
X-RAY DIFFRACTION	f_angle_d	1.029	9254
X-RAY DIFFRACTION	f_dihedral_angle_d	7.486	900
X-RAY DIFFRACTION	f_chiral_restr	0.049	1049
X-RAY DIFFRACTION	f_plane_restr	0.008	1207

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 (%)
2.48-2.51	0.4184	142	0.3865	2194	X-RAY DIFFRACTION	91
2.51-2.54	0.4217	150	0.3875	2124	X-RAY DIFFRACTION	97
2.54-2.58	0.3515	133	0.3582	2289	X-RAY DIFFRACTION	98
2.58-2.61	0.3407	133	0.3298	2241	X-RAY DIFFRACTION	97
2.61-2.65	0.2944	127	0.3304	2368	X-RAY DIFFRACTION	98
2.65-2.69	0.3719	155	0.3212	2197	X-RAY DIFFRACTION	97
2.69-2.73	0.3544	143	0.3233	2192	X-RAY DIFFRACTION	95
2.73-2.77	0.3643	125	0.3229	2090	X-RAY DIFFRACTION	90
2.77-2.82	0.4195	132	0.3282	2201	X-RAY DIFFRACTION	93
2.82-2.87	0.365	131	0.2822	2227	X-RAY DIFFRACTION	98
2.87-2.93	0.3763	154	0.2824	2295	X-RAY DIFFRACTION	99
2.93-2.99	0.273	140	0.2729	2312	X-RAY DIFFRACTION	99
2.99-3.05	0.3275	120	0.2719	2298	X-RAY DIFFRACTION	99
3.05-3.12	0.318	167	0.2517	2262	X-RAY DIFFRACTION	99
3.12-3.2	0.287	140	0.237	2358	X-RAY DIFFRACTION	99
3.2-3.29	0.2433	150	0.2084	2265	X-RAY DIFFRACTION	99
3.29-3.39	0.2976	148	0.2156	2326	X-RAY DIFFRACTION	99
3.39-3.49	0.2674	129	0.198	2263	X-RAY DIFFRACTION	99
3.49-3.62	0.2926	138	0.1963	2334	X-RAY DIFFRACTION	100
3.62-3.76	0.2648	148	0.1844	2331	X-RAY DIFFRACTION	100
3.76-3.94	0.2268	143	0.1874	2269	X-RAY DIFFRACTION	99
3.94-4.14	0.2259	146	0.165	2284	X-RAY DIFFRACTION	99
4.14-4.4	0.2439	136	0.1697	2328	X-RAY DIFFRACTION	99
4.4-4.74	0.2237	148	0.1664	2239	X-RAY DIFFRACTION	97
4.74-5.22	0.2405	127	0.1702	2161	X-RAY DIFFRACTION	93
5.22-5.97	0.2877	142	0.1825	2149	X-RAY DIFFRACTION	93
5.97-7.52	0.2214	142	0.1993	2320	X-RAY DIFFRACTION	100
7.52-47.39	0.2239	146	0.1725	2303	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	4.7575	-0.8244	-2.198	2.7681	2.2871	2.8739	-0.4565	-0.035	-0.5516	0.1941	0.1603	0.405	0.283	0.0409	0.3852	0.5323	-0.1246	0.0007	0.5981	-0.1025	0.4555	22.9565	-2.706	-0.9605
2	2.1209	-0.6483	-1.1225	3.1998	0.7783	4.2301	0.0315	0.2154	0.1133	-0.108	0.1622	-0.1459	-0.1574	-0.0432	-0.1565	0.2459	-0.0241	-0.0003	0.4213	0.0076	0.3343	26.6258	13.581	4.2677
3	1.5611	-0.5286	-1.5497	1.9832	-1.4609	4.2445	-0.2794	1.0039	0.4924	0.1212	0.2263	0.3672	-0.7724	-0.7134	0.0219	0.6988	0.0568	0.0686	0.8328	0.0084	0.4504	16.1911	18.5551	-1.0901
4	2.3836	-0.1546	-0.7004	4.3484	0.8848	2.9818	-0.0597	0.116	-0.2663	0.1645	0.0711	0.0278	0.1949	0.0916	-0.0307	0.2302	0.0075	-0.0142	0.3043	0.0148	0.2811	28.0355	4.5578	9.3478
5	4.4453	-2.4927	0.8953	2.5099	-1.0637	1.4333	-0.5881	-0.0894	0.0904	0.5871	0.1598	-0.1525	0.0604	-0.3469	0.4287	0.6785	-0.0132	-0.0103	0.44	-0.1319	0.5663	10.2221	28.0005	40.7612
6	3.1383	-1.2963	-0.3238	2.3303	0.5905	3.784	0.0094	0.1579	0.1098	0.08	-0.0904	-0.1225	0.1492	-0.1571	0.0663	0.2778	-0.0246	0.0312	0.2817	-0.0027	0.3453	4.7074	21.0359	27.6033
7	4.2303	-2.3609	-2.2869	6.4606	1.6246	2.7599	0.2393	-0.0473	0.9657	-1.4015	-0.1789	-1.8257	-0.9184	0.1101	-0.2366	0.946	0.0291	0.1445	0.5069	0.087	0.9861	16.3649	35.6343	24.1177
8	5.8695	-2.0348	-1.9867	5.1469	-0.8184	4.1978	0.0668	0.4688	0.9928	-0.6088	-0.187	-1.4992	0.2199	0.9635	-0.077	0.8591	0.0368	0.3243	0.7153	0.1438	1.0035	20.0072	24.8299	19.5602
9	3.2767	-0.4502	-0.3852	2.6573	0.7209	4.2507	0.1346	-0.0864	0.2499	-0.0353	-0.0305	-0.1515	-0.026	0.1701	0.019	0.3451	-0.0506	0.0725	0.3329	-0.0039	0.3997	6.09	21.6953	29.1533
10	2.8879	0.5219	-0.3667	4.2127	0.7899	3.3189	-0.0578	-0.2994	-0.094	0.0587	-0.2346	0.3701	0.5331	-0.2691	0.2396	0.4567	0.0077	0.1331	0.4356	-0.0668	0.4378	-1.3138	18.2487	36.815
11	5.2671	1.1626	-0.7344	3.9807	-0.3763	2.1505	0.1241	-0.1054	0.2325	0.9029	0.3467	0.4047	-0.5502	-0.256	-0.5713	0.8574	0.0944	0.281	0.4641	0.1351	0.5487	-9.7929	5.6988	60.8122
12	3.2081	-0.375	-0.9916	3.2293	-0.2528	1.055	-0.1835	-0.0534	-0.2507	0.1412	0.0901	-0.372	0.2093	0.332	-0.0393	0.6707	-0.0024	0.0843	0.4448	-0.0029	0.437	8.5386	-5.9511	55.5362
13	2.2328	-0.0395	0.2572	2.9117	0.0116	3.6974	0.0645	-0.3117	-0.2322	0.6589	-0.1372	0.2626	0.5087	0.1193	0.0843	1.0016	-0.0273	0.2391	0.4899	0.0575	0.5313	-7.6256	-13.4433	64.1616
14	0.363	-0.6401	0.7977	1.2325	-1.8627	3.633	-0.1145	0.1841	-0.0034	0.1897	0.182	0.5429	-0.3906	-0.1923	-0.1294	1.1392	-0.0307	0.2652	0.608	-0.0496	0.6897	-10.9916	-6.9343	48.7284
15	2.5183	-0.5497	-0.1373	2.4364	1.1522	1.6821	0.0957	-0.3926	0.2362	0.2451	0.175	-0.1238	-0.1602	0.2835	-0.2759	0.8724	-0.0042	0.0924	0.4523	0.0293	0.4509	3.3561	-5.1257	64.838
16	7.8673	0.9138	-2.4021	7.3652	-0.6023	8.9709	0.2561	-0.7484	0.0637	1.1805	0.3983	-0.758	-1.0855	0.6516	-0.759	0.68	-0.0803	0.0411	0.496	-0.0591	0.493	6.8121	4.6495	60.8197
17	3.9025	1.2987	-3.0226	3.8776	-1.5559	7.8609	0.4478	-0.3659	0.6812	-0.1308	0.3101	0.2821	-0.4121	0.5588	-0.7485	0.9723	0.0103	0.2527	0.5157	0.0794	0.5363	-0.9373	5.4741	55.5385
18	2.2347	-0.5217	-1.3537	4.8019	-1.4533	1.4625	0.3199	0.1593	0.169	1.4756	-0.0698	-0.5099	-1.185	0.5148	-0.1853	1.2459	-0.0065	-0.3058	0.7061	-0.0165	1.0047	23.4385	-18.3698	27.8111
19	1.009	0.4463	-0.0881	2.5123	1.6959	4.0102	-0.1281	-0.0817	-0.1853	0.6648	-0.1542	0.4771	0.6987	-0.1871	0.2981	0.8881	-0.0429	0.2122	0.3902	0.0108	0.6955	7.7469	-18.7952	28.7265
20	2.1684	0.8836	-0.5677	0.8679	-1.507	3.3921	0.1117	-0.03	-0.4684	1.1359	0.0039	0.3918	0.8878	0.0612	-0.0011	1.8307	-0.0611	0.2275	0.5887	0.0572	0.8963	10.6285	-26.7833	42.2881
21	2.0905	1.0492	0.4815	0.9037	-0.0486	0.3177	-0.2228	-1.8418	0.3914	0.9808	0.1037	0.4352	-0.0889	1.1687	-0.0235	1.4073	0.4243	0.1365	1.365	-0.0908	0.6443	20.5092	-13.2882	38.894
22	2.4304	0.1958	-0.1075	4.3192	1.6749	4.2508	0.0937	0.0261	-0.0583	-0.0744	-0.4185	0.5322	0.4311	-0.2765	0.2754	0.9781	-0.0659	0.3794	0.507	-0.0392	0.8453	5.9604	-19.2321	25.7032

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 48 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 130 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 131 through 159 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 160 through 230 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 5 through 38 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 39 through 110 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 111 through 130 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 131 through 141 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 142 through 200 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 201 through 229 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 4 through 48 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 49 through 76 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 77 through 140 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 141 through 167 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 168 through 200 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 201 through 216 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 217 through 230 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 0 through 23 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 24 through 94 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 95 through 140 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 141 through 167 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 168 through 230 )

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