13CV: Ubiquitin carboxyl-terminal hydrolase isozyme L3

Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(pyridin-2-yl)benzamide bound to Ubiquitin C-terminal Hydrolase-L3. Determined by X-ray diffraction at 1.94 Å resolution. Released 26 Aug 2026.

Method: X-ray diffraction
Resolution: 1.94 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,205
Mol. weight: 108.62 kDa
Ligands: A1DFD
Released: 26 Aug 2026

Explore 13CV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

13CV contains 39 α-helices and 32 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
α-helix	13-22	10
β-strand	25	1	1
β-strand	29-33	5	2
α-helix	39-42	4
β-strand	49-57	9	2
α-helix	60-76	17
α-helix	95-105	11
α-helix	108-110	3
β-strand	113	1	1
α-helix	118-125	8
α-helix	131-140	10
α-helix	162-164	3
β-strand	168-176	9	2
β-strand	179-183	5	2
β-strand	191-195	5	2
α-helix	201-215	15
β-strand	223-229	7	2

Chain B: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
α-helix	13-22	10
β-strand	25	1	3
β-strand	29-34	6	4
α-helix	39-42	4
β-strand	49-57	9	4
α-helix	60-76	17
α-helix	95-105	11
α-helix	108-110	3
β-strand	113	1	3
α-helix	118-126	9
α-helix	131-140	10
β-strand	168-176	9	4
β-strand	179-183	5	4
β-strand	191-195	5	4
α-helix	201-215	15
β-strand	223-229	7	4

Chain C: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
α-helix	13-22	10
β-strand	25	1	5
β-strand	29-33	5	6
α-helix	39-42	4
β-strand	49-57	9	6
α-helix	60-76	17
α-helix	95-105	11
α-helix	108-110	3
β-strand	113	1	5
α-helix	114	1
α-helix	118-126	9
α-helix	131-140	10
β-strand	168-176	9	6
β-strand	179-183	5	6
β-strand	191-195	5	6
α-helix	201-215	15
β-strand	223-229	7	6

Chain D: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
α-helix	13-22	10
β-strand	25	1	7
β-strand	29-34	6	8
α-helix	39-42	4
β-strand	49-57	9	8
α-helix	60-76	17
α-helix	95-105	11
β-strand	113	1	7
α-helix	118-125	8
α-helix	131-140	10
α-helix	159-161	3
α-helix	162-164	3
β-strand	168-176	9	8
β-strand	179-183	5	8
β-strand	191-195	5	8
α-helix	201-214	14
β-strand	223-229	7	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase isozyme L3	A, B, C, D	protein	235	Homo sapiens	P15374 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>13CV_1 Ubiquitin carboxyl-terminal hydrolase isozyme L3 (chains A, B, C, D)
GPLGSMEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLL
FPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFES
GSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVH
VDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA

Ligands and cofactors

ID	Name	Formula	Copies
A1DFD	3-(2-chloroacetamido)-N-(pyridin-2-yl)benzamide	C14 H12 Cl N3 O2	4

Water and common crystallization additives (SO4) are not listed.

Primary citation

Identification, optimization, and structural elucidation of chloroacetamide scaffold as covalent inhibitors for Ubiquitin C-terminal Hydrolase L3. Beeralingappa, N.C., Lu, M., Patel, R. et al. bioRxiv (2026). DOI 10.64898/2026.05.26.727856

Other PDB entries of the same protein (UniProt P15374 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1XD3 1.45 Å, Crystal structure of UCHL3-UbVME complex
7YV4 1.58 Å, Crystal structure of human UCHL3 in complex with Farrerol
1UCH 1.8 Å, Deubiquitinating enzyme uch-L3 (HUMAN) at 1.8 Å resolution
13DF 1.84 Å, Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(3-methoxyphenyl)benzamid…
6ISU 1.87 Å, Crystal structure of Lys27-linked di-ubiquitin in complex with its selective interacting…
13CU 1.95 Å, Crystal structure of covalent inhibitor 2-chloro-N-(3-((pyridin-2-ylthio)methyl)phenyl)ac…
6QML 2.1 Å, UCHL3 in complex with synthetic, K27-linked diubiquitin
13CW 2.48 Å, Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(m-tolyl)benzamide bound…
35YH 2.6 Å, Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(3-hydroxyphenyl)benzamid…

Browse structure collections

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