Crystal structure of covalent inhibitor 2-chloro-N-(3-((pyridin-2-ylthio)methyl)phenyl)acetamide bound to Ubiquitin C-terminal Hydrolase-L3. Determined by X-ray diffraction at 1.95 Å resolution. Released 26 Aug 2026.
Explore 13CU in 3D Show helices and sheets RCSB PDB PDBe
13CU contains 30 α-helices and 24 β-strands across 3 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 6-8 | 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 | 131-139 | 9 | |
| α-helix | 142-144 | 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 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 13-22 | 10 | |
| β-strand | 25 | 1 | 3 |
| β-strand | 29-33 | 5 | 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 | |
| α-helix | 142-144 | 3 | |
| α-helix | 146-147 | 2 | |
| α-helix | 148-151 | 4 | |
| 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 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| 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 | 118-126 | 9 | |
| α-helix | 131-139 | 9 | |
| α-helix | 142-144 | 3 | |
| 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 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Ubiquitin carboxyl-terminal hydrolase isozyme L3 | A, B, C | protein | 238 | Homo sapiens | P15374 (AlphaFold model) |
>13CU_1 Ubiquitin carboxyl-terminal hydrolase isozyme L3 (chains A, B, C) GPLGSPEFMEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAV LLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMH FESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIA LVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA
| ID | Name | Formula | Copies |
|---|---|---|---|
| A1DFC | N-(3-{[(pyridin-2-yl)sulfanyl]methyl}phenyl)propanamide | C14 H13 Cl N2 O S | 2 |
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:
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