Research workbench
Human DPP1 in complex with (2S)-N-((1S)-1-cyano-2-(4-(4-cyanophenyl) PHENYL)ETHYL)PIPERIDINE-2-carboxamide
Analyse Human DPP1 in complex with (2S)-N-((1S)-1-cyano-2-(4-(4-cyanophenyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CDD
- Type
- protein
- Length
- 692 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 1 exclusion domain chain; Dipeptidyl peptidase 1 heavy chain…
- EC
- 3.4.14.1
- UniProt
- P53634
- Ligands
- GDI, NAG, CL
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 1 exclusion domain chain (EC 3.4.14.1) | protein | 118 | 6% helix, 59% strand | P53634 |
| B | Dipeptidyl peptidase 1 heavy chain (EC 3.4.14.1) | protein | 162 | 33% helix, 15% strand | P53634 |
| C, F | Dipeptidyl peptidase 1 light chain (EC 3.4.14.1) | protein | 68 | 4% helix, 41% strand | P53634 |
| D | Dipeptidyl peptidase 1 exclusion domain chain (EC 3.4.14.1) | protein | 115 | 3% helix, 54% strand | P53634 |
| E | Dipeptidyl peptidase 1 heavy chain (EC 3.4.14.1) | protein | 161 | 34% helix, 15% strand | P53634 |
Ligands and binding sites
- GDI · (2S)-N-[(2S)-1-azanylidene-3-[4-(4-cyanophenyl)phenyl]propan-2-yl]piperidine-2-carboxamide · ligand · 2 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, C, B, D, E
- CL · Chloride ion · ion · 2 copies · chains B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.56 | 0.88 | 20 | GDI, CL |
| 2 | 217 | 0.56 | 0.79 | 36 | empty |
| 3 | 194 | 0.56 | 0.80 | 34 | empty |
| 4 | 67 | 0.54 | 0.87 | 24 | GDI, CL |
| 5 | 250 | 0.53 | 0.76 | 38 | empty |
Interfaces
11 interfaces between chains.
- E–F · 3010 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 3002 Ų buried · 58 hydrogen bonds · protein-protein
- D–E · 931 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 919 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 376 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 4CDD · Human DPP1 in complex with (2S)-N-((1S)-1-cyano-2-(4-(4-cyanophenyl)… · the same entry in another collection · chain F against F, TM-score 1.00
- P53634 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 1 (P53634) · a predicted model of the same protein · chain B against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P53634
- Elsewhere: RCSB PDB 4CDD · PDBe 4CDD · UniProt P53634
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.