MolNFT v1 · #87851 · protein
Human DPP1 in complex with (2S,4S)-N-((1S)-1-cyano-2-(4-(4- CYANOPHENYL)PHENYL)ETHYL)-4-hydroxy-piperidine-2-carboxamide
4CDF · Dipeptidyl peptidase 1 exclusion domain chain: “Human DPP1 in complex with (2S,4S)-N-((1S)-1-cyano-2-(4-(4…”. X-ray diffraction, 3 ligands (W2C, NAG, CL), 9 pockets (best druggability 0.61). MolNFT v1 #87851 on GenesisL1: 3D…
- PDB
- 4CDF
- Type
- protein
- Length
- 699 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
- W2C, NAG, CL
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 1 exclusion domain chain (EC 3.4.14.1) | protein | 120 | 6% helix, 57% 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 | 118 | 3% helix, 59% strand | P53634 |
| E | Dipeptidyl peptidase 1 heavy chain (EC 3.4.14.1) | protein | 163 | 35% helix, 13% strand | P53634 |
Ligands and binding sites
- W2C · (2S,4S)-N-[(2S)-1-azanylidene-3-[4-(4-cyanophenyl)phenyl]propan-2-yl]-4-oxidanyl-piperidine-2-carboxamide · ligand · 2 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.61 | 0.90 | 21 | W2C, CL |
| 2 | 245 | 0.59 | 0.79 | 38 | empty |
| 3 | 192 | 0.56 | 0.79 | 26 | empty |
| 4 | 280 | 0.53 | 0.75 | 40 | empty |
| 5 | 186 | 0.51 | 0.78 | 30 | empty |
Interfaces
11 interfaces between chains.
- B–C · 3025 Ų buried · 54 hydrogen bonds · protein-protein
- E–F · 3022 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 941 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 938 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 366 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
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 4CDF · PDBe 4CDF · UniProt P53634
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