MolNFT v1 · #87848 · protein
Human DPP1 in complex with (2S)-2-amino-N-((1S)-1-cyano-2-(4- PHENYLPHENYL)ETHYL)BUTANAMIDE
4CDC · Dipeptidyl peptidase 1 exclusion domain chain: “Human DPP1 in complex with (2S)-2-amino-N-((1S)-1-cyano-2-(4- PHENYLPHENYL)ETHYL)BUTANAMIDE”. X-ray diffraction, 3 ligands (6AO, NAG, CL), 20 pockets (best druggability 0.78). MolNFT…
- PDB
- 4CDC
- Type
- protein
- Length
- 1,373 residues
- Chains
- 12
- 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
- 6AO, NAG, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, J | Dipeptidyl peptidase 1 exclusion domain chain (EC 3.4.14.1) | protein | 114 | 4% helix, 58% strand | P53634 |
| B, H, K | Dipeptidyl peptidase 1 heavy chain (EC 3.4.14.1) | protein | 162 | 31% helix, 15% strand | P53634 |
| C, F, I, L | 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 | 114 | 4% helix, 57% strand | P53634 |
| E | Dipeptidyl peptidase 1 heavy chain (EC 3.4.14.1) | protein | 159 | 34% helix, 15% strand | P53634 |
Ligands and binding sites
- 6AO · (2S)-2-azanyl-N-[(2S)-1-azanylidene-3-(4-phenylphenyl)propan-2-yl]butanamide · ligand · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, C, B, D, H, F, G, I, J, L, E, K
- CL · Chloride ion · ion · 4 copies · chains B, C, E, F, H, I, K, L
- GOL · Glycerol · additive · 4 copies · chains B, C, D, G, H, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.78 | 0.80 | 102 | empty |
| 2 | 1097 | 0.73 | 0.76 | 100 | empty |
| 3 | 263 | 0.56 | 0.77 | 39 | empty |
| 4 | 140 | 0.56 | 0.82 | 20 | empty |
| 5 | 259 | 0.55 | 0.77 | 42 | empty |
Interfaces
36 interfaces between chains.
- B–C · 3045 Ų buried · 58 hydrogen bonds · protein-protein
- E–F · 3042 Ų buried · 56 hydrogen bonds · protein-protein
- H–I · 3026 Ų buried · 56 hydrogen bonds · protein-protein
- K–L · 3012 Ų buried · 49 hydrogen bonds · protein-protein
- J–K · 971 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 7 glycan, 4 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 4CDC · Human DPP1 in complex with (2S)-2-amino-N-((1S)-1-cyano-2-(4… · the same entry in another collection · chain K against K, 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 4CDC · PDBe 4CDC · UniProt P53634
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