MolNFT v1 · #162918 · protein
DPP1 in complex with inhibitor
6RN9 · Dipeptidyl peptidase 1: “DPP1 in complex with inhibitor”. X-ray diffraction, 3 ligands (K9Z, NAG, CL), 5 pockets (best druggability 0.54). MolNFT v1 #162918 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6RN9
- Type
- protein
- Length
- 347 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 1
- EC
- 3.4.14.1
- UniProt
- P53634
- Ligands
- K9Z, NAG, CL
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 1 (EC 3.4.14.1) | protein | 118 | 3% helix, 54% strand | P53634 |
| B | Dipeptidyl peptidase 1 (EC 3.4.14.1) | protein | 161 | 33% helix, 15% strand | P53634 |
| C | Dipeptidyl peptidase 1 (EC 3.4.14.1) | protein | 68 | 4% helix, 41% strand | P53634 |
Ligands and binding sites
- K9Z · (2~{S},4~{S})-~{N}-[(2~{S})-1-azanyl-3-[4-(4-cyanophenyl)phenyl]propan-2-yl]-4-oxidanyl-pyrrolidine-2-carboxamide · ligand · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, B
- CL · Chloride ion · ion · chains B, C
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B, C
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.54 | 0.86 | 21 | K9Z, CL |
| 2 | 105 | 0.43 | 0.77 | 22 | empty |
| 3 | 54 | 0.34 | 0.78 | 17 | ACT |
| 4 | 59 | 0.32 | 0.77 | 17 | DMS |
| 5 | 64 | 0.29 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 3027 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 958 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 324 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 3 glycan, 1 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 6RN9 · PDBe 6RN9 · UniProt P53634
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