MolNFT v1 · #162915 · protein
DPP1 in complex with inhibitor
6RN6 · Dipeptidyl peptidase 1: “DPP1 in complex with inhibitor”. X-ray diffraction, 3 ligands (K9Q, NAG, CL), 9 pockets (best druggability 0.57). MolNFT v1 #162915 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6RN6
- Type
- protein
- Length
- 688 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 1
- EC
- 3.4.14.1
- UniProt
- P53634
- Ligands
- K9Q, NAG, CL
- Pockets
- 9 · best druggability 0.57
Structure
x-ray diffraction · 6 distinct chains · 16% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 1 (EC 3.4.14.1) | protein | 115 | 3% helix, 57% strand | P53634 |
| B | Dipeptidyl peptidase 1 (EC 3.4.14.1) | protein | 163 | 31% helix, 15% strand | P53634 |
| C | Dipeptidyl peptidase 1 (EC 3.4.14.1) | protein | 68 | 4% helix, 40% strand | P53634 |
| D | Dipeptidyl peptidase 1 (EC 3.4.14.1) | protein | 113 | 4% helix, 54% strand | P53634 |
| E | Dipeptidyl peptidase 1 (EC 3.4.14.1) | protein | 162 | 30% helix, 15% strand | P53634 |
| F | Dipeptidyl peptidase 1 (EC 3.4.14.1) | protein | 67 | 4% helix, 42% strand | P53634 |
Ligands and binding sites
- K9Q · (2~{S},4~{R})-~{N}-[(2~{S})-1-azanyl-3-(4-phenylphenyl)propan-2-yl]-4-oxidanyl-pyrrolidine-2-carboxamide · ligand · chains D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, C, B, D
- CL · Chloride ion · ion · 5 copies · chains B, C, D, E, F
- GOL · Glycerol · additive · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.57 | 0.81 | 30 | empty |
| 2 | 165 | 0.57 | 0.81 | 24 | empty |
| 3 | 69 | 0.53 | 0.86 | 22 | K9Q, CL |
| 4 | 263 | 0.52 | 0.75 | 39 | GOL |
| 5 | 69 | 0.52 | 0.86 | 21 | CL |
Interfaces
11 interfaces between chains.
- E–F · 3053 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 3038 Ų buried · 54 hydrogen bonds · protein-protein
- D–E · 940 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 939 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 381 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan, 1 covalent, 1 disulfide (N-glycosylation, covalent ligand, disulfide).
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 6RN6 · PDBe 6RN6 · UniProt P53634
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