MolNFT v1 · #73675 · protein
Crystal structure of human DPP4 bound to tak-100
3O95 · Dipeptidyl peptidase 4: “Crystal structure of human DPP4 bound to tak-100”. X-ray diffraction, 2 ligands (01T, NAG), 20 pockets (best druggability 0.72). MolNFT v1 #73675 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3O95
- Type
- protein
- Length
- 2,913 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- 01T, NAG
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 727 | 17% helix, 36% strand | P27487 |
| B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 733 | 17% helix, 37% strand | P27487 |
| C | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 726 | 17% helix, 36% strand | P27487 |
Ligands and binding sites
- 01T · [5-(aminomethyl)-6-(2,2-dimethylpropyl)-2-ethyl-4-(4-methylphenyl)pyridin-3-yl]acetic acid · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 29 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.72 | 0.99 | 23 | empty |
| 2 | 53 | 0.72 | 0.98 | 21 | empty |
| 3 | 702 | 0.69 | 0.77 | 85 | 01T |
| 4 | 689 | 0.68 | 0.76 | 82 | 01T |
| 5 | 744 | 0.68 | 0.75 | 91 | 01T |
Interfaces
4 interfaces between chains.
- A–B · 2300 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2282 Ų buried · 46 hydrogen bonds · protein-protein
- A–D · 180 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 10 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 20 glycan (disulfide, N-glycosylation).
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 P27487
- Elsewhere: RCSB PDB 3O95 · PDBe 3O95 · UniProt P27487
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