Research workbench
Crystal structure of dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2) (dpp-IV-wt) complex with bms-767778 aka 2-(3- (aminomethyl)-4-(2,4- dichlorophenyl)-2-methyl-5-oxo-5,7-dihydro-6H- PYRROLO[3,4- B]PYRIDIN-6-yl)-N,N-dimethylacetamide
Analyse Crystal structure of dipeptidyl-peptidase 4 (CD26, adenosine deaminase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JH0
- Type
- protein
- Length
- 1,456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 4
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- 1MD
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 18% helix, 36% strand | P27487 |
Ligands and binding sites
- 1MD · 2-[3-(aminomethyl)-4-(2,4-dichlorophenyl)-2-methyl-5-oxo-5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-N,N-dimethylacetamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.73 | 0.77 | 116 | 1MD |
| 2 | 54 | 0.70 | 0.97 | 16 | empty |
| 3 | 505 | 0.65 | 0.77 | 63 | 1MD |
| 4 | 236 | 0.51 | 0.76 | 32 | empty |
| 5 | 206 | 0.51 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2323 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 4JH0 · Crystal structure of dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein… · the same entry in another collection · chain A against A, TM-score 1.00
- P27487 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 4 (P27487) · a predicted model of the same protein · chain A against A, 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 P27487
- Elsewhere: RCSB PDB 4JH0 · PDBe 4JH0 · UniProt P27487
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