MolNFT v1 · #46854 · protein
Crystal structure of dpp-IV complexed with lilly aryl ketone inhibitor
2OGZ · Dipeptidyl peptidase: “Crystal structure of dpp-IV complexed with lilly aryl ketone inhibitor”. X-ray diffraction, 1 ligand (U1N), 17 pockets (best druggability 0.74). MolNFT v1 #46854 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2OGZ
- Type
- protein
- Length
- 1,454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase
- EC
- 3.4.14.5
- UniProt
- P27487
- Ligands
- U1N
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase (EC 3.4.14.5) | protein | 726 | 18% helix, 37% strand | P27487 |
| B | Dipeptidyl peptidase (EC 3.4.14.5) | protein | 728 | 18% helix, 36% strand | P27487 |
Ligands and binding sites
- U1N · 4-[(3R)-3-{[2-(4-fluorophenyl)-2-oxoethyl]amino}butyl]benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.74 | 0.98 | 23 | empty |
| 2 | 839 | 0.71 | 0.76 | 104 | U1N |
| 3 | 476 | 0.66 | 0.78 | 57 | U1N |
| 4 | 121 | 0.56 | 0.83 | 20 | empty |
| 5 | 220 | 0.52 | 0.76 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 2334 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2OGZ · Crystal structure of DPP-IV complexed with Lilly aryl ketone inhibitor · 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 2OGZ · PDBe 2OGZ · UniProt P27487
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