MolNFT v1 · #72994 · protein
Crystal structure of human dpp-IV in complex with sa-(+)-(6- (aminomethyl)-5-(2,4-dichlorophenyl)-7-METHYLIMIDAZO[1,2-A]PYRIMIDIN- 2-YL)(MORPHOLINO)METHANONE
3NOX · Dipeptidyl-peptidase 4 (CD26, adenosine deaminase…: “Crystal structure of human dpp-IV in complex with sa-(+)-(6…”. X-ray diffraction, 2 ligands (6A5, NAG), 16 pockets (best druggability 0.75). MolNFT v1 #72994 on GenesisL1: 3D…
- PDB
- 3NOX
- Type
- protein
- Length
- 1,454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2)
- UniProt
- Q53TN1
- Ligands
- 6A5, NAG
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2) | protein | 727 | 18% helix, 36% strand | Q53TN1 |
Ligands and binding sites
- 6A5 · Sa-(+)-(6-(aminomethyl)-5-(2,4-dichlorophenyl)-7-methylimidazo[1,2-a]pyrimidin-2-yl)(morpholino)methanone · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- GOL · Glycerol · additive · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.75 | 0.97 | 23 | empty |
| 2 | 941 | 0.72 | 0.76 | 114 | 6A5 |
| 3 | 509 | 0.65 | 0.77 | 63 | 6A5 |
| 4 | 354 | 0.59 | 0.77 | 51 | empty |
| 5 | 239 | 0.51 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2292 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 3NOX · Crystal structure of human DPP-IV in complex with… · the same entry in another collection · 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 Q53TN1
- Elsewhere: RCSB PDB 3NOX · PDBe 3NOX · UniProt Q53TN1
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