MolNFT v1 · #47059 · protein
Crystal structure of human dpp-4
2ONC · Dipeptidyl peptidase 4: “Crystal structure of human dpp-4”. X-ray diffraction, 2 ligands (SY1, NAG), 20 pockets (best druggability 0.74). MolNFT v1 #47059 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2ONC
- Type
- protein
- Length
- 2,897 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
- SY1, NAG
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 724 | 17% helix, 36% strand | P27487 |
| B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 18% helix, 37% strand | P27487 |
| C | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 723 | 18% helix, 36% strand | P27487 |
| D | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 722 | 17% helix, 36% strand | P27487 |
Ligands and binding sites
- SY1 · 2-({2-[(3R)-3-aminopiperidin-1-yl]-4-oxoquinazolin-3(4H)-yl}methyl)benzonitrile · ligand · 8 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.74 | 0.98 | 23 | empty |
| 2 | 659 | 0.69 | 0.77 | 77 | SY1 |
| 3 | 667 | 0.68 | 0.77 | 83 | SY1 |
| 4 | 638 | 0.68 | 0.77 | 74 | SY1 |
| 5 | 688 | 0.67 | 0.76 | 78 | SY1 |
Interfaces
3 interfaces between chains.
- A–B · 2292 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 588 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 131 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 18 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 2ONC · PDBe 2ONC · UniProt P27487
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