MolNFT v1 · #64335 · protein
Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinedione inhibitor 1
3G0C · Dipeptidyl peptidase 4: “Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinedione inhibitor 1”. X-ray diffraction, 2 ligands (RUF, NAG), 20 pockets (best druggability 0.73). MolNFT v1 #64335 on GenesisL1: 3D…
- PDB
- 3G0C
- Type
- protein
- Length
- 2,900 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
- RUF, NAG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 723 | 17% helix, 36% strand | P27487 |
| B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 729 | 17% helix, 38% strand | P27487 |
| C, D | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 724 | 18% helix, 37% strand | P27487 |
Ligands and binding sites
- RUF · 7-(2-chlorobenzyl)-1,3-dimethyl-8-piperazin-1-yl-3,7-dihydro-1H-purine-2,6-dione · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.73 | 0.98 | 22 | empty |
| 2 | 702 | 0.69 | 0.77 | 86 | RUF |
| 3 | 633 | 0.69 | 0.77 | 76 | RUF |
| 4 | 617 | 0.68 | 0.77 | 73 | RUF |
| 5 | 569 | 0.67 | 0.77 | 70 | RUF |
Interfaces
3 interfaces between chains.
- A–B · 2319 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 608 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 216 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 17 glycan (disulfide, N-glycosylation).
Compared structures
- 3G0C · Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinedione inhibitor 1 · the same entry in another collection · chain D against D, 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 3G0C · PDBe 3G0C · UniProt P27487
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