MolNFT v1 · #64336 · protein
Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinedione inhibitor 2
3G0D · Dipeptidyl peptidase 4: “Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinedione inhibitor 2”. X-ray diffraction, 2 ligands (XIH, NAG), 20 pockets (best druggability 0.73). MolNFT v1 #64336 on GenesisL1: 3D…
- PDB
- 3G0D
- 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
- XIH, NAG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 723 | 18% helix, 35% strand | P27487 |
| B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 728 | 17% helix, 37% strand | P27487 |
| D | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 723 | 17% helix, 36% strand | P27487 |
Ligands and binding sites
- XIH · 2-({8-[(3R)-3-aminopiperidin-1-yl]-1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydro-7H-purin-7-yl}methyl)benzonitrile · ligand · 4 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 | 0.73 | 0.98 | 23 | empty |
| 2 | 758 | 0.71 | 0.77 | 88 | XIH |
| 3 | 736 | 0.70 | 0.77 | 87 | XIH |
| 4 | 752 | 0.70 | 0.77 | 94 | XIH |
| 5 | 705 | 0.69 | 0.77 | 86 | XIH |
Interfaces
3 interfaces between chains.
- A–B · 2298 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 572 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 144 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 19 glycan (disulfide, N-glycosylation).
Compared structures
- 3G0D · Crystal structure of dipeptidyl peptidase IV in complex with a pyrimidinedione inhibitor 2 · 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 3G0D · PDBe 3G0D · UniProt P27487
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