MolNFT v1 · #124327 · protein
Crystal structure of dipeptidyl peptidase IV in complex with syr-472
5KBY · Dipeptidyl peptidase 4: “Crystal structure of dipeptidyl peptidase IV in complex with syr-472”. X-ray diffraction, 2 ligands (6RL, NAG), 20 pockets (best druggability 0.71). MolNFT v1 #124327 on GenesisL1: 3D structure, binding…
- PDB
- 5KBY
- 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
- 6RL, NAG
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 725 | 18% helix, 38% strand | P27487 |
| B | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 733 | 18% helix, 38% strand | P27487 |
| C | Dipeptidyl peptidase 4 (EC 3.4.14.5) | protein | 717 | 17% helix, 36% strand | P27487 |
Ligands and binding sites
- 6RL · 2-[[6-[(3~{R})-3-azanylpiperidin-1-yl]-3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]methyl]-4-fluoranyl-benzenecarboni trile · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.71 | 0.98 | 22 | empty |
| 2 | 855 | 0.71 | 0.76 | 99 | 6RL |
| 3 | 721 | 0.70 | 0.77 | 88 | 6RL |
| 4 | 661 | 0.69 | 0.77 | 85 | 6RL |
| 5 | 702 | 0.68 | 0.76 | 82 | 6RL |
Interfaces
4 interfaces between chains.
- C–D · 2325 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2290 Ų buried · 45 hydrogen bonds · protein-protein
- A–D · 207 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 glycan, 20 disulfide (N-glycosylation, disulfide).
Compared structures
- 5KBY · Crystal structure of dipeptidyl peptidase IV in complex with SYR-472 · 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 5KBY · PDBe 5KBY · UniProt P27487
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