Research workbench
CD38 structure-based inhibitor design using the N1-cyclic inosine 5'- diphosphate ribose template
Analyse CD38 structure-based inhibitor design using the N1-cyclic inosine 5'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U4H
- Type
- protein
- Length
- 497 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyl cyclase 1
- EC
- 3.2.2.5
- UniProt
- P28907
- Ligands
- C8R
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosyl cyclase 1 (EC 3.2.2.5) | protein | 245 | 43% helix, 16% strand | P28907 |
| B | ADP-ribosyl cyclase 1 (EC 3.2.2.5) | protein | 252 | 41% helix, 13% strand | P28907 |
Ligands and binding sites
- C8R · 8-Amino-N1-Cyclic Inosine 5'-Diphosphoribose · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.73 | 0.77 | 78 | C8R |
| 2 | 353 | 0.60 | 0.77 | 39 | C8R |
| 3 | 137 | 0.55 | 0.82 | 21 | empty |
| 4 | 119 | 0.54 | 0.82 | 17 | empty |
| 5 | 89 | 0.38 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 562 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3U4H · CD38 structure-based inhibitor design using the N1-cyclic inosine 5'-diphosphate ribose… · the same entry in another collection · chain A against A, TM-score 1.00
- P28907 · AlphaFold monomer V2.0 prediction for ADP-ribosyl CYCLASE/CYCLIC ADP- ribose hydrolase 1… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P28907
- Elsewhere: RCSB PDB 3U4H · PDBe 3U4H · UniProt P28907
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