MolNFT v1 · #77764 · protein
Crystal structure of human CD38 in complex with compound cz-48
3ROM · ADP-ribosyl cyclase 1: “Crystal structure of human CD38 in complex with compound cz-48”. X-ray diffraction, 1 ligand (48Z), 7 pockets (best druggability 0.73). MolNFT v1 #77764 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3ROM
- Type
- protein
- Length
- 505 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
- 48Z
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosyl cyclase 1 (EC 3.2.2.5) | protein | 252 | 42% helix, 14% strand | P28907 |
| B | ADP-ribosyl cyclase 1 (EC 3.2.2.5) | protein | 253 | 42% helix, 13% strand | P28907 |
Ligands and binding sites
- 48Z · 2-deoxy-2-fluoro-5-O-thiophosphono-alpha-D-arabinofuranose · 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 | 620 | 0.73 | 0.80 | 73 | 48Z |
| 2 | 287 | 0.61 | 0.79 | 36 | 48Z |
| 3 | 68 | 0.56 | 0.88 | 14 | empty |
| 4 | 104 | 0.52 | 0.82 | 15 | empty |
| 5 | 82 | 0.38 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 680 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 3ROM · Crystal structure of human CD38 in complex with compound CZ-48 · 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 B 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 3ROM · PDBe 3ROM · UniProt P28907
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