Research workbench
Human CD38 complexed with inhibitor 2 [4-[(2,6-DIMETHYLBENZYL)AMINO]- 2-methylquinoline-8-carboxamide]
Analyse Human CD38 complexed with inhibitor 2 [4-[(2,6-DIMETHYLBENZYL)AMINO]… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XJT
- Type
- protein
- Length
- 241 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyl CYCLASE/CYCLIC ADP-ribose hydrolase 1
- EC
- 3.2.2.6, 2.4.99.20
- UniProt
- P28907
- Ligands
- 41Z, NA7
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosyl CYCLASE/CYCLIC ADP-ribose hydrolase 1 (EC 3.2.2.6, 2.4.99.20) | protein | 241 | 44% helix, 16% strand | P28907 |
Ligands and binding sites
- 41Z · 4-[(2,6-dimethylbenzyl)amino]-2-methylquinoline-8-carboxamide · ligand · chains A
- NA7 · [(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxy-4-(phosphonooxy)tetrahydrofuran-2-yl]methyl [(2R,3S,4S)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.56 | 0.89 | 16 | empty |
| 2 | 240 | 0.54 | 0.77 | 41 | 41Z, NA7 |
| 3 | 70 | 0.33 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 5 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 4XJT · Human CD38 complexed with inhibitor 2 [4-[(2,6-dimethylbenzyl)amino]-2-methylquinoline-8-c… · 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 0.97
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 4XJT · PDBe 4XJT · UniProt P28907
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