Research workbench
X-ray co-crystal structure of compound 5 with mcl-1
Analyse X-ray co-crystal structure of compound 5 with mcl-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UDY
- Type
- protein
- Length
- 301 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Induced myeloid leukemia cell differentiation protein mcl- 1
- UniProt
- Q07820
- Ligands
- Q54
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 151 | 79% helix, 0% strand | Q07820 |
| B | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 150 | 79% helix, 0% strand | Q07820 |
Ligands and binding sites
- Q54 · (3S)-6'-chloro-5-(cyclobutylmethyl)-3',4,4',5-tetrahydro-2H,2'H-spiro[1,5-benzoxazepine-3,1'-naphthalene]-7-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.62 | 0.82 | 21 | Q54 |
| 2 | 182 | 0.62 | 0.83 | 22 | Q54 |
| 3 | 63 | 0.32 | 0.76 | 16 | empty |
| 4 | 54 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 617 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6UDY · X-ray co-crystal structure of compound 5 with Mcl-1 · the same entry in another collection · 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 Q07820
- Elsewhere: RCSB PDB 6UDY · PDBe 6UDY · UniProt Q07820
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