Research workbench
Mcl-1 complexed with small molecules
Analyse Mcl-1 complexed with small molecules in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BW2
- Type
- protein
- Length
- 595 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Induced myeloid leukemia cell differentiation protein mcl- 1
- UniProt
- Q07820
- Ligands
- ECY
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 150 | 79% helix, 0% strand | Q07820 |
| B, D | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 148 | 78% helix, 0% strand | Q07820 |
| C | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 149 | 78% helix, 0% strand | Q07820 |
Ligands and binding sites
- ECY · 3-({11-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1-oxo-7-(1,3,5-trimethyl-1H-pyrazol-4-yl)-4,5-dihydro-1H-[1, 4]diazepino[1,2-a]indol-2(3H)-yl}methyl)benzoic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.69 | 0.87 | 19 | ECY |
| 2 | 466 | 0.67 | 0.79 | 52 | empty |
| 3 | 188 | 0.65 | 0.84 | 21 | ECY |
| 4 | 165 | 0.63 | 0.84 | 19 | ECY |
| 5 | 150 | 0.61 | 0.83 | 18 | ECY |
Interfaces
3 interfaces between chains.
- B–C · 604 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 308 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 284 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6BW2 · Mcl-1 complexed with small molecules · 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 6BW2 · PDBe 6BW2 · UniProt Q07820
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