Research workbench
Mcl-1 complexed with small molecule inhibitor
Analyse Mcl-1 complexed with small molecule inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FDO
- Type
- protein
- Length
- 572 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
- 5X2
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 142 | 81% helix, 0% strand | Q07820 |
| B | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 150 | 78% helix, 0% strand | Q07820 |
| C | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 143 | 80% helix, 0% strand | Q07820 |
| D | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 137 | 85% helix, 0% strand | Q07820 |
Ligands and binding sites
- 5X2 · 3-[3-(4-chloranyl-3,5-dimethyl-phenoxy)propyl]-~{N}-(phenylsulfonyl)-1~{H}-indole-2-carboxamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.66 | 0.82 | 37 | 5X2 |
| 2 | 261 | 0.65 | 0.82 | 28 | 5X2 |
| 3 | 154 | 0.65 | 0.85 | 20 | 5X2 |
| 4 | 184 | 0.63 | 0.83 | 24 | 5X2 |
| 5 | 94 | 0.40 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 574 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 139 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 46 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5FDO · Mcl-1 complexed with small molecule inhibitor · 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 5FDO · PDBe 5FDO · UniProt Q07820
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