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
- 4ZBF
- Type
- protein
- Length
- 1,806 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Induced myeloid leukemia cell differentiation protein mcl- 1
- UniProt
- Q07820
- Ligands
- 4M7
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 153 | 76% helix, 0% strand | Q07820 |
| B, E, G, H, I, J, K, L | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 151 | 77% helix, 0% strand | Q07820 |
| C | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 149 | 78% helix, 0% strand | Q07820 |
| D, F | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 148 | 79% helix, 0% strand | Q07820 |
Ligands and binding sites
- 4M7 · (1R)-7-[3-(naphthalen-1-yloxy)propyl]-3,4-dihydro-2H-[1,4]thiazepino[2,3,4-hi]indole-6-carboxylic acid 1-oxide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.74 | 0.79 | 65 | 4M7 |
| 2 | 1161 | 0.73 | 0.77 | 111 | empty |
| 3 | 185 | 0.69 | 0.86 | 19 | 4M7 |
| 4 | 200 | 0.68 | 0.85 | 20 | 4M7 |
| 5 | 133 | 0.68 | 0.88 | 18 | 4M7 |
Interfaces
19 interfaces between chains.
- E–L · 618 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 610 Ų buried · 9 hydrogen bonds · protein-protein
- B–G · 502 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 491 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 415 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4ZBF · 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 4ZBF · PDBe 4ZBF · UniProt Q07820
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