Research workbench
Discovery of potent mcl-1 inhibitors using fragment-based methods and structure-based design
Analyse Discovery of potent mcl-1 inhibitors using fragment-based methods and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HW3
- Type
- protein
- Length
- 1,804 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
- 19G
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, H | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 150 | 77% helix, 0% strand | Q07820 |
| B, E, F, G, K | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 151 | 77% helix, 0% strand | Q07820 |
| D | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 153 | 75% helix, 0% strand | Q07820 |
| I | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 147 | 78% helix, 0% strand | Q07820 |
| J | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 150 | 78% helix, 0% strand | Q07820 |
| L | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 149 | 77% helix, 0% strand | Q07820 |
Ligands and binding sites
- 19G · 3-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1-benzothiophene-2-carboxylic acid · ligand · 12 copies · chains A, B, D, C, E, F, G, H, I, K, J, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.85 | 0.86 | 88 | 19G |
| 2 | 909 | 0.80 | 0.82 | 88 | empty |
| 3 | 765 | 0.78 | 0.82 | 60 | 19G |
| 4 | 621 | 0.76 | 0.82 | 51 | 19G |
| 5 | 135 | 0.69 | 0.89 | 19 | 19G |
Interfaces
22 interfaces between chains.
- A–K · 625 Ų buried · 8 hydrogen bonds · protein-protein
- H–J · 571 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 559 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 537 Ų buried · 8 hydrogen bonds · protein-protein
- D–L · 521 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4HW3 · Discovery of potent Mcl-1 inhibitors using fragment-based methods and structure-based… · 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 4HW3 · PDBe 4HW3 · UniProt Q07820
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.