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
- 5FDR
- 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
- 5X3
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 155 | 76% helix, 0% strand | Q07820 |
| B | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 149 | 77% helix, 0% strand | Q07820 |
| C | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 143 | 83% helix, 0% strand | Q07820 |
| D | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 148 | 80% helix, 0% strand | Q07820 |
Ligands and binding sites
- 5X3 · 5-[[6-chloranyl-3-[3-(4-chloranyl-3,5-dimethyl-phenoxy)propyl]-7-(3,5-dimethyl-1~{H}-pyrazol-4-yl)-1~{H}-indol-2-yl]carbonylsulfamoyl]furan-2-carboxylic 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.82 | 0.83 | 77 | 5X3 |
| 2 | 183 | 0.67 | 0.86 | 21 | 5X3 |
| 3 | 221 | 0.65 | 0.83 | 22 | 5X3 |
| 4 | 179 | 0.47 | 0.76 | 20 | empty |
| 5 | 110 | 0.39 | 0.75 | 19 | empty |
Interfaces
5 interfaces between chains.
- B–C · 659 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 588 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 464 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 206 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 124 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5FDR · 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 5FDR · PDBe 5FDR · UniProt Q07820
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