Research workbench
Mcl-1 bound to compound 17
Analyse Mcl-1 bound to compound 17 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U63
- Type
- protein
- Length
- 570 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
- Q0D
- Pockets
- 8 · best druggability 0.69
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 | 146 | 80% helix, 0% strand | Q07820 |
| B | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 141 | 84% helix, 0% strand | Q07820 |
| C | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 138 | 79% helix, 0% strand | Q07820 |
| D | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 145 | 79% helix, 0% strand | Q07820 |
Ligands and binding sites
- Q0D · 2-{[(naphthalen-2-yl)sulfonyl]amino}-5-[(2-phenylethyl)sulfanyl]benzoic acid · ligand · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.69 | 0.74 | 80 | empty |
| 2 | 145 | 0.54 | 0.80 | 22 | Q0D |
| 3 | 120 | 0.52 | 0.81 | 17 | Q0D |
| 4 | 101 | 0.51 | 0.81 | 14 | Q0D |
| 5 | 112 | 0.51 | 0.80 | 17 | Q0D |
Interfaces
4 interfaces between chains.
- A–D · 424 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 411 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 119 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 43 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6U63 · Mcl-1 bound to compound 17 · 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 6U63 · PDBe 6U63 · UniProt Q07820
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