Research workbench
Structure of mcl-1 in complex with compound 2G
Analyse Structure of mcl-1 in complex with compound 2G in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YBG
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Induced myeloid leukemia cell differentiation protein mcl- 1
- UniProt
- Q07820
- Ligands
- OJT, CL
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 143 | 84% helix, 0% strand | Q07820 |
| B | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 144 | 83% helix, 0% strand | Q07820 |
Ligands and binding sites
- OJT · (2~{R})-2-[5-[3-chloranyl-2-methyl-4-[2-(4-methylpiperazin-1-yl)ethoxy]phenyl]-6-(3-chlorophenyl)thieno[2,3-d]pyrimidin-4-yl]oxy-3-(2-methoxyphenyl)propanoic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.60 | 0.82 | 29 | CL |
| 2 | 151 | 0.54 | 0.80 | 17 | OJT |
| 3 | 139 | 0.50 | 0.78 | 13 | OJT |
| 4 | 91 | 0.42 | 0.78 | 18 | empty |
| 5 | 87 | 0.36 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 518 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6YBG · Structure of Mcl-1 in complex with compound 2g · 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 6YBG · PDBe 6YBG · UniProt Q07820
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