Research workbench
Structure of mbp-mcl-1 in complex with compound 4D
Analyse Structure of mbp-mcl-1 in complex with compound 4D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YBK
- Type
- protein
- Length
- 515 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,INDUCED myeloid leukemia cell…
- UniProt
- P0AEY0, Q07820
- Ligands
- OK2, GLC, CL
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,INDUCED myeloid leukemia cell differentiation protein mcl-1 | protein | 515 | 55% helix, 14% strand | P0AEY0, Q07820 |
Ligands and binding sites
- OK2 · (2~{R})-2-[5-[3-chloranyl-2-methyl-4-[2-(4-methylpiperazin-1-yl)ethoxy]phenyl]-6-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4-yl]oxy-3-[2-(pyrazin-2-ylmethoxy)phenyl]propanoic acid · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.71 | 0.85 | 26 | GLC |
| 2 | 469 | 0.65 | 0.78 | 40 | empty |
| 3 | 125 | 0.48 | 0.78 | 15 | OK2 |
| 4 | 57 | 0.47 | 0.84 | 16 | empty |
| 5 | 53 | 0.40 | 0.82 | 14 | empty |
Compared structures
- 6YBK · Structure of MBP-Mcl-1 in complex with compound 4d · 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 P0AEY0
- Every structure of UniProt Q07820
- Elsewhere: RCSB PDB 6YBK · PDBe 6YBK · UniProt P0AEY0 · UniProt Q07820
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