MolNFT v1 · #170564 · protein
Structure of mbp-mcl-1 in complex with compound 3E
6YBJ · MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,INDUCED…: “Structure of mbp-mcl-1 in complex with compound 3E”. X-ray diffraction, 3 ligands (OJW, GLC, CL), 4 pockets (best druggability 0.71). MolNFT v1 #170564 on GenesisL1: 3D…
- PDB
- 6YBJ
- Type
- protein
- Length
- 514 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
- OJW, GLC, CL
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MALTOSE/MALTODEXTRIN-binding periplasmic PROTEIN,INDUCED myeloid leukemia cell differentiation protein mcl-1 | protein | 514 | 55% helix, 13% strand | P0AEY0, Q07820 |
Ligands and binding sites
- OJW · (2~{R})-2-[5-[3-chloranyl-2-methyl-4-[2-(4-methylpiperazin-1-yl)ethoxy]phenyl]-6-(5-fluoranylfuran-2-yl)thieno[2,3-d]pyrimidin-4-yl]oxy-3-[2-[(2-methylpyrazol-3-yl)methoxy]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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.71 | 0.85 | 30 | GLC |
| 2 | 403 | 0.62 | 0.77 | 33 | empty |
| 3 | 110 | 0.47 | 0.79 | 13 | OJW |
| 4 | 61 | 0.28 | 0.73 | 14 | empty |
Compared structures
- 6YBJ · Structure of MBP-Mcl-1 in complex with compound 3e · 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 6YBJ · PDBe 6YBJ · UniProt P0AEY0 · UniProt Q07820
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