MolNFT v1 · #137301 · protein
Crystal structure of mcl-1 in complex with a bim competitive inhibitor
5VKC · Induced myeloid leukemia cell differentiation protein mcl- 1: “Crystal structure of mcl-1 in complex with a bim competitive inhibitor”. X-ray diffraction, 2 ligands (9EA, ZN), 2 pockets (best druggability 0.64). MolNFT v1 #137301 on…
- PDB
- 5VKC
- Type
- protein
- Length
- 288 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
- 9EA, ZN
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 144 | 81% helix, 0% strand | Q07820 |
Ligands and binding sites
- 9EA · 7-(3-{[4-(4-acetylpiperazin-1-yl)phenoxy]methyl}-1,5-dimethyl-1H-pyrazol-4-yl)-3-{3-[(naphthalen-1-yl) oxy]propyl}-1-[(pyridin-3-yl)methyl]-1H-indole-2-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.64 | 0.82 | 25 | 9EA |
| 2 | 151 | 0.64 | 0.85 | 17 | 9EA |
Interfaces
1 interface between chains.
- A–B · 222 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5VKC · Crystal structure of MCL-1 in complex with a BIM competitive 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 5VKC · PDBe 5VKC · UniProt Q07820
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