MolNFT v1 · #124943 · protein
Crystal structure of MCL1 with compound 1
5KU9 · Induced myeloid leukemia cell differentiation protein mcl- 1: “Crystal structure of MCL1 with compound 1”. X-ray diffraction, 2 ligands (6XJ, NA), 4 pockets (best druggability 0.70). MolNFT v1 #124943 on GenesisL1: 3D structure…
- PDB
- 5KU9
- Type
- protein
- Length
- 285 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Induced myeloid leukemia cell differentiation protein mcl- 1
- EC
- 3.6.1.11
- Ligands
- 6XJ, NA
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Induced myeloid leukemia cell differentiation protein mcl- 1 (EC 3.6.1.11) | protein | 149 | 78% helix, 0% strand | — |
| B | Induced myeloid leukemia cell differentiation protein mcl- 1 (EC 3.6.1.11) | protein | 136 | 77% helix, 0% strand | — |
Ligands and binding sites
- 6XJ · (3~{S})-3-azanyl-4-(4-bromophenyl)-~{N}-[(3~{S})-1-[2-[[(2~{R})-1-(3,4-dichlorophenyl)-4-(methylamino)-4-oxidanylidene-butan-2-yl]amino]-2-oxidanylidene-ethyl]-2-oxidanylidene-4,5-dihydro-3~{H}-1-benzazepin-3-yl]butanamide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.70 | 0.83 | 40 | empty |
| 2 | 54 | 0.39 | 0.80 | 13 | empty |
| 3 | 55 | 0.37 | 0.79 | 11 | empty |
| 4 | 51 | 0.32 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 644 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5KU9 · Crystal structure of MCL1 with compound 1 · 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
- Elsewhere: RCSB PDB 5KU9 · PDBe 5KU9
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