Research workbench
Structure of mcl-1 complex with compound 6B
Analyse Structure of mcl-1 complex with compound 6B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NB7
- Type
- protein
- Length
- 604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Induced myeloid leukemia cell differentiation protein mcl- 1
- UniProt
- Q07820
- Ligands
- U6N
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 151 | 79% helix, 0% strand | Q07820 |
Ligands and binding sites
- U6N · (2~{R})-2-[[7-but-2-ynyl-5-(3-chloranyl-2-methyl-phenyl)-6-ethyl-pyrrolo[2,3-d]pyrimidin-4-yl]amino]-3-phenyl-propanoic acid · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.79 | 0.80 | 74 | U6N |
| 2 | 1158 | 0.76 | 0.78 | 75 | U6N |
| 3 | 135 | 0.50 | 0.79 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 500 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 450 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 446 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 66 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 56 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7NB7 · Structure of Mcl-1 complex with compound 6b · 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 7NB7 · PDBe 7NB7 · UniProt Q07820
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