Research workbench
MCL1-scfv complex with an indole acid inhibitor
Analyse MCL1-scfv complex with an indole acid inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QB4
- Type
- protein
- Length
- 373 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Induced myeloid leukemia cell differentiation protein mcl- 1; SCFV55
- UniProt
- Q07820
- Ligands
- HVN
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 142 | 82% helix, 0% strand | Q07820 |
| X | SCFV55 | protein | 231 | 6% helix, 51% strand | — |
Ligands and binding sites
- HVN · 3-[3-[[(1~{R})-1,2,3,4-tetrahydronaphthalen-1-yl]oxy]propyl]-7-(1,3,5-trimethylpyrazol-4-yl)-1~{H}-indole-2-carboxylic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.62 | 0.83 | 19 | HVN |
| 2 | 175 | 0.49 | 0.77 | 27 | empty |
| 3 | 87 | 0.41 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–X · 781 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6QB4 · Mcl1-scFv complex with an indole acid 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 6QB4 · PDBe 6QB4 · UniProt Q07820
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