MolNFT v1 · #136124 · protein
Structure of a mcl-1 inhibitor binding to site 3 of human serum albumin
5UJB: “Structure of a mcl-1 inhibitor binding to site 3 of human serum albumin”. X-ray diffraction, 2 ligands (6AK, PO4), 20 pockets (best druggability 0.82). MolNFT v1 #136124 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5UJB
- Type
- protein
- Length
- 1,133 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serum albumin
- UniProt
- P02768
- Ligands
- 6AK, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serum albumin | protein | 568 | 70% helix, 0% strand | P02768 |
| B | Serum albumin | protein | 565 | 71% helix, 0% strand | P02768 |
Ligands and binding sites
- 6AK · 4-{8-chloro-11-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1-oxo-7-(1,3,5-trimethyl-1H-pyrazol-4-yl)-4,5-dihydro-1H-[1,4]diazepino[1,2-a]indol-2(3H)-yl}-1-methyl-1H-indole-6-carboxylic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.82 | 0.91 | 54 | empty |
| 2 | 386 | 0.80 | 0.89 | 49 | empty |
| 3 | 88 | 0.71 | 0.94 | 23 | empty |
| 4 | 104 | 0.68 | 0.91 | 23 | empty |
| 5 | 172 | 0.67 | 0.86 | 28 | 6AK |
Interfaces
1 interface between chains.
- A–B · 494 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide (disulfide).
Compared structures
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 P02768
- Elsewhere: RCSB PDB 5UJB · PDBe 5UJB · UniProt P02768
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