MolNFT v1 · #122093 · protein
Discovery of potent myeloid cell leukemia-1 (mcl-1) inhibitors using structure-based design
5IEZ · Induced myeloid leukemia cell differentiation protein mcl- 1: “Discovery of potent myeloid cell leukemia-1 (mcl-1) inhibitors using structure-based design”. X-ray diffraction, 1 ligand (6AL), 10 pockets (best druggability 0.70).…
- PDB
- 5IEZ
- Type
- protein
- Length
- 601 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
- 6AL
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 151 | 78% helix, 0% strand | Q07820 |
| B, C | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 152 | 76% helix, 0% strand | Q07820 |
| D | Induced myeloid leukemia cell differentiation protein mcl- 1 | protein | 146 | 78% helix, 0% strand | Q07820 |
Ligands and binding sites
- 6AL · 3-({6-chloro-3-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-7-(1,3,5-trimethyl-1H-pyrazol-4-yl)-1H-indole-2-carbonyl}amino)benzoic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.70 | 0.78 | 61 | empty |
| 2 | 186 | 0.66 | 0.85 | 22 | 6AL |
| 3 | 164 | 0.65 | 0.85 | 21 | 6AL |
| 4 | 152 | 0.63 | 0.84 | 19 | 6AL |
| 5 | 142 | 0.62 | 0.85 | 18 | 6AL |
Interfaces
4 interfaces between chains.
- B–C · 502 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 343 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 225 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5IEZ · Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) inhibitors using Structure-Based… · 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 5IEZ · PDBe 5IEZ · UniProt Q07820
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