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Discovery of potent mcl-1 inhibitors using fragment-based methods and structure-based design

Analyse Discovery of potent mcl-1 inhibitors using fragment-based methods and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HW2
Type: protein
Length: 902 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Induced myeloid leukemia cell differentiation protein mcl- 1
UniProt: Q07820
Ligands: 19H
Pockets: 13 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 75% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Induced myeloid leukemia cell differentiation protein mcl- 1	protein	149	74% helix, 0% strand	Q07820
B, D, E	Induced myeloid leukemia cell differentiation protein mcl- 1	protein	151	75% helix, 0% strand	Q07820
C, F	Induced myeloid leukemia cell differentiation protein mcl- 1	protein	150	76% helix, 0% strand	Q07820

Ligands and binding sites

19H · 6-chloro-3-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1H-indole-2-carboxylic acid · ligand · 6 copies · chains A, B, C, D, E, F
PGE · Triethylene glycol · additive · 3 copies · chains A, B
EDO · 1,2-ethanediol · additive · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1077	0.75	0.78	102	empty
2	228	0.74	0.88	27	19H
3	864	0.73	0.78	70	empty
4	162	0.66	0.86	19	19H
5	166	0.64	0.84	18	19H

Interfaces

9 interfaces between chains.

E–F · 339 Å² buried · 1 hydrogen bond · protein-protein
A–B · 280 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 252 Å² buried · 1 hydrogen bond · protein-protein
A–F · 185 Å² buried · 0 hydrogen bonds · protein-protein
C–E · 169 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4HW2 · Discovery of potent Mcl-1 inhibitors using fragment-based methods and 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 4HW2 · PDBe 4HW2 · UniProt Q07820

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