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Crystal structure of Mcl1 with inhibitor 9

Analyse Crystal structure of Mcl1 with inhibitor 9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OQC
Type: protein
Length: 303 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.8
Source: Homo sapiens
Molecule: Induced myeloid leukemia cell differentiation protein Mcl-1
UniProt: Q07820
Ligands: N0S
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · resolution 1.8 · 2 distinct chains · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Induced myeloid leukemia cell differentiation protein Mcl-1	protein	152	78% helix, 0% strand	Q07820
B	Induced myeloid leukemia cell differentiation protein Mcl-1	protein	151	79% helix, 0% strand	Q07820

Ligands and binding sites

N0S · (4s,7ar,9ar,10s,11e,15r)-6'-chloro-10-hydroxy-15-methyl-3',4',7A,8,9,9A,10,13,14,15-decahydro-2'H,3H, 5H-spiro[1,19-(ethanediylidene)-16lambda~6~-cyclobuta[i][1,4]oxazepino[3,4-F][1,2, 7]thiadiazacyclohexadecine-4,1'-naphthalene]-16,16, 18(7H,17H)-trione · ligand · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	209	0.64	0.83	36	N0S
2	162	0.61	0.83	18	N0S
3	105	0.39	0.76	19	empty
4	114	0.38	0.74	21	empty

Interfaces

1 interface between chains.

A–B · 608 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6OQC · Crystal structure of MCL1 with inhibitor 9 · the same entry in another collection · chain A against A, TM-score 1.00
Q07820 · AlphaFold monomer V2.0 prediction for induced myeloid leukemia cell differentiation… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 6OQC · PDBe 6OQC · UniProt Q07820

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