MolNFT v1 · #118826 · protein

Mcl-1 complexed with small molecule inhibitor

5FDR · Induced myeloid leukemia cell differentiation protein mcl- 1: “Mcl-1 complexed with small molecule inhibitor”. X-ray diffraction, 1 ligand (5X3), 6 pockets (best druggability 0.82). MolNFT v1 #118826 on GenesisL1: 3D structure…

PDB: 5FDR
Type: protein
Length: 595 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: 5X3
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Induced myeloid leukemia cell differentiation protein mcl- 1	protein	155	76% helix, 0% strand	Q07820
B	Induced myeloid leukemia cell differentiation protein mcl- 1	protein	149	77% helix, 0% strand	Q07820
C	Induced myeloid leukemia cell differentiation protein mcl- 1	protein	143	83% helix, 0% strand	Q07820
D	Induced myeloid leukemia cell differentiation protein mcl- 1	protein	148	80% helix, 0% strand	Q07820

Ligands and binding sites

5X3 · 5-[[6-chloranyl-3-[3-(4-chloranyl-3,5-dimethyl-phenoxy)propyl]-7-(3,5-dimethyl-1~{H}-pyrazol-4-yl)-1~{H}-indol-2-yl]carbonylsulfamoyl]furan-2-carboxylic 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

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	958	0.82	0.83	77	5X3
2	183	0.67	0.86	21	5X3
3	221	0.65	0.83	22	5X3
4	179	0.47	0.76	20	empty
5	110	0.39	0.75	19	empty

Interfaces

5 interfaces between chains.

B–C · 659 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 588 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 464 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 206 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 124 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5FDR · Mcl-1 complexed with small molecule 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 5FDR · PDBe 5FDR · UniProt Q07820

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