MolNFT v1 · #83460 · protein

Crystal structure of mcl-1 in complex with compound 10

3WIY · Induced myeloid leukemia cell differentiation protein mcl- 1: “Crystal structure of mcl-1 in complex with compound 10”. X-ray diffraction, 1 ligand (LC6), 13 pockets (best druggability 0.77). MolNFT v1 #83460 on GenesisL1: 3D…

PDB: 3WIY
Type: protein
Length: 905 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: LC6
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	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	77% helix, 0% strand	Q07820
C, D, F	Induced myeloid leukemia cell differentiation protein mcl- 1	protein	150	78% helix, 0% strand	Q07820

Ligands and binding sites

LC6 · 7-(4-{[(4-{[(2R)-4-(dimethylamino)-1-(phenylsulfanyl)butan-2-yl]amino}-3-nitrophenyl)sulfonyl]carbamoyl}-2-methylphenyl)-3-[3-(naphthalen-1-yloxy)propyl]pyrazolo[1,5-a]pyridine-2-carboxylic acid · ligand · 6 copies · chains A, B, D, C, E, F

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	1022	0.77	0.79	78	empty
2	574	0.71	0.79	55	LC6
3	209	0.67	0.84	19	LC6
4	169	0.66	0.85	18	LC6
5	183	0.64	0.84	18	LC6

Interfaces

8 interfaces between chains.

A–B · 641 Å² buried · 12 hydrogen bonds · protein-protein
C–E · 613 Å² buried · 8 hydrogen bonds · protein-protein
B–E · 463 Å² buried · 4 hydrogen bonds · protein-protein
B–F · 310 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 197 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3WIY · Crystal structure of Mcl-1 in complex with compound 10 · 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 3WIY · PDBe 3WIY · UniProt Q07820

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