MolNFT v1 · #126835 · protein

MCL1 Fab complex in complex with compound 21

5MEV · Induced myeloid leukemia cell differentiation protein mcl-1…: “MCL1 Fab complex in complex with compound 21”. X-ray diffraction, 1 ligand (7LW), 4 pockets (best druggability 0.57). MolNFT v1 #126835 on GenesisL1: 3D structure…

PDB: 5MEV
Type: protein
Length: 571 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Induced myeloid leukemia cell differentiation protein mcl-1 HOMOLOG,INDUCED myeloid…
UniProt: P97287, Q07820
Ligands: 7LW
Pockets: 4 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Induced myeloid leukemia cell differentiation protein mcl-1 HOMOLOG,INDUCED myeloid leukemia cell differentiation protein mcl-1	protein	151	72% helix, 0% strand	P97287, Q07820
H	Fab heavy chain	protein	207	4% helix, 54% strand	—
L	Fab light chain	protein	213	4% helix, 43% strand	—

Ligands and binding sites

7LW · (5~{R},13~{S},17~{S})-5-[(3,4-dichlorophenyl)methyl]-8-methyl-13-[(4-methylsulfonylphenyl)methyl]-1,4,8,12, 16-pentazatricyclo[15.8.1.0^{20,25}]hexacosa-20,22,24-triene-3,7,15,26-tetrone · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	459	0.57	0.74	45	empty
2	91	0.41	0.77	22	empty
3	55	0.36	0.78	12	empty
4	76	0.35	0.76	17	empty

Interfaces

3 interfaces between chains.

H–L · 1755 Å² buried · 12 hydrogen bonds · protein-protein
A–H · 766 Å² buried · 15 hydrogen bonds · protein-protein
A–L · 135 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5MEV · MCL1 Fab complex in complex with compound 21 · the same entry in another collection · chain A against A, TM-score 1.00
P97287 · AlphaFold monomer V2.0 prediction for induced myeloid leukemia cell differentiation… · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P97287
Every structure of UniProt Q07820
Elsewhere: RCSB PDB 5MEV · PDBe 5MEV · UniProt P97287 · UniProt Q07820

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