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MCL1 Fab complex in complex with compound 29

Analyse MCL1 Fab complex in complex with compound 29 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5MES
Type: protein
Length: 577 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: 7LT
Pockets: 5 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 25% helix, 38% 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	77% helix, 0% strand	P97287, Q07820
H	Heavy chain	protein	213	8% helix, 52% strand	—
L	Light chain	protein	213	6% helix, 51% strand	—

Ligands and binding sites

7LT · (5~{R},13~{S},17~{S})-5-[[4-chloranyl-3-(2-phenylethyl)phenyl]methyl]-13-[(4-chlorophenyl) methyl]-8-methyl-1,4,8,12,16-pentazatricyclo[15.8.1.0^{20,25}]hexacosa-20(25),21, 23-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

5 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	466	0.58	0.74	56	empty
2	82	0.51	0.83	17	empty
3	107	0.43	0.78	23	empty
4	130	0.40	0.74	22	empty
5	75	0.34	0.75	15	empty

Interfaces

3 interfaces between chains.

H–L · 1731 Å² buried · 9 hydrogen bonds · protein-protein
A–H · 763 Å² buried · 16 hydrogen bonds · protein-protein
A–L · 142 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5MES · MCL1 Fab complex in complex with compound 29 · the same entry in another collection · chain H against H, 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 0.97

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 5MES · PDBe 5MES · UniProt P97287 · UniProt Q07820

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