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Structure of hdmx with dimer inducing indolyl hydantoin ro-2443

Analyse Structure of hdmx with dimer inducing indolyl hydantoin ro-2443 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3U15
Type: protein
Length: 327 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein MDM4
UniProt: O15151
Ligands: 03M, SO4
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Protein MDM4	protein	82	46% helix, 13% strand	O15151
D	Protein MDM4	protein	81	44% helix, 12% strand	O15151

Ligands and binding sites

03M · (5Z)-5-[(6-chloro-7-methyl-1H-indol-3-yl)methylidene]-3-(3,4-difluorobenzyl)imidazolidine-2,4-dione · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D

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

Pockets

3 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	570	0.77	0.83	44	03M
2	550	0.76	0.83	46	03M
3	65	0.29	0.74	15	empty

Interfaces

3 interfaces between chains.

C–D · 469 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 437 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 321 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3U15 · Structure of hDMX with Dimer Inducing Indolyl Hydantoin RO-2443 · the same entry in another collection · chain D against D, TM-score 1.00
O15151 · AlphaFold monomer V2.0 prediction for protein MDM4 (O15151) · 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 O15151
Elsewhere: RCSB PDB 3U15 · PDBe 3U15 · UniProt O15151

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