MolNFT v1 · #142224 · protein

The 1.25A crystal structure of HIS6-tagged MDM2 in complex with nutlin-3A

5ZXF · E3 ubiquitin-protein ligase MDM2: “The 1.25A crystal structure of HIS6-tagged MDM2 in complex with nutlin-3A”. X-ray diffraction, 1 ligand (NUT), 1 pocket (best druggability 0.43). MolNFT v1 #142224 on GenesisL1: 3D structure…

PDB: 5ZXF
Type: protein
Length: 87 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase MDM2
EC: 2.3.2.27
UniProt: Q00987
Ligands: NUT
Pockets: 1 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27)	protein	87	44% helix, 18% strand	Q00987

Ligands and binding sites

NUT · 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one · ligand · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	106	0.43	0.77	16	NUT

Compared structures

5ZXF · The 1.25A Crystal structure of His6-tagged Mdm2 in complex with nutlin-3a · 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 Q00987
Elsewhere: RCSB PDB 5ZXF · PDBe 5ZXF · UniProt Q00987

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