MolNFT v1 · #125507 · protein

Novel SPIRO[3H-indole-3,2 -pyrrolidin]-2(1H)-one inhibitors of the MDM2-P53 interaction: HDM2 (MDM2) in complex with compound 6B

5LAV · E3 ubiquitin-protein ligase MDM2: “Novel SPIRO[3H-indole-3,2 -pyrrolidin]-2(1H)-one inhibitors of the MDM2-P53 interaction: HDM2 (MDM2) in…”. X-ray diffraction, 2 ligands (6SK, SO4), 1 pocket (best druggability 0.47). MolNFT v1…

PDB: 5LAV
Type: protein
Length: 93 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase MDM2
EC: 6.3.2.-
UniProt: Q00987
Ligands: 6SK, SO4
Pockets: 1 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-)	protein	93	45% helix, 18% strand	Q00987

Ligands and binding sites

6SK · (3~{S},3'~{S},4'~{S})-4'-azanyl-6-chloranyl-3'-(3-chlorophenyl)-1'-(2,2-dimethylpropyl)spiro[1~{H}-indole-3,2'-pyrrolidine]-2-one · ligand · chains A
SO4 · Sulfate ion · ion · 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	122	0.47	0.77	15	6SK

Compared structures

5LAV · Novel Spiro[3H-indole-3,2 -pyrrolidin]-2(1H)-one Inhibitors of the MDM2-p53 Interaction… · 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 5LAV · PDBe 5LAV · UniProt Q00987

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