MolNFT v1 · #182959 · protein

HDM2 in complex with compound 62

7NA3 · Isoform 11 of E3 ubiquitin-protein ligase MDM2: “HDM2 in complex with compound 62”. X-ray diffraction, 2 ligands (1I3, SO4), 1 pocket (best druggability 0.49). MolNFT v1 #182959 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7NA3
Type: protein
Length: 96 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isoform 11 of E3 ubiquitin-protein ligase MDM2
EC: 2.3.2.27
UniProt: Q00987
Ligands: 1I3, SO4
Pockets: 1 · best druggability 0.49

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Isoform 11 of E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27)	protein	96	44% helix, 18% strand	Q00987

Ligands and binding sites

1I3 · 3-[4-(5-chloropyridin-3-yl)-2-[(2S)-1-methoxypropan-2-yl]-3-{(1R)-1-[(1r,4R)-4-methylcyclohexyl]ethyl}-3H-imidazo[4,5-c]pyridin-6-yl]-1,2,4-oxadiazol-5(4H)-one · ligand · chains A
SO4 · Sulfate ion · ion · 4 copies · 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	148	0.49	0.77	18	1I3

Compared structures

7NA3 · HDM2 in complex with compound 62 · 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 7NA3 · PDBe 7NA3 · UniProt Q00987

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