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HDM2 in complex with compound 56

Analyse HDM2 in complex with compound 56 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7NA2
Type: protein
Length: 192 residues
Chains: 2
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: 1I0
Pockets: 1 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Isoform 11 of E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27)	protein	96	45% helix, 17% strand	Q00987

Ligands and binding sites

1I0 · 3-[4-(5-chloropyridin-3-yl)-2-[(4ar,7ar)-hexahydrocyclopenta[b][1,4]oxazin-4(4ah)-yl]-3-{[(1R, 4R)-4-methylcyclohexyl]methyl}-3H-imidazo[4,5-c]pyridin-6-yl]-1,2,4-oxadiazol-5(4H)-one · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1056	0.85	0.86	52	1I0

Interfaces

1 interface between chains.

A–B · 786 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

7NA2 · HDM2 in complex with compound 56 · 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 7NA2 · PDBe 7NA2 · UniProt Q00987

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