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HDM2 in complex with compound 2

Analyse HDM2 in complex with compound 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7NA1
Type: protein
Length: 178 residues
Chains: 2
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: 1GI, SO4
Pockets: 1 · best druggability 0.79

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27)	protein	89	44% helix, 18% strand	Q00987

Ligands and binding sites

1GI · 8-(1-benzothiophen-5-yl)-7-[(4-chlorophenyl)methyl]-6-{[(1R)-1-cyclopropylethyl]amino}-7H-purine-2-carboxylic acid · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · chains A
CIT · Citric acid · additive · chains A, B
GOL · Glycerol · additive · chains 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	879	0.79	0.81	53	1GI, CIT, GOL

Interfaces

1 interface between chains.

A–B · 606 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7NA1 · HDM2 in complex with compound 2 · 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 7NA1 · PDBe 7NA1 · UniProt Q00987

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