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Crystal structure of MDM2 in complex with compound 13.

Analyse Crystal structure of MDM2 in complex with compound 13. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6I3S
Type: protein
Length: 94 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: H28, SO4
Pockets: 1 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27)	protein	94	45% helix, 19% strand	Q00987

Ligands and binding sites

H28 · (3~{S},3'~{R},3'~{A}~{S},6'~{A}~{R})-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-(cyclopropylmethyl) spiro[1~{h}-indole-3,2'-3~{A},6~{A}-dihydro-3~{H}-pyrrolo[3,4-b]pyrrole]-2,4'-dione · ligand · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A
GOL · Glycerol · additive · 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	128	0.50	0.79	17	H28

Compared structures

6I3S · Crystal structure of MDM2 in complex with compound 13. · 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 6I3S · PDBe 6I3S · UniProt Q00987

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