8GCG: MDM2

MDM2 bound to inhibitor. Determined by X-ray diffraction at 1.47 Å resolution. Released 23 Oct 2024.

Method: X-ray diffraction
Resolution: 1.47 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 881
Mol. weight: 13.78 kDa
Released: 23 Oct 2024

Explore 8GCG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8GCG contains 5 α-helices and 6 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	27-28	2	1
β-strand	29-30	2	2
α-helix	32-40	9
β-strand	48-49	2	1
α-helix	50-63	14
α-helix	69-71	3
β-strand	74-76	3	3
α-helix	81-86	6
β-strand	90-92	3	3
α-helix	96-104	9
β-strand	107-108	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase Mdm2	A	protein	109	Homo sapiens	Q00987 (AlphaFold model)
macrocyclic peptide inhibitor	B	protein	9	synthetic construct

Sequence of entity 1 (A), FASTA

>8GCG_1 E3 ubiquitin-protein ligase Mdm2 (chains A)
SQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVY
CSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQESSDSGTSVSEN

Sequence of entity 2 (B), FASTA

>8GCG_2 macrocyclic peptide inhibitor (chains B)
VWFGXFXXX

Primary citation

DNA-Encoded Macrocyclic Peptide Libraries Enable the Discovery of a Neutral MDM2-p53 Inhibitor. Silvestri, A.P., Zhang, Q., Ping, Y. et al. ACS Med Chem Lett (2023) 14:820-826. DOI 10.1021/acsmedchemlett.3c00117 · PubMed

Other PDB entries of the same protein (UniProt Q00987 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q9L 1.13 Å, HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 9 AT 1.13A; Structural states of Hdm2…
5C5A 1.15 Å, Crystal Structure of HDM2 in complex with Nutlin-3a
6Q9O 1.21 Å, HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 10 AT 1.21A; Structural states of Hdm2…
5ZXF 1.25 Å, The 1.25A Crystal structure of His6-tagged Mdm2 in complex with nutlin-3a
7QDQ 1.26 Å, Crystal Structure of HDM2 in complex with Caylin-1
8F10 1.28 Å, Structure of the MDM2 P53 binding domain in complex with H102, an all-D Helicon…
8P0D 1.31 Å, Human 14-3-3 sigma in complex with human MDM2 peptide
5Z02 1.35 Å, Crystal structure of HIS6-tagged Mdm2 with nutlin-3a
8J81 1.35 Å, MDM2 bound with a peptoid
4OGN 1.38 Å, Co-Crystal Structure of MDM2 with Inhbitor Compound 3
2AXI 1.4 Å, HDM2 in complex with a beta-hairpin
7KJM 1.4 Å, Crystal structure of human MDM2 in complex with D-peptide inhibitor (dpmi-omega)

Browse structure collections

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