8PWC: MDM2 with Brigimadlin

Crystal structure of MDM2 with Brigimadlin. Determined by X-ray diffraction at 1.46 Å resolution. Released 2 Oct 2024.

Method: X-ray diffraction
Resolution: 1.46 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,618
Mol. weight: 39.55 kDa
Ligands: G7I
Released: 2 Oct 2024

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

Secondary structure: helices and β-sheets

8PWC contains 15 α-helices and 16 β-strands across 3 chains. 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.

Chains A and B: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	27-28	2	1
β-strand	30	1	2
α-helix	32-40	9
β-strand	48-49	2	1
α-helix	50-63	14
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	1	2

Chain C: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
β-strand	27-28	2	7
α-helix	32-40	9
β-strand	48-49	2	7
α-helix	50-63	14
β-strand	74-76	3	8
α-helix	81-86	6
β-strand	90-92	3	8
α-helix	96-104	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase Mdm2	A, B, C	protein	110	Homo sapiens	Q00987 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>8PWC_1 E3 ubiquitin-protein ligase Mdm2 (chains A, B, C)
GSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIV
YCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQESSDSGTSVSEN

Ligands and cofactors

ID	Name	Formula	Copies
G7I	Brigimadlin	C31 H25 Cl2 F N4 O3	3

Primary citation

Discovery and Characterization of Brigimadlin, a Novel and Highly Potent MDM2-p53 Antagonist Suitable for Intermittent Dose Schedules. Gollner, A., Rudolph, D., Weyer-Czernilofsky, U. et al. Mol Cancer Ther (2024) 23:1689-1702. DOI 10.1158/1535-7163.MCT-23-0783 · 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)

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