7KJM: Human MDM2

Crystal structure of human MDM2 in complex with D-peptide inhibitor (dpmi-omega). Determined by X-ray diffraction at 1.4 Å resolution. Released 17 Nov 2021.

Method: X-ray diffraction
Resolution: 1.4 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 1,866
Mol. weight: 23.72 kDa
Ligands: IPA
Released: 17 Nov 2021

Explore 7KJM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KJM contains 10 α-helices and 14 β-strands across 4 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.

Chain A: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
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	67-68	2	3
β-strand	71-76	6	3
α-helix	81-86	6
β-strand	90-92	3	3
α-helix	96-104	9
β-strand	107	1	2

Chains B and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	4
β-strand	30	1	5
α-helix	32-39	8
β-strand	48	1	4
α-helix	50-63	14
β-strand	67	1	6
β-strand	74-76	3	6
α-helix	81-86	6
β-strand	90-92	3	6
α-helix	96-104	9
β-strand	107	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase Mdm2	A, C	protein	85	Homo sapiens	Q00987 (AlphaFold model)
D-PMI-omega	B, D	protein	12	synthetic construct

Sequence of entity 1 (A, C), FASTA

>7KJM_1 E3 ubiquitin-protein ligase Mdm2 (chains A, C)
ETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGD
LFGVPSFSVKEHRKIYTMIYRNLVV

Sequence of entity 2 (B, D), FASTA

>7KJM_2 D-PMI-omega (chains B, D)
EFWYVEXEKLLR

Ligands and cofactors

ID	Name	Formula	Copies
IPA	Isopropyl alcohol	C3 H8 O	1

Water and common crystallization additives (CL, PEG) are not listed.

Primary citation

A Dual-Specificity d-Peptide Antagonist of MDM2 and MDMX for Antitumor Immunotherapy. Liao, C., Yan, J., Tolbert, W.D. et al. J Med Chem (2025). DOI 10.1021/acs.jmedchem.4c02057 · 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
8F13 1.4 Å, Structure of the MDM2 P53 binding domain in complex with H103, an all-D Helicon…

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