4WT2: Co-crystal Structure of MDM2

Co-crystal Structure of MDM2 in Complex with AM-7209. Determined by X-ray diffraction at 1.42 Å resolution. Released 3 Dec 2014.

Method: X-ray diffraction
Resolution: 1.42 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,044
Mol. weight: 12.98 kDa
Ligands: 3UD
Released: 3 Dec 2014

Explore 4WT2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WT2 contains 6 α-helices and 7 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: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	1
β-strand	13-15	3	1
α-helix	22-25	4
β-strand	27-30	4	2
α-helix	32-40	9
β-strand	48-49	2	2
α-helix	50-63	14
α-helix	70-72	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	107-109	3	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase Mdm2	A	protein	105	Homo sapiens	Q00987 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4WT2_1 E3 ubiquitin-protein ligase Mdm2 (chains A)
MSVPTDGAVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKR
LYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVV

Ligands and cofactors

ID	Name	Formula	Copies
3UD	4-({[(3R,5R,6S)-1-[(1S)-2-(tert-butylsulfonyl)-1-cyclopropylethyl]-6-(4-chloro-…	C37 H41 Cl2 F N2 O7 S	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Discovery of AM-7209, a Potent and Selective 4-Amidobenzoic Acid Inhibitor of the MDM2-p53 Interaction. Rew, Y., Sun, D., Yan, X. et al. J Med Chem (2014) 57:10499-10511. DOI 10.1021/jm501550p · 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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