PDBsum entry 4j7e

Ligase/antagonist

PDB id: 4j7e

Contents

Protein chain

86 a.a.

Ligands

I29

SO4

Waters ×62

PDB id:

4j7e

Name:

Ligase/antagonist

Title:

The 1.63a crystal structure of humanized xenopus mdm2 with a nutlin fragment, ro5524529

Structure:

E3 ubiquitin-protein ligase mdm2. Chain: a. Fragment: n-terminal domain (unp residues 21-105). Synonym: double minute 2 protein, xdm2, p53-binding protein mdm2. Engineered: yes. Mutation: yes

Source:

Xenopus laevis. Clawed frog,common platanna,platanna. Organism_taxid: 8355. Gene: mdm2. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.63Å R-factor: 0.223 R-free: 0.237

Authors:

C.Janson,C.Lukacs,B.Graves

Key ref:

D.C.Fry et al. (2013). Deconstruction of a nutlin: dissecting the binding determinants of a potent protein-protein interaction inhibitor. Acs Med Chem Lett, 4, 660-665. PubMed id: 24900726 DOI: 10.1021/ml400062c

Date:

13-Feb-13 Release date: 07-Aug-13

Protein chain

P56273  (MDM2_XENLA) -  E3 ubiquitin-protein ligase Mdm2 from Xenopus laevis

Seq: 473 a.a.

Struc: 86 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine

DOI no: 10.1021/ml400062c

Acs Med Chem Lett 4:660-665 (2013)

PubMed id: 24900726

Deconstruction of a nutlin: dissecting the binding determinants of a potent protein-protein interaction inhibitor.

D.C.Fry, C.Wartchow, B.Graves, C.Janson, C.Lukacs, U.Kammlott, C.Belunis, S.Palme, C.Klein, B.Vu.

ABSTRACT

Protein-protein interaction (PPI) systems represent a rich potential source of targets for drug discovery, but historically have proven to be difficult, particularly in the lead identification stage. Application of the fragment-based approach may help toward success with this target class. To provide an example toward understanding the potential issues associated with such an application, we have deconstructed one of the best established protein-protein inhibitors, the Nutlin series that inhibits the interaction between MDM2 and p53, into fragments, and surveyed the resulting binding properties using heteronuclear single quantum coherence nuclear magnetic resonance (HSQC NMR), surface plasmon resonance (SPR), and X-ray crystallography. We report the relative contributions toward binding affinity for each of the key substituents of the Nutlin molecule and show that this series could hypothetically have been discovered via a fragment approach. We find that the smallest fragment of Nutlin that retains binding accesses two subpockets of MDM2 and has a molecular weight at the high end of the range that normally defines fragments.