7NA1

HDM2 in complex with compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.354 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of MK-4688 : an Efficient Inhibitor of the HDM2-p53 Protein-Protein Interaction.

Reutershan, M.H.Machacek, M.R.Altman, M.D.Bogen, S.Cai, M.Cammarano, C.Chen, D.Christopher, M.Cryan, J.Daublain, P.Fradera, X.Geda, P.Goldenblatt, P.Hill, A.D.Kemper, R.A.Kutilek, V.Li, C.Martinez, M.McCoy, M.Nair, L.Pan, W.Thompson, C.F.Scapin, G.Shizuka, M.Spatz, M.L.Steinhuebel, D.Sun, B.Voss, M.E.Wang, X.Yang, L.Yeh, T.C.Dussault, I.Marshall, C.G.Trotter, B.W.

(2021) J Med Chem 64: 16213-16241

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01524
  • Primary Citation of Related Structures:  
    7NA1, 7NA2, 7NA3, 7NA4

  • PubMed Abstract: 

    Identification of low-dose, low-molecular-weight, drug-like inhibitors of protein-protein interactions (PPIs) is a challenging area of research. Despite the challenges, the therapeutic potential of PPI inhibition has driven significant efforts toward this goal. Adding to recent success in this area, we describe herein our efforts to optimize a novel purine carboxylic acid-derived inhibitor of the HDM2-p53 PPI into a series of low-projected dose inhibitors with overall favorable pharmacokinetic and physical properties. Ultimately, a strategy focused on leveraging known binding hot spots coupled with biostructural information to guide the design of conformationally constrained analogs and a focus on efficiency metrics led to the discovery of MK-4688 (compound 56 ), a highly potent, selective, and low-molecular-weight inhibitor suitable for clinical investigation.


  • Organizational Affiliation

    Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Mdm2
A, B
109Homo sapiensMutation(s): 2 
Gene Names: MDM2
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens)
Explore Q00987 
Go to UniProtKB:  Q00987
PHAROS:  Q00987
GTEx:  ENSG00000135679 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00987
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1GI (Subject of Investigation/LOI)
Query on 1GI

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
8-(1-benzothiophen-5-yl)-7-[(4-chlorophenyl)methyl]-6-{[(1R)-1-cyclopropylethyl]amino}-7H-purine-2-carboxylic acid
C26 H22 Cl N5 O2 S
VYDVBUHEXZQWED-CQSZACIVSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
E [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
1GI BindingDB:  7NA1 IC50: 259.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.354 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.260 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.349α = 90
b = 39.432β = 90
c = 160.389γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2021-11-10 
  • Deposition Author(s): Scapin, G.

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2021-11-24
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection