3W69

Crystal structure of human mdm2 with a dihydroimidazothiazole inhibitor

PDB DOI: https://doi.org/10.2210/pdb3W69/pdb

Classification: LIGASE/LIGASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-02-12 Released: 2013-06-05
Deposition Author(s): Shimizu, H., Katakura, S., Miyazaki, M., Naito, H., Sugimoto, Y., Kawato, H., Okayama, T., Soga, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.238
R-Value Work: 0.209
R-Value Observed: 0.210

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Synthesis and evaluation of novel orally active p53-MDM2 interaction inhibitors

Miyazaki, M., Naito, H., Sugimoto, Y., Yoshida, K., Kawato, H., Okayama, T., Shimizu, H., Miyazaki, M., Kitagawa, M., Seki, T., Fukutake, S., Shiose, Y., Aonuma, M., Soga, T.

(2013) Bioorg Med Chem 21: 4319-4331

PubMed: 23685175 Search on PubMed
DOI: https://doi.org/10.1016/j.bmc.2013.04.056
Primary Citation of Related Structures:
3W69

PubMed Abstract:
We have discovered and reported potent p53-MDM2 interaction inhibitors possessing dihydroimidazothiazole scaffold. Our lead showed strong activity in vitro, but did not exhibit antitumor efficacy in vivo for the low metabolic stability. In order to obtain orally active compounds, we executed further optimization of our lead by the improvement of physicochemical properties. Thus we furnished optimal compounds by introducing an alkyl group onto the pyrrolidine at the C-2 substituent to prevent the metabolism; and modifying the terminal substituent of the proline motif improved solubility. These optimal compounds exhibited good PK profiles and significant antitumor efficacy with oral administration on a xenograft model using MV4-11 cells having wild type p53.

Organizational Affiliation

Medicinal Chemistry Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd, 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan. miyazaki.masaki.p3@daiichisankyo.co.jp

Macromolecule Content

Total Structure Weight: 22.09 kDa
Atom Count: 1,658
Modelled Residue Count: 170
Deposited Residue Count: 174
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase Mdm2	A, B	87	Homo sapiens	Mutation(s): 1 Gene Names: MDM2 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q00987
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LTZ Query on LTZ Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	(5R,6S)-2-[((2S,5R)-2-{[(3R)-4-acetyl-3-methylpiperazin-1-yl]carbonyl}-5-ethylpyrrolidin-1-yl)carbonyl]-5,6-bis(4-chlorophenyl)-3-isopropyl-6-methyl-5,6-dihydroimidazo[2,1-b][1,3]thiazole C₃₆ H₄₃ Cl₂ N₅ O₃ S NYMONQQQYOURJF-GTVZXTIFSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	D [auth A], F [auth B], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
LTZ	PDBBind: 3W69	IC50: 58 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.238
R-Value Work: 0.209
R-Value Observed: 0.210
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.562	α = 90
b = 65.761	β = 90
c = 81.436	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
PROCESS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-06-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-06-05
Type: Initial release
Version 1.1: 2014-04-30
Changes: Database references
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description