6I29 | pdb_00006i29

X-ray structure of the p53-MDM2 inhibitor NMI801 bound to HDM2 at 2.1A resolution

PDB DOI: https://doi.org/10.2210/pdb6I29/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2018-11-01 Released: 2019-11-20
Deposition Author(s): Kallen, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.277 (Depositor), 0.267 (DCC)
R-Value Work:
0.243 (Depositor), 0.236 (DCC)
R-Value Observed:
0.244 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

p53 dynamics vary between tissues and are linked with radiation sensitivity

Ornstein, J., Iwamoto, Y., Prytyskach, M., Miller, M., Kallen, J., Ferretti, S., Holzer, P., Forrester, W., Weissleder, R., Lahav, G.

To be published.

Macromolecule Content

Total Structure Weight: 11.89 kDa
Atom Count: 861
Modeled Residue Count: 93
Deposited Residue Count: 96
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human E3 Ubiquitin-Protein Ligase MDM2	A	96	Homo sapiens	Mutation(s): 0 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00987
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H0W (Subject of Investigation/LOI) Query on H0W Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	6-chloranyl-3-[3-[(1~{S})-1-(4-chlorophenyl)ethyl]-5-phenyl-imidazol-4-yl]-~{N}-[2-[4-(2-oxidanylidene-1,3-oxazinan-3-yl)piperidin-1-yl]pyridin-3-yl]-1~{H}-indole-2-carboxamide C₄₀ H₃₇ Cl₂ N₇ O₃ PEGKHNWZGSKUJH-VWLOTQADSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.277 (Depositor), 0.267 (DCC)
R-Value Work: 0.243 (Depositor), 0.236 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.883	α = 90
b = 121.883	β = 90
c = 121.883	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-11-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-11-20
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.