5ZGG

NMR structure of p75NTR transmembrane domain in complex with NSC49652

• PDB DOI:  https://doi.org/10.2210/pdb5ZGG/pdb
• BMRB: 36172

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2018-03-08 Released: 2019-03-13 
• Deposition Author(s): Lin, Z., Ibanez, C.
• Funding Organization(s): Tianjin

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

A Small Molecule Targeting the Transmembrane Domain of Death Receptor p75NTRInduces Melanoma Cell Death and Reduces Tumor Growth.

Goh, E.T.H., Lin, Z., Ahn, B.Y., Lopes-Rodrigues, V., Dang, N.H., Salim, S., Berger, B., Dymock, B., Senger, D.L., Ibanez, C.F.

(2018) Cell Chem Biol 25: 1485-1494.e5

• PubMed: 30293939 
• DOI: https://doi.org/10.1016/j.chembiol.2018.09.007
• Primary Citation of Related Structures:  
  5ZGG


• PubMed Abstract: 
  

Small molecules offer powerful ways to alter protein function. However, most proteins in the human proteome lack small-molecule probes, including the large class of non-catalytic transmembrane receptors, such as death receptors. We hypothesized that small molecules targeting the interfaces between transmembrane domains (TMDs) in receptor complexes may induce conformational changes that alter receptor function. Applying this concept in a screening assay, we identified a compound targeting the TMD of death receptor p75 ^NTR that induced profound conformational changes and receptor activity. The compound triggered apoptotic cell death dependent on p75 ^NTR and JNK activity in neurons and melanoma cells, and inhibited tumor growth in a melanoma mouse model. Due to their small size and crucial role in receptor activation, TMDs represent attractive targets for small-molecule manipulation of receptor function.

---

Organizational Affiliation: 

Department of Physiology, National University of Singapore, Singapore 117597, Singapore; Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore; Department of Cell and Molecular Biology, Karolinska Institute, Stockholm 17165, Sweden. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 7.66 kDa 
• Atom Count: 539 
• Modelled Residue Count: 68 
• Deposited Residue Count: 68 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 16	A, B	34	Homo sapiens	Mutation(s): 0  Gene Names: NGFR, TNFRSF16 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P08138 (Homo sapiens) Explore P08138  Go to UniProtKB:  P08138
PHAROS:  P08138

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9F6 (Subject of Investigation/LOI)	C [auth B]	(2E)-1-(2-hydroxyphenyl)-3-(pyridin-3-yl)prop-2-en-1-one C14 H11 N O2 CRWNZUBUBIULHB-BQYQJAHWSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-13 
Deposition Author(s): Lin, Z., Ibanez, C.

---

Funding Organization	Location	Grant Number
Tianjin	China	17JCYBJC24200

Revision History  

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2019-09-25
  Changes: Data collection, Database references