7CMF | pdb_00007cmf

Crystal structure of human P-cadherin REC12 (monomer) in complex with 2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine (inhibitor)

• PDB DOI: https://doi.org/10.2210/pdb7CMF/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-27 Released: 2021-09-15 
• Deposition Author(s): Senoo, A., Ito, S., Ueno, G., Nagatoishi, S., Tsumoto, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.283 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: experimental

Literature

Regulation of cadherin dimerization by chemical fragments as a trigger to inhibit cell adhesion

Senoo, A., Ito, S., Nagatoishi, S., Saito, Y., Ueno, G., Kuroda, D., Yoshida, K., Tashima, T., Kudo, S., Sando, S., Tsumoto, K.

(2021) Commun Biol 4: 1041

• DOI: https://doi.org/10.1038/s42003-021-02575-3

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 23.82 kDa 
• Atom Count: 1,664 
• Modeled Residue Count: 212 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cadherin-3	A	214	Homo sapiens	Mutation(s): 0  Gene Names: CDH3, CDHP
UniProt & NIH Common Fund Data Resources
Find proteins for P22223 (Homo sapiens) Explore P22223  Go to UniProtKB:  P22223
PHAROS:  P22223 GTEx:  ENSG00000062038

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G60 (Subject of Investigation/LOI)	F [auth A]	2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine C11 H13 Cl N2 PPPQHAMKVHECAL-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.283 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.311	α = 90
b = 40.764	β = 97.39
c = 72.567	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-15 
Deposition Author(s): Senoo, A., Ito, S., Ueno, G., Nagatoishi, S., Tsumoto, K.

Revision History  

• Version 1.0: 2021-09-15
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description