7CME

Crystal structure of human P-cadherin MEC12 (X dimer) in complex with 2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine (inhibitor)

PDB DOI: https://doi.org/10.2210/pdb7CME/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.249
R-Value Work: 0.209
R-Value Observed: 0.211

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 47.87 kDa
Atom Count: 3,388
Modelled Residue Count: 428
Deposited Residue Count: 428
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cadherin-3	A, B	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22223
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G60 (Subject of Investigation/LOI) Query on G60 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	2-(5-chloro-2-methyl-1H-indol-3-yl)ethan-1-amine C₁₁ H₁₃ Cl N₂ PPPQHAMKVHECAL-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B]	C [auth A], J [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	G [auth A] H [auth A] I [auth A] K [auth B] L [auth B] G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]