6RD2

ENAH EVH1 in complex with Ac-[2-Cl-F]-[ProM-2]-[ProM-1]-TEDEL-NH2

PDB DOI: https://doi.org/10.2210/pdb6RD2/pdb

Classification: CELL ADHESION
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-04-12 Released: 2020-05-13
Deposition Author(s): Barone, M., Roske, Y.
Funding Organization(s): German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.224
R-Value Work: 0.198
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Designed nanomolar small-molecule inhibitors of Ena/VASP EVH1 interaction impair invasion and extravasation of breast cancer cells.

Barone, M., Muller, M., Chiha, S., Ren, J., Albat, D., Soicke, A., Dohmen, S., Klein, M., Bruns, J., van Dinther, M., Opitz, R., Lindemann, P., Beerbaum, M., Motzny, K., Roske, Y., Schmieder, P., Volkmer, R., Nazare, M., Heinemann, U., Oschkinat, H., Ten Dijke, P., Schmalz, H.G., Kuhne, R.

(2020) Proc Natl Acad Sci U S A 117: 29684-29690

PubMed: 33184177 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.2007213117
Primary Citation of Related Structures:
5N91, 5N9C, 5N9P, 5NAJ, 5NBF, 5NBX, 5NC2, 5NC7, 5NCF, 5NCG, 5NCP, 5ND0, 5NDU, 5NEG, 6RCF, 6RCJ, 6RD2, 6XVT, 6XXR, 7A5M, 7AKI

PubMed Abstract:

Battling metastasis through inhibition of cell motility is considered a promising approach to support cancer therapies. In this context, Ena/VASP-depending signaling pathways, in particular interactions with their EVH1 domains, are promising targets for pharmaceutical intervention. However, protein-protein interactions involving proline-rich segments are notoriously difficult to address by small molecules. Hence, structure-based design efforts in combination with the chemical synthesis of additional molecular entities are required. Building on a previously developed nonpeptidic micromolar inhibitor, we determined 22 crystal structures of ENAH EVH1 in complex with inhibitors and rationally extended our library of conformationally defined proline-derived modules (ProMs) to succeed in developing a nanomolar inhibitor ([Formula: see text] Da). In contrast to the previous inhibitor, the optimized compounds reduced extravasation of invasive breast cancer cells in a zebrafish model. This study represents an example of successful, structure-guided development of low molecular weight inhibitors specifically and selectively addressing a proline-rich sequence-recognizing domain that is characterized by a shallow epitope lacking defined binding pockets. The evolved high-affinity inhibitor may now serve as a tool in validating the basic therapeutic concept, i.e., the suppression of cancer metastasis by inhibiting a crucial protein-protein interaction involved in actin filament processing and cell migration.

Related Citations:

A modular toolkit to inhibit proline-rich motif-mediated protein-protein interactions.
Opitz, R., Mueller, M., Reuter, C., Barone, M., Soicke, A., Roske, Y., Piotukh, K., Huy, P., Beerbaum, M., Wiesner, B., Beyermann, M., Schmieder, P., Freund, C., Volkmer, R., Oschkinat, H., Schmalz, H.G., Kuehne, R.
(2015) Proc Natl Acad Sci U S A 112: 5011

Organizational Affiliation:

Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; kuehne@fmp-berlin.de p.ten_dijke@lumc.nl schmalz@uni-koeln.de.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein enabled homolog	A [auth B], B [auth A]	113	Homo sapiens	Mutation(s): 0 Gene Names: ENAH, MENA
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N8S7 (Homo sapiens) Explore Q8N8S7 Go to UniProtKB: Q8N8S7
PHAROS: Q8N8S7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N8S7
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
THR-GLU-ASP-GLU-NLW	C, D	5	synthetic construct	Mutation(s): 0
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K1N Query on K1N Download Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain S [auth D] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D]	R [auth C], S [auth D]	(3~{S},7~{R},10~{R},13~{S})-4-[(3~{S},6~{R},8~{a}~{S})-1'-[(2~{S})-2-acetamido-3-(2-chlorophenyl)propanoyl]-5-oxidanylidene-spiro[1,2,3,8~{a}-tetrahydroindolizine-6,2'-pyrrolidine]-3-yl]carbonyl-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-ene-13-carboxylic acid C₃₅ H₄₀ Cl N₅ O₇ AYDUPBNKBXOHLZ-QHVDBZGRSA-N		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A]	K [auth B], P [auth A], Q [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A]	E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], L [auth A], M [auth A], N [auth A], O [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Ligand Interaction