8BK0

Crystal structure of human Ephrin type-A receptor 2 (EPHA2) Kinase domain in complex with LDN-211904

PDB DOI: https://doi.org/10.2210/pdb8BK0/pdb

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

Deposited: 2022-11-08 Released: 2022-11-16
Deposition Author(s): Zhubi, R., Gerninghaus, J., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)
Funding Organization(s): The Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.195
R-Value Work: 0.167
R-Value Observed: 0.168

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of human Ephrin type-A receptor 2 (EPHA2) Kinase domain in complex with LDN-211904

Zhubi, R., Gerninghaus, J., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 35.31 kDa
Atom Count: 2,294
Modelled Residue Count: 266
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-A receptor 2	A	306	Homo sapiens	Mutation(s): 0 Gene Names: EPHA2, ECK EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29317 (Homo sapiens) Explore P29317 Go to UniProtKB: P29317
PHAROS: P29317 GTEx: ENSG00000142627
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29317
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QJI (Subject of Investigation/LOI) Query on QJI Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	~{N}-(2-chlorophenyl)-6-piperidin-4-yl-imidazo[1,2-a]pyridine-3-carboxamide C₁₉ H₁₉ Cl N₄ O DGSMEFWSLXFLQA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A]