6Q7B | pdb_00006q7b

Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712 derivative ATDL09

PDB DOI: https://doi.org/10.2210/pdb6Q7B/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2018-12-13 Released: 2020-01-15
Deposition Author(s): Kudlinzki, D., Troester, A., Witt, K., Linhard, V.L., Gande, S.L., Saxena, K., Schwalbe, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.01 Å
R-Value Free:
0.203 (Depositor), 0.201 (DCC)
R-Value Work:
0.187 (Depositor), 0.186 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Effects of NVP-BHG712 chemical modifications on EPHA2 binding and affinity

Troester, A., Kudlinzki, D., Saxena, K., Gande, S., Schwalbe, H.

To be published.

Macromolecule Content

Total Structure Weight: 34.99 kDa
Atom Count: 2,674
Modeled Residue Count: 279
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29317
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HO5 Query on HO5 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	3-[[4-imidazol-1-yl-6-[(3~{S})-3-oxidanylpyrrolidin-1-yl]-1,3,5-triazin-2-yl]amino]-4-methyl-~{N}-[3-(trifluoromethyl)phenyl]benzamide C₂₅ H₂₃ F₃ N₈ O₂ IOGRLXUUAIVKHX-IBGZPJMESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.01 Å
R-Value Free: 0.203 (Depositor), 0.201 (DCC)
R-Value Work: 0.187 (Depositor), 0.186 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.8	α = 90
b = 106.807	β = 108.74
c = 40.402	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-01-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-01-15
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.