6Q7E | pdb_00006q7e

Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712 derivative ATDL14

PDB DOI: https://doi.org/10.2210/pdb6Q7E/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: 1.06 Å
R-Value Free:
0.211 (Depositor), 0.210 (DCC)
R-Value Work:
0.192 (Depositor), 0.190 (DCC)
R-Value Observed:
0.193 (Depositor)

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

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: 2,687
Modeled Residue Count: 272
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

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(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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HMW Query on HMW 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~{R})-3-oxidanylpyrrolidin-1-yl]-1,3,5-triazin-2-yl]amino]-4-methyl-~{N}-[3-(trifluoromethyl)phenyl]benzamide C₂₅ H₂₃ F₃ N₈ O₂ IOGRLXUUAIVKHX-LJQANCHMSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.06 Å
R-Value Free: 0.211 (Depositor), 0.210 (DCC)
R-Value Work: 0.192 (Depositor), 0.190 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.868	α = 90
b = 107.211	β = 108.85
c = 40.516	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

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

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.