3DZQ | pdb_00003dzq

Human EphA3 kinase domain in complex with inhibitor AWL-II-38.3

PDB DOI: https://doi.org/10.2210/pdb3DZQ/pdb

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

Deposited: 2008-07-30 Released: 2008-08-26
Deposition Author(s): Walker, J.R., Syeda, F., Gray, N., Mansoor, W., Mackenzie, F., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.193 (Depositor), 0.196 (DCC)
R-Value Work:
0.161 (Depositor), 0.165 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Kinase Domain of Human Ephrin Type-A Receptor 3 (Epha3) in Complex with ALW-II-38-3.

Walker, J.R., Syeda, F., Gray, N., Mansoor, W., Mackenzie, F., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

To be published.

Macromolecule Content

Total Structure Weight: 40.93 kDa
Atom Count: 2,482
Modeled Residue Count: 268
Deposited Residue Count: 361
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EPH receptor A3	A	361	Homo sapiens	Mutation(s): 0 Gene Names: EPHA3 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29320 (Homo sapiens) Explore P29320 Go to UniProtKB: P29320
PHAROS: P29320 GTEx: ENSG00000044524
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29320
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IFC Query on IFC 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]	N-[2-methyl-5-({[3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl]carbonyl}amino)phenyl]isoxazole-5-carboxamide C₂₃ H₁₈ F₃ N₅ O₃ IYUFHBXMTTXZBE-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.193 (Depositor), 0.196 (DCC)
R-Value Work: 0.161 (Depositor), 0.165 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.4	α = 90
b = 38.093	β = 101.75
c = 75.983	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-08-26

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-08-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description