4G2F: Human EphA3 kinase domain

Human EphA3 kinase domain in complex with compound 7. Determined by X-ray diffraction at 1.7 Å resolution. Released 24 Oct 2012.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,462
Mol. weight: 40.78 kDa
Ligands: C07
Released: 24 Oct 2012

Explore 4G2F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4G2F contains 20 α-helices and 16 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 20 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	614	1
β-strand	615	1	1
α-helix	616-617	2
α-helix	618-620	3
β-strand	621-629	9	1
β-strand	634-641	8	1
β-strand	647-654	8	1
α-helix	655-656	2
α-helix	661-674	14
β-strand	682	1	2
α-helix	683-684	2
β-strand	685-689	5	1
β-strand	696-700	5	1
β-strand	706	1	2
α-helix	707-712	6
α-helix	720-739	20
β-strand	742-743	2	3
α-helix	749-751	3
β-strand	752-754	3	2
β-strand	760-762	3	2
β-strand	769-770	2	3
α-helix	788-790	3
α-helix	793-798	6
α-helix	803-818	16
α-helix	822-823	2
α-helix	830-838	9
β-strand	842	1	4
α-helix	843-846	4
β-strand	850	1	5
α-helix	851-860	10
α-helix	865-867	3
α-helix	869-870	2
α-helix	871-883	13
α-helix	885-887	3
β-strand	891	1	5
β-strand	902	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
EPH receptor A3	A	protein	361	Homo sapiens	P29320 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4G2F_1 EPH receptor A3 (chains A)
MGSSHHHHHHSSGLVPRGSTQTVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKLPSKK
EISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGS
LDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFG
LSRVLEDDPEAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYW
EMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPG
SLKIITSAAARPSNLLLDQSNVDITTFRTTGDWLNGVWTAHCKEIFTGVEYSSCDTIAKI
S

Ligands and cofactors

ID	Name	Formula	Copies
C07	1-amino-5-(5-hydroxy-2-methylphenyl)-7,8,9,10-tetrahydropyrimido[4,5-c]isoquino…	C18 H18 N4 O2	1

Primary citation

Discovery of a novel chemotype of tyrosine kinase inhibitors by fragment-based docking and molecular dynamics. Zhao, H., Dong, J., Lafleur, K. et al. ACS Med Chem Lett (2012) 3:834-838. DOI 10.1021/ml3001984 · PubMed

Other PDB entries of the same protein (UniProt P29320 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2QOL 1.07 Å, Human EphA3 kinase and juxtamembrane region, Y596:Y602:S768G triple mutant
2QOD 1.15 Å, Human EphA3 kinase and juxtamembrane region, Y602F mutant
2QOF 1.2 Å, Human EphA3 kinase and juxtamembrane region, Y596F mutant
2QOK 1.2 Å, Human EphA3 kinase and juxtamembrane region, Y596F:Y602F:S768A triple mutant
2QOC 1.25 Å, Human EphA3 kinase domain, phosphorylated, AMP-PNP bound structure
2QOI 1.25 Å, Human EphA3 kinase and juxtamembrane region, Y596F:Y602F double mutant
2QOO 1.25 Å, Human EphA3 kinase and juxtamembrane region, Y596F:Y602F:Y742F triple mutant
4P5Q 1.35 Å, Human EphA3 Kinase domain in complex with quinoxaline derivatives
6IN0 1.5 Å, Crystal structure of EphA3 in complex with 18-Crown-6
2QO9 1.55 Å, Human EphA3 kinase and juxtamembrane region, phosphorylated, AMP-PNP bound
4P4C 1.6 Å, Human EphA3 Kinase domain in complex with quinoxaline derivatives
2QO2 1.6 Å, Human EphA3 kinase and juxtamembrane region, dephosphorylated, apo structure

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