2XVD: EphB4 kinase domain inhibitor complex

ephB4 kinase domain inhibitor complex. Determined by X-ray diffraction at 1.7 Å resolution. Released 8 Jun 2011.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: HOMO SAPIENS
Chains: 1
Atoms: 2,334
Mol. weight: 34.52 kDa
Ligands: AS6, MG
Released: 8 Jun 2011

Explore 2XVD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2XVD contains 18 α-helices and 12 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: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	609	1	1
α-helix	612-614	3
β-strand	615-623	9	1
β-strand	628-634	7	1
β-strand	642-648	7	1
α-helix	655-668	14
β-strand	676	1	2
α-helix	677-678	2
β-strand	679-683	5	1
β-strand	690-694	5	1
β-strand	700	1	2
α-helix	701-707	7
α-helix	714-733	20
α-helix	743-745	3
β-strand	746-748	3	2
β-strand	754-756	3	2
α-helix	762-765	4
α-helix	784-786	3
α-helix	789-794	6
α-helix	799-814	16
α-helix	818-819	2
α-helix	826-834	9
α-helix	839-842	4
β-strand	846	1	3
α-helix	847-856	10
α-helix	861-863	3
α-helix	865-866	2
α-helix	867-879	13
α-helix	881-885	5
β-strand	887	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ephrin type-B receptor 4	A	protein	302	HOMO SAPIENS	P54760 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2XVD_1 EPHRIN TYPE-B RECEPTOR 4 (chains A)
DPNEAVREFAKEIDVSYVKIEEVIGAGEFGEVCRGRLKAPGKKESCVAIKTLKGGYTERQ
RREFLSEASIMGQFEHPNIIRLEGVVTNSMPVMILTEFMENGALDSFLRLNDGQFTVIQL
VGMLRGIASGMRYLAEMSYVHRDLAARNILVNSNLVCKVSDFGLSRFLEENSSDPTETSS
LGGKIPIRWTAPEAIAFRKFTSASDAWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQDY
RLPPPPDCPTSLHQLMLDCWQKDRNARPRFPQVVSALDKMIRNPASLKIVARENGGASHP
LL

Ligands and cofactors

ID	Name	Formula	Copies
AS6	{4-methyl-3-[(1-METHYLETHYL)(2-{[3-(methylsulfonyl)-5-morpholin-4-ylphenyl]amin…	C26 H33 N5 O4 S	1
MG	Magnesium ion	Mg	3

Primary citation

Inhibitors of the Tyrosine Kinase Ephb4. Part 4: Discovery and Optimization of a Benzylic Alcohol Series. Barlaam, B., Ducray, R., Lambert-Van Der Brempt, C. et al. Bioorg Med Chem Lett (2011) 21:2207. DOI 10.1016/J.BMCL.2011.03.009 · PubMed

Other PDB entries of the same protein (UniProt P54760 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6FNK 1.05 Å, Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with a…
6FNM 1.16 Å, Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with Dasatinib
6FNJ 1.24 Å, Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with an isomer of…
6FNL 1.27 Å, Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase
6FNI 1.47 Å, Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with NVP-BHG712
2BBA 1.65 Å, Crystal Structure and Thermodynamic Characterization of the EphB4 Receptor in Complex…
2VWX 1.65 Å, ephB4 kinase domain inhibitor complex
2VWY 1.65 Å, ephB4 kinase domain inhibitor complex
2VWZ 1.65 Å, ephB4 kinase domain inhibitor complex
2VX1 1.65 Å, ephB4 kinase domain inhibitor complex
4BB4 1.65 Å, ephB4 kinase domain inhibitor complex
2X9F 1.75 Å, ephB4 kinase domain inhibitor complex

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