3BE2: VEGFR2 kinase domain

Crystal structure of the VEGFR2 kinase domain in complex with a benzamide inhibitor. Determined by X-ray diffraction at 1.75 Å resolution. Released 8 Apr 2008.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,654
Mol. weight: 36.82 kDa
Ligands: RAJ
Released: 8 Apr 2008

Explore 3BE2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3BE2 contains 20 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: 20 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	817-819	3
α-helix	824-827	4
β-strand	828	1	1
α-helix	831-833	3
β-strand	834-843	10	1
β-strand	846-854	9	1
β-strand	862-870	9	1
α-helix	871	1
α-helix	876-892	17
β-strand	898	1	2
β-strand	901-905	5	1
β-strand	913-917	5	1
β-strand	923	1	2
α-helix	924-930	7
β-strand	935	1	3
α-helix	993-996	4
β-strand	1000	1	3
α-helix	1002-1021	20
α-helix	1031-1033	3
β-strand	1034-1036	3	2
α-helix	1038-1040	3
β-strand	1042-1044	3	2
α-helix	1069-1071	3
α-helix	1074-1079	6
α-helix	1084-1098	15
α-helix	1103-1104	2
α-helix	1113-1121	9
α-helix	1125-1128	4
α-helix	1133-1142	10
α-helix	1147-1149	3
α-helix	1151-1152	2
α-helix	1153-1170	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor receptor 2	A	protein	314	Homo sapiens	P35968 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3BE2_1 Vascular endothelial growth factor receptor 2 (chains A)
EHAERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTVAVKMLKEGA
THSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVITEFCKFGNLSTYLRSKRNE
FVPYKVAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKI
CDFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGAS
PYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLL
QANAQQDRHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
RAJ	N-{3-[3-(dimethylamino)propyl]-5-(trifluoromethyl)phenyl}-4-methyl-3-[(3-pyrimi…	C29 H29 F3 N6 O	1

Primary citation

Naphthamides as novel and potent vascular endothelial growth factor receptor tyrosine kinase inhibitors: design, synthesis, and evaluation. Harmange, J.C., Weiss, M.M., Germain, J. et al. J Med Chem (2008) 51:1649-1667. DOI 10.1021/jm701097z · PubMed

Other PDB entries of the same protein (UniProt P35968 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2XIR 1.5 Å, Crystal structure of the VEGFR2 kinase domain in complex with PF- 00337210…
3VO3 1.52 Å, Crystal Structure of the Kinase domain of Human VEGFR2 with imidazo[1,2-b]pyridazine…
6GQQ 1.52 Å, Crystal structure of human KDR (VEGFR2) kinase domain in complex with AZD3229-analogue…
3VHE 1.55 Å, Crystal structure of human VEGFR2 kinase domain with a novel pyrrolopyrimidine inhibitor.
3WZD 1.57 Å, KDR in complex with ligand lenvatinib
3EWH 1.6 Å, Crystal structure of the VEGFR2 kinase domain in complex with a pyridyl-pyrimidine…
3VNT 1.64 Å, Crystal Structure of the Kinase domain of Human VEGFR2 with a…
1YWN 1.71 Å, Vegfr2 in complex with a novel 4-amino-furo[2,3-d]pyrimidine
6XVJ 1.78 Å, Crystal structure of the KDR (VEGFR2) kinase domain in complex with a type-II inhibitor
4ASE 1.83 Å, Crystal structure of VEGFR2 (juxtamembrane and kinase domains) in complex with tivozanib…
6GQO 1.87 Å, Crystal structure of human KDR (VEGFR2) kinase domain in complex with AZD3229-analogue…
3WZE 1.9 Å, KDR in complex with ligand sorafenib

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