2OH4: Vegfr2 with a benzimidazole-urea inhibitor

Crystal structure of Vegfr2 with a benzimidazole-urea inhibitor. Determined by X-ray diffraction at 2.05 Å resolution. Released 18 Sept 2007.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,661
Mol. weight: 37.1 kDa
Ligands: GIG
Released: 18 Sept 2007

Explore 2OH4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2OH4 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
α-helix	822-825	4
β-strand	826	1	1
α-helix	829-831	3
β-strand	832-841	10	1
β-strand	844-852	9	1
β-strand	860-867	8	1
α-helix	868-869	2
α-helix	874-890	17
β-strand	896	1	2
β-strand	899-903	5	1
β-strand	911-915	5	1
β-strand	920-921	2	2
α-helix	922-928	7
β-strand	933	1	3
β-strand	998	1	3
α-helix	1000-1019	20
α-helix	1029-1031	3
β-strand	1032-1034	3	2
α-helix	1036-1038	3
β-strand	1040-1042	3	2
α-helix	1066-1069	4
α-helix	1072-1076	5
α-helix	1082-1097	16
α-helix	1101-1102	2
α-helix	1111-1119	9
α-helix	1123-1126	4
α-helix	1131-1140	10
α-helix	1145-1147	3
α-helix	1149-1150	2
α-helix	1151-1165	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor receptor 2	A	protein	316	Homo sapiens	P35968 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2OH4_1 Vascular endothelial growth factor receptor 2 (chains A)
HMDPDELPLDEHCERLPYDASKWEFPRDRLNLGKPLGRGAFGQVIEADAFGIDKTATCRT
VAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNL
STYLRSKRNEFVPYKTPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNIL
LSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLL
WEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSE
LVEHLGNLLQANAQQD

Ligands and cofactors

ID	Name	Formula	Copies
GIG	Methyl (5-{4-[({[2-fluoro-5-(trifluoromethyl)phenyl]amino}carbonyl)amino]phenox…	C23 H17 F4 N5 O4	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Discovery of Novel Benzimidazoles as Potent Inhibitors of TIE-2 and VEGFR-2 Tyrosine Kinase Receptors. Hasegawa, M., Nishigaki, N., Washio, Y. et al. J Med Chem (2007) 50:4453-4470. DOI 10.1021/jm0611051 · 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
3BE2 1.75 Å, Crystal structure of the VEGFR2 kinase domain in complex with a benzamide inhibitor
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…

Browse structure collections

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