3VNT: Vascular endothelial growth factor receptor 2

Crystal Structure of the Kinase domain of Human VEGFR2 with a [1,3]thiazolo[5,4-b]pyridine derivative. Determined by X-ray diffraction at 1.64 Å resolution. Released 11 Apr 2012.

Method: X-ray diffraction
Resolution: 1.64 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,757
Mol. weight: 37.09 kDa
Ligands: 0JA
Released: 11 Apr 2012

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

Secondary structure: helices and β-sheets

3VNT contains 21 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: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	813-815	3
α-helix	817-819	3
α-helix	824-827	4
β-strand	828	1	1
α-helix	831-833	3
β-strand	834-842	9	1
β-strand	846-854	9	1
β-strand	862-870	9	1
β-strand	872	1	2
β-strand	874	1	2
α-helix	876-892	17
β-strand	898	1	3
α-helix	899-900	2
β-strand	901-905	5	1
β-strand	913-917	5	1
β-strand	922-923	2	3
α-helix	924-930	7
β-strand	935	1	4
β-strand	1000	1	4
α-helix	1002-1021	20
α-helix	1031-1033	3
β-strand	1034-1036	3	3
α-helix	1038-1040	3
β-strand	1042-1044	3	3
α-helix	1048-1050	3
β-strand	1060-1062	3	5
β-strand	1065-1067	3	5
α-helix	1069-1071	3
α-helix	1074-1079	6
α-helix	1084-1099	16
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	1153-1167	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor receptor 2	A	protein	318	Homo sapiens	P35968 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3VNT_1 Vascular endothelial growth factor receptor 2 (chains A)
GAMDPDELPLDEHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCR
TVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGN
LSTYLRSKRNEFVPYKEAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARN
ILLSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGV
LLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTF
SELVEHLGNLLQANAQQD

Ligands and cofactors

ID	Name	Formula	Copies
0JA	2-chloro-3-(1-cyanocyclopropyl)-N-[5-({2-[(cyclopropylcarbonyl)amino][1,3]thiaz…	C27 H19 Cl F N5 O3 S	1

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

Primary citation

Design and synthesis of novel DFG-out RAF/vascular endothelial growth factor receptor 2 (VEGFR2) inhibitors. 1. Exploration of [5,6]-fused bicyclic scaffolds. Okaniwa, M., Hirose, M., Imada, T. et al. J Med Chem (2012) 55:3452-3478. DOI 10.1021/jm300126x · 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…
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…
3WZE 1.9 Å, KDR in complex with ligand sorafenib

Browse structure collections

About this viewer

MolViewer shows 3VNT directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.