6GQO: Human KDR (VEGFR2) kinase domain

Crystal structure of human KDR (VEGFR2) kinase domain in complex with AZD3229-analogue (compound 18). Determined by X-ray diffraction at 1.87 Å resolution. Released 19 Sept 2018.

Method: X-ray diffraction
Resolution: 1.87 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,647
Mol. weight: 37.47 kDa
Ligands: F82
Released: 19 Sept 2018

Explore 6GQO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GQO contains 22 α-helices and 14 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: 22 helices, 14 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	834-839	6	1
β-strand	846-854	9	1
β-strand	862-870	9	1
α-helix	876-892	17
β-strand	898	1	2
α-helix	899-900	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	943-946	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	1048-1050	3
β-strand	1060-1062	3	4
β-strand	1065-1067	3	4
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	322	Homo sapiens	P35968 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6GQO_1 Vascular endothelial growth factor receptor 2 (chains A)
MDPDELPLDEHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTV
AVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLS
TYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNIL
LSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLL
WEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSE
LVEHLGNLLQANAQQDENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
F82	2-[4-(6,7-dimethoxyquinazolin-4-yl)oxy-2-methoxy-phenyl]-~{N}-(1-propan-2-ylpyr…	C25 H27 N5 O5	1

Primary citation

Discovery of N-(4-{[5-Fluoro-7-(2-methoxyethoxy)quinazolin-4-yl]amino}phenyl)-2-[4-(propan-2-yl)-1 H-1,2,3-triazol-1-yl]acetamide (AZD3229), a Potent Pan-KIT Mutant Inhibitor for the Treatment of Gastrointestinal Stromal Tumors. Kettle, J.G., Anjum, R., Barry, E. et al. J Med Chem (2018) 61:8797-8810. DOI 10.1021/acs.jmedchem.8b00938 · 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…
3WZE 1.9 Å, KDR in complex with ligand sorafenib

Browse structure collections

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