1YWN: Vegfr2

Vegfr2 in complex with a novel 4-amino-furo[2,3-d]pyrimidine. Determined by X-ray diffraction at 1.71 Å resolution. Released 23 Aug 2005.

Method: X-ray diffraction
Resolution: 1.71 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,512
Mol. weight: 36.89 kDa
Ligands: LIF
Released: 23 Aug 2005

Explore 1YWN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YWN 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	832-840	9	1
β-strand	845-852	8	1
β-strand	860-867	8	1
α-helix	874-890	17
β-strand	896	1	2
β-strand	899-903	5	1
β-strand	911-915	5	1
β-strand	921	1	2
α-helix	922-928	7
α-helix	930-932	3
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	1072-1077	6
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

>1YWN_1 Vascular endothelial growth factor receptor 2 (chains A)
MDPDELPLDEHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTV
AVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLS
TYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNIL
LSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLL
WEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSE
LVEHLGNLLQANAQQD

Ligands and cofactors

ID	Name	Formula	Copies
LIF	N-{4-[4-amino-6-(4-METHOXYPHENYL)FURO[2,3-d]pyrimidin-5-yl]phenyl}-N'-[2-fluoro…	C27 H19 F4 N5 O3	1

Primary citation

Novel 4-amino-furo[2,3-d]pyrimidines as Tie-2 and VEGFR2 dual inhibitors. Miyazaki, Y., Matsunaga, S., Tang, J. et al. Bioorg Med Chem Lett (2005) 15:2203-2207. DOI 10.1016/j.bmcl.2005.03.034 · 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…
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

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