3HNG: VEGFR1

Crystal structure of VEGFR1 in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide. Determined by X-ray diffraction at 2.7 Å resolution. Released 30 Jun 2009.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,357
Mol. weight: 41.45 kDa
Ligands: 8ST
Released: 30 Jun 2009

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

Secondary structure: helices and β-sheets

3HNG contains 23 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: 23 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	806-809	4
α-helix	817-820	4
β-strand	821	1	1
α-helix	824-826	3
β-strand	827-835	9	1
β-strand	839-847	9	1
α-helix	849-851	3
β-strand	855-863	9	1
α-helix	864	1
α-helix	869-883	15
β-strand	891	1	2
α-helix	892-893	2
β-strand	894-898	5	1
α-helix	904-905	2
β-strand	906-910	5	1
β-strand	916	1	2
α-helix	917-922	6
α-helix	996-1014	19
α-helix	1025-1027	3
β-strand	1028-1030	3	2
α-helix	1032-1034	3
β-strand	1036-1038	3	2
α-helix	1042-1044	3
β-strand	1054-1055	2	3
β-strand	1060-1061	2	3
α-helix	1063-1065	3
α-helix	1068-1073	6
α-helix	1078-1093	16
α-helix	1097-1098	2
α-helix	1107-1113	7
α-helix	1119-1121	3
α-helix	1127-1136	10
α-helix	1141-1143	3
α-helix	1145-1146	2
α-helix	1147-1157	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vascular endothelial growth factor receptor 1	A	protein	360	Homo sapiens	P17948 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3HNG_1 Vascular endothelial growth factor receptor 1 (chains A)
SMPDEVPLDEQCERLPYDASKWEFARERLKLGKSLGRGAFGKVVQASAFGIKKSPTCRTV
AVKMLKEGATASEYKALMTELKILTHIGHHLNVVNLLGACTKQGGPLMVIVEYCKYGNLS
NYLKSKRDLFFLNKDAALHMEPKKEKMEPGLEQGKKPRLDSVTSSESFASSGFQEDKSLS
DVEEEEDSDGFYKEPITMEDLISYSFQVARGMEFLSSRKCIHRDLAARNILLSENNVVKI
CDFGLARDIYKNPDYVRKGDTRLPLKWMAPESIFDKIYSTKSDVWSYGVLLWEIFSLGGS
PYPGVQMDEDFCSRLREGMRMRAPEYSTPEIYQIMLDCWHRDPKERPRFAELVEKLGDLL

Ligands and cofactors

ID	Name	Formula	Copies
8ST	N-(4-chlorophenyl)-2-[(pyridin-4-ylmethyl)amino]benzamide	C19 H16 Cl N3 O	1

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

Primary citation

Crystal structure of VEGFR1 in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide. Tresaugues, L., Roos, A., Arrowsmith, C.H. et al. To be published.

Other PDB entries of the same protein (UniProt P17948 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1FLT 1.7 Å, Vegf in complex with domain 2 of the flt-1 receptor
5ABD 2.0 Å, Crystal structure of vegfr-1 domain 2 in presence of CU
4CL7 2.0 Å, Crystal structure of VEGFR-1 domain 2 in presence of Cobalt
4CKV 2.06 Å, Crystal structure of VEGFR-1 domain 2 in presence of Zn
5EX3 2.41 Å, Crystal structure of human SMYD3 in complex with a VEGFR1 peptide
1RV6 2.45 Å, Crystal Structure of PlGF in Complex with Domain 2 of VEGFR1
1QTY 2.7 Å, Vascular endothelial growth factor in complex with domain 2 of the flt-1 receptor
2XAC 2.71 Å, Structural Insights into the Binding of VEGF-B by VEGFR-1D2: Recognition and Specificity
5T89 4.0 Å, Crystal structure of VEGF-A in complex with VEGFR-1 domains D1-6
1QSV The vegf-binding domain of flt-1, 20 NMR structures
1QSZ The vegf-binding domain of flt-1 (minimized mean)

Browse structure collections

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