9F6B: Neuropilin-1

Human neuropilin-1 in a complex with a quinoline based antagonists. Determined by X-ray diffraction at 1.57 Å resolution. Released 14 May 2025.

Method: X-ray diffraction
Resolution: 1.57 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,023
Mol. weight: 37.03 kDa
Ligands: A1IAT
Released: 14 May 2025

Explore 9F6B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F6B contains 6 α-helices and 30 β-strands across 2 chains. 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.

Chains A and B: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	277-278	2	1
α-helix	288-290	3
β-strand	291-293	3	1
α-helix	299-301	3
α-helix	303-306	4
β-strand	307	1	1
β-strand	315	1	2
β-strand	326-342	17	1
β-strand	344-345	2	3
β-strand	352-353	2	3
β-strand	354-363	10	1
β-strand	370-371	2	1
β-strand	373-374	2	4
β-strand	377-378	2	4
β-strand	381-382	2	1
β-strand	391-412	22	1
β-strand	417	1	2
β-strand	418-424	7	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-1	A, B	protein	158	Homo sapiens	O14786 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9F6B_1 Neuropilin-1 (chains A, B)
GHMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVD
LGLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTD
VVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT

Ligands and cofactors

ID	Name	Formula	Copies
A1IAT	(2~{S})-2-[[3-[[6-[3-(aminomethyl)phenyl]quinolin-8-yl]sulfonylamino]thiophen-2…	C27 H29 N7 O5 S2	2

Primary citation

Quinoline-Based Neuropilin‐1 Antagonists Exhibit a Pure Antagonist Profile and Block Vascular Endothelial Growth Factor-Induced Pain. Hestehave, S., Dragoni, S., Fallon, P. et al. Acs Pharmacol Transl Sci (2025) 8:3844-3871. DOI 10.1021/acsptsci.5c00029 · PubMed

Other PDB entries of the same protein (UniProt O14786 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6FMC 0.9 Å, Neuropilin1-b1 domain in complex with EG01377, 0.9 Angstrom structure
6TKK 1.06 Å, Neuropilin 1-b1 domain in a complex with the C-terminal VEGFB186 peptide
8PFE 1.35 Å, Crystal Structure of an Hexavariant of the b1 Domain of Human Neuropilin-1 in Complex…
5JGI 1.38 Å, X-ray structure of neuropilin-1 b1 domain complexed with M45 compound
5C7G 1.45 Å, Crystal Structure of the b1 Domain of Human Neuropilin-1 in complex with a bicine molecule
5IJR 1.52 Å, X-ray structure of neuropilin-1 b1 domain complexed with Arg-1 ligand.
9EOU 1.55 Å, Crystal Structure of the b1b2 domains from Human Neuropilin-1 in complex with a peptide.
7O1N 1.56 Å, Crystal Structure of Human Neuropilin-1 b1 Domain mutant - Y297A
9S57 1.57 Å, The b1 and b2 domains of neuropilin-1 with a bound VGF TLQP-21 peptide
5IYY 1.6 Å, X-ray structure of neuropilin-1 b1 domain complexed with Arg-4 ligand.
5JGQ 1.6 Å, X-ray structure of neuropilin-1 b1 domain complexed with Arg-7 ligand.
7P5U 1.6 Å, Neuropilin-b1 in a complex with a VEGFB-derived peptide

Browse structure collections

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