9F6B | pdb_00009f6b

Human neuropilin-1 in a complex with a quinoline based antagonists

• PDB DOI: https://doi.org/10.2210/pdb9F6B/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-30 Released: 2025-05-14 
• Deposition Author(s): Djordjevic, S., Selwood, D., Hubbard, P., Leonard, P., Mota, F.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.239 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Quinoline based neuropilin-1 antagonists exhibit a pure antagonist profile and block pain transmission

Mota, F., Selwood, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.03 kDa 
• Atom Count: 3,023 
• Modeled Residue Count: 310 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuropilin-1	A, B	158	Homo sapiens	Mutation(s): 0  Gene Names: NRP1, NRP, VEGF165R
UniProt & NIH Common Fund Data Resources
Find proteins for O14786 (Homo sapiens) Explore O14786  Go to UniProtKB:  O14786
PHAROS:  O14786 GTEx:  ENSG00000099250

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IAT (Subject of Investigation/LOI)	C [auth A], D [auth B]	(2~{S})-2-[[3-[[6-[3-(aminomethyl)phenyl]quinolin-8-yl]sulfonylamino]thiophen-2-yl]carbonylamino]-5-carbamimidamido-pentanoic acid C27 H29 N7 O5 S2 FXBLSUJMVWPWDW-NRFANRHFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.239 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.57	α = 90
b = 92.22	β = 94.84
c = 40.83	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Djordjevic, S., Selwood, D., Hubbard, P., Leonard, P., Mota, F.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release