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- PDB-9f6b: Human neuropilin-1 in a complex with a quinoline based antagonists -

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Basic information

Entry
Database: PDB / ID: 9f6b
TitleHuman neuropilin-1 in a complex with a quinoline based antagonists
ComponentsNeuropilin-1
KeywordsSIGNALING PROTEIN / NRP-1 small molecule antagonist pain transmission
Function / homology
Function and homology information


endothelial tip cell fate specification / basal dendrite development / otic placode development / protein localization to early endosome / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration ...endothelial tip cell fate specification / basal dendrite development / otic placode development / protein localization to early endosome / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / trigeminal nerve structural organization / sensory neuron axon guidance / postsynapse organization / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / negative regulation of axon extension involved in axon guidance / axon extension involved in axon guidance / renal artery morphogenesis / VEGF-activated neuropilin signaling pathway / neurofilament / sympathetic neuron projection extension / regulation of vascular endothelial growth factor receptor signaling pathway / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / endothelial cell chemotaxis / motor neuron migration / neural crest cell migration involved in autonomic nervous system development / sympathetic ganglion development / positive regulation of axon extension involved in axon guidance / axonogenesis involved in innervation / CHL1 interactions / semaphorin receptor complex / regulation of vesicle-mediated transport / Signaling by ROBO receptors / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / neuropilin signaling pathway / substrate-dependent cell migration, cell extension / hepatocyte growth factor receptor signaling pathway / coronary artery morphogenesis / angiogenesis involved in coronary vascular morphogenesis / CRMPs in Sema3A signaling / semaphorin receptor activity / commissural neuron axon guidance / outflow tract septum morphogenesis / motor neuron axon guidance / regulation of Cdc42 protein signal transduction / axonal fasciculation / cell migration involved in sprouting angiogenesis / neural crest cell migration / sprouting angiogenesis / positive regulation of filopodium assembly / artery morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / cellular response to hepatocyte growth factor stimulus / retinal ganglion cell axon guidance / branching involved in blood vessel morphogenesis / positive regulation of smooth muscle cell migration / positive chemotaxis / growth factor binding / cytokine binding / sorting endosome / semaphorin-plexin signaling pathway / platelet-derived growth factor receptor signaling pathway / Sema3A PAK dependent Axon repulsion / cellular response to vascular endothelial growth factor stimulus / positive regulation of focal adhesion assembly / vascular endothelial growth factor receptor signaling pathway / vasculogenesis / positive regulation of phosphorylation / coreceptor activity / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / GTPase activator activity / axon guidance / animal organ morphogenesis / Signal transduction by L1 / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / mitochondrial membrane / vascular endothelial growth factor receptor activity / response to wounding / neuron migration / positive regulation of angiogenesis / cell-cell signaling / heparin binding / cytoplasmic vesicle / angiogenesis / negative regulation of neuron apoptotic process / postsynaptic membrane / Attachment and Entry / early endosome / receptor complex / positive regulation of ERK1 and ERK2 cascade / neuron projection
Similarity search - Function
Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. ...Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsDjordjevic, S. / Selwood, D. / Hubbard, P. / Leonard, P. / Mota, F.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Quinoline based neuropilin-1 antagonists exhibit a pure antagonist profile and block pain transmission
Authors: Mota, F. / Selwood, D.
History
DepositionApr 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuropilin-1
B: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0264
Polymers35,8352
Non-polymers1,1912
Water8,287460
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-3 kcal/mol
Surface area15140 Å2
Unit cell
Length a, b, c (Å)40.570, 92.220, 40.830
Angle α, β, γ (deg.)90.00, 94.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Neuropilin-1 / Vascular endothelial cell growth factor 165 receptor


Mass: 17917.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP1, NRP, VEGF165R / Production host: Escherichia coli (E. coli) / References: UniProt: O14786
#2: Chemical ChemComp-A1IAT / (2~{S})-2-[[3-[[6-[3-(aminomethyl)phenyl]quinolin-8-yl]sulfonylamino]thiophen-2-yl]carbonylamino]-5-carbamimidamido-pentanoic acid


Mass: 595.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H29N7O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium Chloride, 14% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.57→20.51 Å / Num. obs: 41294 / % possible obs: 99 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.3
Reflection shellResolution: 1.57→1.6 Å / Rmerge(I) obs: 0.21 / Num. unique obs: 1640

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→20.51 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23905 2060 5 %RANDOM
Rwork0.19305 ---
obs0.19534 39098 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.874 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å2-0.13 Å2
2---0.43 Å20 Å2
3---0.2 Å2
Refinement stepCycle: 1 / Resolution: 1.57→20.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 82 460 3000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022636
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3441.9763592
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4645316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04424.018112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76215431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0461514
X-RAY DIFFRACTIONr_chiral_restr0.1580.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212012
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 147 -
Rwork0.238 2480 -
obs--87.83 %

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