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- PDB-3i97: B1 domain of human Neuropilin-1 bound with small molecule EG00229 -

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Basic information

Entry
Database: PDB / ID: 3i97
TitleB1 domain of human Neuropilin-1 bound with small molecule EG00229
ComponentsNeuropilin-1
KeywordsSIGNALING PROTEIN / Neuropilin-1 / Drug / VEGF / Angiogenesis / Neuropilin / Alternative splicing / Cell membrane / Developmental protein / Differentiation / Disulfide bond / Glycoprotein / Heparan sulfate / Membrane / Neurogenesis / Phosphoprotein / Polymorphism / Proteoglycan / Receptor / Secreted / Transmembrane / MEMBRANE PROTEIN
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 / regulation of vascular endothelial growth factor receptor signaling pathway / dorsal root ganglion morphogenesis ...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 / regulation of vascular endothelial growth factor receptor signaling pathway / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / neurofilament / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / renal artery morphogenesis / postsynapse organization / negative regulation of axon extension involved in axon guidance / VEGF-activated neuropilin signaling pathway / axon extension involved in axon guidance / sympathetic neuron projection extension / vascular endothelial growth factor binding / Neurophilin interactions with VEGF and VEGFR / 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 / vascular endothelial growth factor receptor activity / outflow tract septum morphogenesis / regulation of vesicle-mediated transport / Signaling by ROBO receptors / semaphorin receptor complex / angiogenesis involved in coronary vascular morphogenesis / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / neuropilin signaling pathway / hepatocyte growth factor receptor signaling pathway / coronary artery morphogenesis / substrate-dependent cell migration, cell extension / semaphorin receptor activity / CRMPs in Sema3A signaling / commissural neuron axon guidance / axonal fasciculation / cell migration involved in sprouting angiogenesis / regulation of Cdc42 protein signal transduction / motor neuron axon guidance / sprouting angiogenesis / neural crest cell migration / positive regulation of filopodium assembly / artery morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / cellular response to hepatocyte growth factor stimulus / branching involved in blood vessel morphogenesis / retinal ganglion cell axon guidance / positive chemotaxis / positive regulation of smooth muscle cell migration / cytokine binding / growth factor binding / sorting endosome / positive regulation of focal adhesion assembly / Sema3A PAK dependent Axon repulsion / platelet-derived growth factor receptor signaling pathway / semaphorin-plexin signaling pathway / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / coreceptor activity / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / GTPase activator activity / Signal transduction by L1 / axon guidance / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / animal organ morphogenesis / mitochondrial membrane / neuron migration / response to wounding / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell signaling / heparin binding / cytoplasmic vesicle / angiogenesis / postsynaptic membrane / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / Attachment and Entry / early endosome / receptor complex / 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) / : / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 2. ...Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / : / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 2. / 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 domain-like / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-8DR / Neuropilin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAllerston, C.K. / Djordjevic, S.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Small molecule inhibitors of the neuropilin-1 vascular endothelial growth factor A (VEGF-A) interaction.
Authors: Jarvis, A. / Allerston, C.K. / Jia, H. / Herzog, B. / Garza-Garcia, A. / Winfield, N. / Ellard, K. / Aqil, R. / Lynch, R. / Chapman, C. / Hartzoulakis, B. / Nally, J. / Stewart, M. / Cheng, ...Authors: Jarvis, A. / Allerston, C.K. / Jia, H. / Herzog, B. / Garza-Garcia, A. / Winfield, N. / Ellard, K. / Aqil, R. / Lynch, R. / Chapman, C. / Hartzoulakis, B. / Nally, J. / Stewart, M. / Cheng, L. / Menon, M. / Tickner, M. / Djordjevic, S. / Driscoll, P.C. / Zachary, I. / Selwood, D.L.
History
DepositionJul 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)36,9225
Polymers35,8352
Non-polymers1,0873
Water1448
1
A: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5073
Polymers17,9171
Non-polymers5902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neuropilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4152
Polymers17,9171
Non-polymers4981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.000, 89.600, 41.600
Angle α, β, γ (deg.)90.00, 97.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUTHRTHRAA5 - 448 - 47
21GLUGLUTHRTHRBB5 - 448 - 47
12ILEILESERSERAA54 - 9157 - 94
22ILEILESERSERBB54 - 9157 - 94
13GLYGLYTYRTYRAA111 - 150114 - 153
23GLYGLYTYRTYRBB111 - 150114 - 153

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 17917.291 Da / Num. of mol.: 2 / Fragment: domain B1, F5/8 type C 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NP1-B1, NRP, NRP1, VEGF165R / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: O14786
#2: Chemical ChemComp-8DR / (S)-2-(3-(benzo[c][1,2,5]thiadiazole-4-sulfonamido)thiophene-2-carboxamido)-5-guanidinopentanoic acid / (2S)-2-[[3-(2,1,3-benzothiadiazol-4-ylsulfonylamino)thiophen-2-yl]carbonylamino]-5-carbamimidamido-pentanoic acid


Mass: 497.572 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19N7O5S3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 293.15 K / pH: 6
Details: 100 mM MES (pH 6.0), 10% PEG 8K and 200 mM Zn(AcO, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 2008 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→30.33 Å / Num. obs: 5852 / % possible obs: 88 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 4 / % possible all: 85.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KEX

1kex


Resolution: 2.9→30.33 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.829 / SU B: 30.153 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R Free: 0.585 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 278 4.8 %RANDOM
Rwork0.216 ---
obs0.219 5573 87.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å2-0.14 Å2
2---0.82 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 70 8 2533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222588
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.973513
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4325306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.51324.182110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54315438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7841514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021954
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.31156
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3320.51784
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.5148
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.320.340
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.52
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.40521569
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6632510
X-RAY DIFFRACTIONr_scbond_it0.35521195
X-RAY DIFFRACTIONr_scangle_it0.56131003
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1316tight positional0.040.05
2300tight positional0.060.05
3321tight positional0.040.05
1316tight thermal0.070.5
2300tight thermal0.190.5
3321tight thermal0.160.5
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 15 -
Rwork0.297 396 -
obs--83.2 %

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