Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T15023 | Target Info | |||
| Target Name | Neuropilin-1 (NRP1) | ||||
| Synonyms | Vascular endothelial cell growth factor 165 receptor; VEGF165R; Platelet-derived endothelial cell growth factor receptor; NRP; Membrane-bound; CD304 | ||||
| Target Type | Successful Target | ||||
| Gene Name | NRP1 | ||||
| Biochemical Class | Neuropilin and tolloid-like | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: L-Homoarginine | Ligand Info | |||||
| Structure Description | X-ray structure of neuropilin-1 b1 domain complexed with Arg-1 ligand. | PDB:5IJR | ||||
| Method | X-ray diffraction | Resolution | 1.52 Å | Mutation | No | [1] |
| PDB Sequence |
KCMEALGMES
283 GEIHSDQITA293 SSQYSTNWSA303 ERSRLNYPEN313 GWTPGEDSYR323 EWIQVDLGLL 333 RFVTAVGTQG343 AISKETKKKY353 YVKTYKIDVS363 SNGEDWITIK373 EGNKPVLFQG 383 NTNPTDVVVA393 VFPKPLITRF403 VRIKPATWET413 GISMRFEVYG423 CKIT |
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| Ligand Name: Tris(hydroxyethyl)aminomethane | Ligand Info | |||||
| Structure Description | MAM domain of human neuropilin-1 | PDB:5L73 | ||||
| Method | X-ray diffraction | Resolution | 2.24 Å | Mutation | No | [2] |
| PDB Sequence |
QDEFPDYGFN
649 CEFGWGSHKT659 FCHWEHDNHV669 QLKWSVLTSK679 TGPIQDHTGD689 GNFIYSQADE 699 NQKGKVARLV709 SPVVYSQNSA719 HCMTFWYHMS729 GSHVGTLRVK739 LRYQKPEEYD 749 QLVWMAIGHQ759 GDHWKEGRVL769 LHKSLKLYQV779 IFEGEIGKGN789 LGGIAVDDIS 799 INNHISQEDC809 AKPA
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| Ligand Name: (2~{S})-2-[[3-[[5-[4-(aminomethyl)phenyl]-1-benzofuran-7-yl]sulfonylamino]thiophen-2-yl]carbonylamino]-5-carbamimidamido-pentanoic acid | Ligand Info | |||||
| Structure Description | Neuropilin1-b1 domain in complex with EG01377, 0.9 Angstrom structure | PDB:6FMC | ||||
| Method | X-ray diffraction | Resolution | 0.90 Å | Mutation | No | [3] |
| PDB Sequence |
GHMFKCMEAL
279 GMESGEIHSD289 QITASSQYST299 NWSAERSRLN309 YPENGWTPGE319 DSYREWIQVD 329 LGLLRFVTAV339 GTQGAISKET349 KKKYYVKTYK359 IDVSSNGEDW369 ITIKEGNKPV 379 LFQGNTNPTD389 VVVAVFPKPL399 ITRFVRIKPA409 TWETGISMRF419 EVYGCKIT |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DUE or .DUE2 or .DUE3 or :3DUE;style chemicals stick;color identity;select .A:297 or .A:301 or .A:316 or .A:320 or .A:346 or .A:348 or .A:349 or .A:351 or .A:353 or .A:414 or .A:415; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: L-Arginine, N2-[(phenylmethoxy)carbonyl]- | Ligand Info | |||||
| Structure Description | X-ray structure of neuropilin-1 b1 domain complexed with Arg-4 ligand. | PDB:5IYY | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [1] |
| PDB Sequence |
MFKCMEALGM
281 ESGEIHSDQI291 TASSQYSTNW301 SAERSRLNYP311 ENGWTPGEDS321 YREWIQVDLG 331 LLRFVTAVGT341 QGAISKETKK351 KYYVKTYKID361 VSSNGEDWIT371 IKEGNKPVLF 381 QGNTNPTDVV391 VAVFPKPLIT401 RFVRIKPATW411 ETGISMRFEV421 YGCKIT |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .R40 or .R402 or .R403 or :3R40;style chemicals stick;color identity;select .A:297 or .A:301 or .A:316 or .A:320 or .A:346 or .A:348 or .A:349 or .A:351 or .A:353 or .A:413 or .A:414 or .A:415; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Hippuryl-L-arginine | Ligand Info | |||||
| Structure Description | X-ray structure of neuropilin-1 b1 domain complexed with Arg-6 ligand. | PDB:5JHK | ||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [1] |
| PDB Sequence |
KCMEALGMES
283 GEIHSDQITA293 SSQYSTNWSA303 ERSRLNYPEN313 GWTPGEDSYR323 EWIQVDLGLL 333 RFVTAVGTQG343 AISKETKKKY353 YVKTYKIDVS363 SNGEDWITIK373 EGNKPVLFQG 383 NTNPTDVVVA393 VFPKPLITRF403 VRIKPATWET413 GISMRFEVYG423 CKIT |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6K8 or .6K82 or .6K83 or :36K8;style chemicals stick;color identity;select .A:297 or .A:300 or .A:301 or .A:316 or .A:320 or .A:346 or .A:348 or .A:349 or .A:351 or .A:353 or .A:414 or .A:415; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: CID 6992570 | Ligand Info | |||||
| Structure Description | X-ray structure of neuropilin-1 b1 domain complexed with Arg-5 ligand. | PDB:5J1X | ||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | No | [1] |
| PDB Sequence |
FKCMEALGME
282 SGEIHSDQIT292 ASSQYSTNWS302 AERSRLNYPE312 NGWTPGEDSY322 REWIQVDLGL 332 LRFVTAVGTQ342 GAISKETKKK352 YYVKTYKIDV362 SSNGEDWITI372 KEGNKPVLFQ 382 GNTNPTDVVV392 AVFPKPLITR402 FVRIKPATWE412 TGISMRFEVY422 GCKIT |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AR5 or .AR52 or .AR53 or :3AR5;style chemicals stick;color identity;select .A:297 or .A:301 or .A:316 or .A:320 or .A:346 or .A:348 or .A:349 or .A:351 or .A:353 or .A:413 or .A:414 or .A:415; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Trifluoroacetic Acid | Ligand Info | |||||
| Structure Description | Neuropilin-1 b1 domain in complex with EG01377; 2.8 Angstrom structure | PDB:6FMF | ||||
| Method | X-ray diffraction | Resolution | 2.81 Å | Mutation | No | [3] |
| PDB Sequence |
FKCMEALGME
282 SGEIHSDQIT292 ASSQYSTNWS302 AERSRLNYPE312 NGWTPGEDSY322 REWIQVDLGL 332 LRFVTAVGTQ342 GAISKETKKK352 YYVKTYKIDV362 SSNGEDWITI372 KEGNKPVLFQ 382 GNTNPTDVVV392 AVFPKPLITR402 FVRIKPATWE412 TGISMRFEVY422 GCKIT |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TFA or .TFA2 or .TFA3 or :3TFA;style chemicals stick;color identity;select .A:296 or .A:297 or .A:298 or .A:299; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (S)-2-(3-(Benzo[c][1,2,5]thiadiazole-4-sulfonamido)thiophene-2-carboxamido)-5-guanidinopentanoic Acid | Ligand Info | |||||
| Structure Description | B1 domain of human Neuropilin-1 bound with small molecule EG00229 | PDB:3I97 | ||||
| Method | X-ray diffraction | Resolution | 2.90 Å | Mutation | No | [4] |
| PDB Sequence |
KCMEALGMES
11 GEIHSDQITA21 SSQYSTNWSA31 ERSRLNYPEN41 GWTPGEDSYR51 EWIQVDLGLL 61 RFVTAVGTQG71 AISKETKKKY81 YVKTYKIDVS91 SNGEDWITIK101 EGNKPVLFQG 111 NTNPTDVVVA121 VFPKPLITRF131 VRIKPATWET141 GISMRFEVYG151 CKIT |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8DR or .8DR2 or .8DR3 or :38DR;style chemicals stick;color identity;select .A:25 or .A:26 or .A:28 or .A:29 or .A:44 or .A:45 or .A:48 or .A:74 or .A:76 or .A:77 or .A:79 or .A:81 or .A:141 or .A:142 or .A:143; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Architecture and hydration of the arginine-binding site of neuropilin-1. FEBS J. 2018 Apr;285(7):1290-1304. | ||||
| REF 2 | Crystal Structure of the Neuropilin-1 MAM Domain: Completing the Neuropilin-1 Ectodomain Picture. Structure. 2016 Nov 1;24(11):2008-2015. | ||||
| REF 3 | Small Molecule Neuropilin-1 Antagonists Combine Antiangiogenic and Antitumor Activity with Immune Modulation through Reduction of Transforming Growth Factor Beta (TGFbeta) Production in Regulatory T-Cells. J Med Chem. 2018 May 10;61(9):4135-4154. | ||||
| REF 4 | Small molecule inhibitors of the neuropilin-1 vascular endothelial growth factor A (VEGF-A) interaction. J Med Chem. 2010 Mar 11;53(5):2215-26. | ||||
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