Structure of PDB 5jgq Chain B Binding Site BS01

Receptor Information
>5jgq Chain B (length=154) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYR
EWIQVDLGLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWITIK
EGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYG
CKIT
Ligand information
Ligand ID6JY
InChIInChI=1S/C13H18N4O3/c14-13(15)16-8-4-7-10(12(19)20)17-11(18)9-5-2-1-3-6-9/h1-3,5-6,10H,4,7-8H2,(H,17,18)(H,19,20)(H4,14,15,16)/t10-/m0/s1
InChIKeyRSYYQCDERUOEFI-JTQLQIEISA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC(=N)NCCC[C@H](NC(=O)c1ccccc1)C(O)=O
CACTVS 3.385NC(=N)NCCC[CH](NC(=O)c1ccccc1)C(O)=O
OpenEye OEToolkits 2.0.4c1ccc(cc1)C(=O)NC(CCCNC(=N)N)C(=O)O
ACDLabs 12.01N/C(NCCCC(NC(=O)c1ccccc1)C(=O)O)=N
OpenEye OEToolkits 2.0.4[H]/N=C(/N)\NCCC[C@@H](C(=O)O)NC(=O)c1ccccc1
FormulaC13 H18 N4 O3
NameN~2~-(benzenecarbonyl)-L-arginine
ChEMBLCHEMBL25380
DrugBank
ZINCZINC000001677520
PDB chain5jgq Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5jgq Architecture and hydration of the arginine-binding site of neuropilin-1.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		Y297 T316 D320 S346 T349 Y353 G414 I415
Binding residue
(residue number reindexed from 1)		Y24 T43 D47 S73 T76 Y80 G141 I142
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.62,Kd=24uM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:5jgq, PDBe:5jgq, PDBj:5jgq
PDBsum5jgq
PubMed29430837
UniProtO14786|NRP1_HUMAN Neuropilin-1 (Gene Name=NRP1)

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