Structure of PDB 5iyy Chain A Binding Site BS01

Receptor Information
>5iyy Chain A (length=156) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDS
YREWIQVDLGLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWIT
IKEGNKPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEV
YGCKIT
Ligand information
Ligand IDR40
InChIInChI=1S/C14H20N4O4/c15-13(16)17-8-4-7-11(12(19)20)18-14(21)22-9-10-5-2-1-3-6-10/h1-3,5-6,11H,4,7-9H2,(H,18,21)(H,19,20)(H4,15,16,17)/t11-/m0/s1
InChIKeySJSSFUMSAFMFNM-NSHDSACASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4c1ccc(cc1)COC(=O)NC(CCCNC(=N)N)C(=O)O
OpenEye OEToolkits 2.0.4[H]/N=C(\N)/NCCC[C@@H](C(=O)O)NC(=O)OCc1ccccc1
CACTVS 3.385NC(=N)NCCC[CH](NC(=O)OCc1ccccc1)C(O)=O
ACDLabs 12.01N=C(/NCCCC(NC(=O)OCc1ccccc1)C(=O)O)N
CACTVS 3.385NC(=N)NCCC[C@H](NC(=O)OCc1ccccc1)C(O)=O
FormulaC14 H20 N4 O4
NameN~2~-[(benzyloxy)carbonyl]-L-arginine
ChEMBLCHEMBL1423296
DrugBank
ZINCZINC000001540612
PDB chain5iyy Chain A 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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PDB5iyy Architecture and hydration of the arginine-binding site of neuropilin-1.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		Y297 W301 T316 D320 S346 T349 Y353 G414 I415
Binding residue
(residue number reindexed from 1)		Y26 W30 T45 D49 S75 T78 Y82 G143 I144
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.77,Kd=17uM
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:5iyy, PDBe:5iyy, PDBj:5iyy
PDBsum5iyy
PubMed29430837
UniProtO14786|NRP1_HUMAN Neuropilin-1 (Gene Name=NRP1)

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