Structure of PDB 7lrf Chain B Binding Site BS02

Receptor Information
>7lrf Chain B (length=411) Species: 9031 (Gallus gallus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PDPCYDEHGLPRRCIPDFVNSAFGKEVKVSSTCGKPPSRYCVVTEKGEEQ
VRSCHLCNASDPKRAHPPSFLTDLNNPHNLTCWQSDSYVQYPHNVTLTLS
LGKKFEVTYVSLQFCSPRPESMAIYKSMDYGKTWVPFQFYSTQCRKMYNK
PSRAAITKQNEQEAICTDSHTDVRPLSGGLIAFSTLDGRPTAHDFDNSPV
LQDWVTATDIKVTFSRLHTFGDEARDSYFYAVSDLQVGGRCKCNGHASRC
VRDRDDNLVCDCKHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCN
LHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGFYRDLSKP
ISHRKACKECDCHPVGAAGQTCNQTTGQCPCKDGVTGITCNRCAKGYQQS
RSPIAPCIKIP
Ligand information
Ligand IDGU4
InChIInChI=1S/C6H12O18S4/c7-6-5(24-28(17,18)19)4(23-27(14,15)16)3(22-26(11,12)13)2(21-6)1-20-25(8,9)10/h2-7H,1H2,(H,8,9,10)(H,11,12,13)(H,14,15,16)(H,17,18,19)/t2-,3-,4+,5-,6+/m1/s1
InChIKeySPIXVQOXHJQNTH-DVKNGEFBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C(C1C(C(C(C(O1)O)OS(=O)(=O)O)OS(=O)(=O)O)OS(=O)(=O)O)OS(=O)(=O)O
ACDLabs 12.01OC1OC(COS(=O)(=O)O)C(OS(=O)(=O)O)C(OS(=O)(O)=O)C1OS(=O)(=O)O
OpenEye OEToolkits 2.0.7C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)OS(=O)(=O)O)OS(=O)(=O)O)OS(=O)(=O)O)OS(=O)(=O)O
CACTVS 3.385O[CH]1O[CH](CO[S](O)(=O)=O)[CH](O[S](O)(=O)=O)[CH](O[S](O)(=O)=O)[CH]1O[S](O)(=O)=O
CACTVS 3.385O[C@H]1O[C@H](CO[S](O)(=O)=O)[C@@H](O[S](O)(=O)=O)[C@H](O[S](O)(=O)=O)[C@H]1O[S](O)(=O)=O
FormulaC6 H12 O18 S4
Name2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose;
2,3,4,6-tetra-O-sulfonato-alpha-D-glucose;
2,3,4,6-tetra-O-sulfonato-D-glucose;
2,3,4,6-tetra-O-sulfonato-glucose
ChEMBL
DrugBank
ZINCZINC000058632064
PDB chain7lrf Chain L Residue 1 [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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PDB7lrf The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation.
Resolution3.21 Å
Binding residue
(original residue number in PDB)
R350 R374 R400
Binding residue
(residue number reindexed from 1)
R304 R328 R354
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:7lrf, PDBe:7lrf, PDBj:7lrf
PDBsum7lrf
PubMed36869049
UniProtQ90922|NET1_CHICK Netrin-1 (Gene Name=NTN1)

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