Structure of PDB 1syo Chain B Binding Site BS01

Receptor Information
>1syo Chain B (length=408) Species: 9913 (Bos taurus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEFPELCSYTWEAVDTKNNMLYKINICGNMGVAQCGPSSAVCMHDLKTDS
FHSVGDSLLKTASRSLLEFNTTVNIQSSITFLCGKTLGTPEFVTATDCVH
YFEWRTTAACKKNIFKANKEVPCYAFDRELKKHDLNPLIKTSGAYLVDDS
DPDTSLFINVCRDIEVLRASSPQVRVCPTGAAACLVRGDRAFDVGRPQEG
LKLVSNDRLVLSYVKFCDGHSPAVTITFVCPSERREGTIPKLTAKSNCRF
EIEWVTEYACHRDYLESRSCSLSSAQHDVAVDLQPLSRVSLFYTSEADEY
TYYLSICGGSQAPICNKKDAAVCQVKKADSTQVKVAGRPQNLTLRYSDGD
LTLIYFGGEECSSGFQRMSVINFECNQTAGNNGRGAPVFTGEVDCTYFFT
WDTKYACV
Ligand information
Ligand IDM6P
InChIInChI=1S/C6H13O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-10H,1H2,(H2,11,12,13)/t2-,3-,4+,5+,6+/m1/s1
InChIKeyNBSCHQHZLSJFNQ-PQMKYFCFSA-N
SMILES
SoftwareSMILES
CACTVS 3.341O[CH]1O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341O[C@H]1O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(O1)O)O)O)O)OP(=O)(O)O
ACDLabs 10.04O=P(O)(O)OCC1OC(O)C(O)C(O)C1O
FormulaC6 H13 O9 P
Name6-O-phosphono-alpha-D-mannopyranose;
ALPHA-D-MANNOSE-6-PHOSPHATE;
6-O-phosphono-alpha-D-mannose;
6-O-phosphono-D-mannose;
6-O-phosphono-mannose
ChEMBLCHEMBL402001
DrugBankDB02900
ZINCZINC000004096188
PDB chain1syo Chain B Residue 1500 [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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PDB1syo The N-terminal carbohydrate recognition site of the cation-independent mannose 6-phosphate receptor
Resolution2.2 Å
Binding residue
(original residue number in PDB)		Y1324 Q1348 C1385 S1386 R1391 E1416 C1419 Y1421
Binding residue
(residue number reindexed from 1)		Y300 Q324 C361 S362 R367 E392 C395 Y397
Annotation score4
Binding affinityMOAD: Kd~1nM
PDBbind-CN: -logKd/Ki=9.00,Kd~1nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005537 D-mannose binding
GO:0038023 signaling receptor activity
Biological Process
GO:0007041 lysosomal transport

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1syo, PDBe:1syo, PDBj:1syo
PDBsum1syo
PubMed15169779
UniProtP08169|MPRI_BOVIN Cation-independent mannose-6-phosphate receptor (Gene Name=IGF2R)

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