Structure of PDB 1gyk Chain D Binding Site BS03

Receptor Information
>1gyk Chain D (length=204) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLF
SYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWES
SSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSF
VGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKP
LVWV
Ligand information
Ligand IDCDG
InChIInChI=1S/C10H16O8/c1-10(9(13)14)16-3-4-7(18-10)5(11)6(12)8(15-2)17-4/h4-8,11-12H,3H2,1-2H3,(H,13,14)/t4-,5-,6-,7+,8-,10-/m1/s1
InChIKeyZDZVLEQWFATHTF-IJWOWSJNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1(OCC2C(O1)C(C(C(O2)OC)O)O)C(=O)O
CACTVS 3.341CO[C@@H]1O[C@@H]2CO[C@](C)(O[C@@H]2[C@H](O)[C@H]1O)C(O)=O
OpenEye OEToolkits 1.5.0C[C@]1(OC[C@@H]2[C@H](O1)[C@@H]([C@H]([C@@H](O2)OC)O)O)C(=O)O
CACTVS 3.341CO[CH]1O[CH]2CO[C](C)(O[CH]2[CH](O)[CH]1O)C(O)=O
ACDLabs 10.04O=C(O)C1(OCC2OC(OC)C(O)C(O)C2O1)C
FormulaC10 H16 O8
NameMETHYL 4,6-O-[(1R)-1-CARBOXYETHYLIDENE]-BETA-D-GALACTOPYRANOSIDE
ChEMBL
DrugBankDB01651
ZINC
PDB chain1gyk Chain D Residue 1207 [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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PDB1gyk The Structures of Crystalline Complexes of Human Serum Amyloid P Component with its Carbohydrate Ligand, the Cyclic Pyruvate Acetal of Galactose
Resolution2.2 Å
Binding residue
(original residue number in PDB)		N59 E136 D138 Q148
Binding residue
(residue number reindexed from 1)		N59 E136 D138 Q148
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001849 complement component C1q complex binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0030246 carbohydrate binding
GO:0042802 identical protein binding
GO:0046790 virion binding
GO:0046872 metal ion binding
GO:0051082 unfolded protein binding
Biological Process
GO:0002674 negative regulation of acute inflammatory response
GO:0006457 protein folding
GO:0006953 acute-phase response
GO:0044869 negative regulation by host of viral exo-alpha-sialidase activity
GO:0044871 negative regulation by host of viral glycoprotein metabolic process
GO:0045087 innate immune response
GO:0045656 negative regulation of monocyte differentiation
GO:0046597 negative regulation of viral entry into host cell
GO:0048525 negative regulation of viral process
GO:0051131 chaperone-mediated protein complex assembly
GO:0061045 negative regulation of wound healing
GO:1903016 negative regulation of exo-alpha-sialidase activity
GO:1903019 negative regulation of glycoprotein metabolic process
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0062023 collagen-containing extracellular matrix
GO:0070062 extracellular exosome
GO:0072562 blood microparticle

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1gyk, PDBe:1gyk, PDBj:1gyk
PDBsum1gyk
PubMed12126626
UniProtP02743|SAMP_HUMAN Serum amyloid P-component (Gene Name=APCS)

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