Structure of PDB 2a3x Chain D Binding Site BS03

Receptor Information
>2a3x 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 IDCPK
InChIInChI=1S/C18H26N2O12/c1-17(13(21)22)27-7-11(8-28-17)31-15(25)19-3-5-20(6-4-19)16(26)32-12-9-29-18(2,14(23)24)30-10-12/h11-12H,3-10H2,1-2H3,(H,21,22)(H,23,24)/t11-,12-,17+,18+
InChIKeyGNQQJZKGGHOMBD-RDAHUFKRSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[C]1(OC[CH](CO1)OC(=O)N2CCN(CC2)C(=O)O[CH]3CO[C](C)(OC3)C(O)=O)C(O)=O
CACTVS 3.341C[C@@]1(OC[C@H](CO1)OC(=O)N2CCN(CC2)C(=O)O[C@H]3CO[C@](C)(OC3)C(O)=O)C(O)=O
ACDLabs 10.04O=C(OC1COC(OC1)(C(=O)O)C)N3CCN(C(=O)OC2COC(OC2)(C(=O)O)C)CC3
OpenEye OEToolkits 1.5.0CC1(OCC(CO1)OC(=O)N2CCN(CC2)C(=O)OC3COC(OC3)(C)C(=O)O)C(=O)O
FormulaC18 H26 N2 O12
NameBIS-1,2-{[(Z)-2CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBONYL}-PIPERAZINE
ChEMBL
DrugBankDB07580
ZINCZINC000100035677
PDB chain2a3x Chain I Residue 401 [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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PDB2a3x Ligand-assisted Aggregation of Proteins: DIMERIZATION OF SERUM AMYLOID P COMPONENT BY BIVALENT LIGANDS.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		N59 Y74 E136 D138 Q148
Binding residue
(residue number reindexed from 1)		N59 Y74 E136 D138 Q148
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.92,IC50=0.12uM
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:2a3x, PDBe:2a3x, PDBj:2a3x
PDBsum2a3x
PubMed16036920
UniProtP02743|SAMP_HUMAN Serum amyloid P-component (Gene Name=APCS)

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