Structure of PDB 4avt Chain B Binding Site BS03

Receptor Information
>4avt Chain B (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 IDGHE
InChIInChI=1S/C16H24N2O6/c19-13(17-9-3-5-11(17)15(21)22)7-1-2-8-14(20)18-10-4-6-12(18)16(23)24/h11-12H,1-10H2,(H,21,22)(H,23,24)/t11-,12-/m1/s1
InChIKeyHZLAWYIBLZNRFZ-VXGBXAGGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2C1C[C@@H](N(C1)C(=O)CCCCC(=O)N2CCC[C@@H]2C(=O)O)C(=O)O
CACTVS 3.385OC(=O)[C@H]1CCCN1C(=O)CCCCC(=O)N2CCC[C@@H]2C(O)=O
CACTVS 3.385OC(=O)[CH]1CCCN1C(=O)CCCCC(=O)N2CCC[CH]2C(O)=O
ACDLabs 12.01O=C(N1C(C(=O)O)CCC1)CCCCC(=O)N2C(C(=O)O)CCC2
OpenEye OEToolkits 1.9.2C1CC(N(C1)C(=O)CCCCC(=O)N2CCCC2C(=O)O)C(=O)O
FormulaC16 H24 N2 O6
Name(2R)-1-[6-[(2R)-2-carboxypyrrolidin-1-yl]-6-oxidanylidene-hexanoyl]pyrrolidine-2-carboxylic acid
ChEMBLCHEMBL25263
DrugBankDB13087
ZINCZINC000003972138
PDB chain4avt Chain B 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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PDB4avt Interaction of Serum Amyloid P Component with Hexanoyl Bis(D-Proline) (Cphpc)
Resolution3.2 Å
Binding residue
(original residue number in PDB)		N59 Y64 E136 D138 Q148
Binding residue
(residue number reindexed from 1)		N59 Y64 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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4avt, PDBe:4avt, PDBj:4avt
PDBsum4avt
PubMed25084341
UniProtP02743|SAMP_HUMAN Serum amyloid P-component (Gene Name=APCS)

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