Structure of PDB 6c02 Chain A Binding Site BS05

Receptor Information
>6c02 Chain A (length=815) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSCRKKCFDASFRGLENCRCDVACKDRGDCCWDFEDTCVESTRIWMCNKF
RCGETRLEASLCSCSDDCLQRKDCCADYKSVCQGETSWLEENCDQCPEGF
DLPPVILFSMDGFRAEYLYTWDTLMPNINKLKTCGIHSKYMRAMYPTKAF
PNHYTIVTGLYPESHGIIDNNMYDVNLNKNFSLSSKEQNNPAWWHGQPMW
LTAMYQGLKAATYFWPGSEVAINGSFPSIYMPYNGSVPFEERISTLLKWL
DLPKAERPRFYTMYFEEPDSSGHAGGPVSARVIKALQVVDHAFGMLMEGL
KQRNLHNCVNIILLADHGMDQTYCNKMEYMTDYFPRINFFYMYEGPAPRI
RAHNIPHDFFSFNSEEIVRNLSCRKPDQHFKPYLTPDLPKRLHYAKNVRI
DKVHLFVDQQWLAVRSKSNTNCGGGNHGYNNEFRSMEAIFLAHGPSFKEK
TEVEPFENIEVYNLMCDLLRIQPAPNNGTHGSLNHLLKVPFYEPSHAEEV
SKFSVCGFANPLPTESLDCFCPHLQNSTQLEQVNQMLSLTQEEITATVKV
NLPFGRPRVLQKNVDHCLLYHREYVSGFGKAMRMPMWSSYTVPQLGDTSP
LPPTVPDCLRADVRVPPSESQKCSFYLADKNITHGFLYPPASNRTSDSQY
DALITSNLVPMYEEFRKMWDYFHSVLLIKHATERNGVNVVSGPIFDYNYD
GHFDAPDEITKHLANTDVPIPTHYFVVLTSCKNKSHTPENCPGWLDVLPF
IIPHRPTNVESCPEGKPEALWVEERFTAHIARVRDVELLTGLDFYQDKVQ
PVSEILQLKTYLPTF
Ligand information
Ligand IDAPC
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1
InChIKeyCAWZRIXWFRFUQB-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
FormulaC11 H18 N5 O12 P3
NameDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL132722
DrugBankDB02596
ZINCZINC000008295117
PDB chain6c02 Chain A Residue 927 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6c02 Structural basis for nucleotide recognition by the ectoenzyme CD203c.
Resolution1.942 Å
Binding residue
(original residue number in PDB)		K204 A205 F206 N226 E275 Y289 Y320 D325 H483
Binding residue
(residue number reindexed from 1)		K148 A149 F150 N170 E219 Y233 Y264 D269 H427
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.4.1: phosphodiesterase I.
3.6.1.9: nucleotide diphosphatase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0004081 bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity
GO:0004528 phosphodiesterase I activity
GO:0005509 calcium ion binding
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0034432 bis(5'-adenosyl)-pentaphosphatase activity
GO:0036219 GTP diphosphatase activity
GO:0036221 UTP diphosphatase activity
GO:0046872 metal ion binding
GO:0047429 nucleoside triphosphate diphosphatase activity
GO:0047693 ATP diphosphatase activity
GO:0047710 bis(5'-adenosyl)-triphosphatase activity
Biological Process
GO:0002276 basophil activation involved in immune response
GO:0006220 pyrimidine nucleotide metabolic process
GO:0006796 phosphate-containing compound metabolic process
GO:0009143 nucleoside triphosphate catabolic process
GO:0030505 inorganic diphosphate transport
GO:0033007 negative regulation of mast cell activation involved in immune response
GO:0046034 ATP metabolic process
GO:0050728 negative regulation of inflammatory response
GO:0055062 phosphate ion homeostasis
GO:0070667 negative regulation of mast cell proliferation
Cellular Component
GO:0005576 extracellular region
GO:0005886 plasma membrane
GO:0009897 external side of plasma membrane
GO:0016324 apical plasma membrane
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6c02, PDBe:6c02, PDBj:6c02
PDBsum6c02
PubMed29717535
UniProtO14638|ENPP3_HUMAN Ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (Gene Name=ENPP3)

[Back to BioLiP]