Structure of PDB 6f2y Chain A Binding Site BS01

Receptor Information
>6f2y Chain A (length=720) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WVTEACAPQCPEGFDQPPVILFSMDGFRAEYLQTWSTLLPNINKLKTCGL
HSKYMRAVYPTKAFPNHYTIVTGLYPESHGIIDNNMYDVYLNKNFSLSSV
EKSNPAWWSGQPIWLTAMYQGLKAASYYWPGSDVAVNGSFPNIYRNYSNS
VPYESRIATLLQWLDLPKAERPSFYTIYVEEPDSAGHKSGPVSAGVIKAL
QLVDDAFGMLMEGLKQRNLHNCVNIIVLADHGMDQTSCDRVEYMTDYFPE
INFYMYQGPAPRIRTRNIPQDFFTFNSEEIVRDLSCRKSDQHFKPYLTPD
LPKRLHYAKNVRIDKVHLMVDRQWLAYRNKNCEGGTHGYNNEFKSMEAIF
LAHGPSFKEKTVIEPFENIEVYNLLCDLLHIQPAPNNGSHGSLNHLLKAP
FYQPSHAEELSKSAGCGFTTPLPKDSLNCSCLALQEQVNQRLNLNRGEVS
ATEKTNLPFGRPRVIQKNKDHCLLYHREYVSGFGKAMKMPMWSSYTVPKP
GDTSSLPPTVPDCLRADVRVDPSESQKCSFYLADQNIDHGFLYPPAIKGN
NESQYDALITSNLVPMYKEFKKMWDYFHKVLLIKYAIERNGVNVVSGPIF
DYNYDGHFDAPDEITNYVAGTDVPVPTHYFVVLTSCKNKTHTPDSCPGWL
DVLPFVVPHRPTNVESCPENKAEDLWVEERFKAHIARVRDVELLTGLDFY
QEKTQPVSEILQLKTYLPTF
Ligand information
Ligand IDB4P
InChIInChI=1S/C20H28N10O19P4/c21-15-9-17(25-3-23-15)29(5-27-9)19-13(33)11(31)7(45-19)1-43-50(35,36)47-52(39,40)49-53(41,42)48-51(37,38)44-2-8-12(32)14(34)20(46-8)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-34H,1-2H2,(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKeyYOAHKNVSNCMZGQ-XPWFQUROSA-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)(O)O[P@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)[C@@H](O)[C@H]3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)N
FormulaC20 H28 N10 O19 P4
NameBIS(ADENOSINE)-5'-TETRAPHOSPHATE
ChEMBLCHEMBL339385
DrugBank
ZINCZINC000096014967
PDB chain6f2y Chain A Residue 1001 [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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PDB6f2y Crystal structure and substrate binding mode of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3).
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D168 K205 A206 F207 N227 Y290 Y321 D326 H330 H374 T379 N477 E479 G480 G481 T482 H483
Binding residue
(residue number reindexed from 1)		D25 K62 A63 F64 N84 Y147 Y178 D183 H187 H231 T236 N331 E333 G334 G335 T336 H337
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:0016787 hydrolase activity
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:6f2y, PDBe:6f2y, PDBj:6f2y
PDBsum6f2y
PubMed30022031
UniProtP97675|ENPP3_RAT Ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (Gene Name=Enpp3)

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