Structure of PDB 6pcl Chain A Binding Site BS01

Receptor Information
>6pcl Chain A (length=135) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QTRTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEE
EPSVAAVREVCEEAGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDW
EDSVNIGRKREWFKIEDAIKVLQYHKPVQASYFET
Ligand information
Ligand IDI7P
InChIInChI=1S/C6H19O27P7/c7-34(8,9)27-1-2(28-35(10,11)12)4(30-37(16,17)18)6(32-40(25,26)33-39(22,23)24)5(31-38(19,20)21)3(1)29-36(13,14)15/h1-6H,(H,25,26)(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2+,3-,4-,5+,6+
InChIKeyUPHPWXPNZIOZJL-KXXVROSKSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OC1C(OP(=O)(O)O)C(OP(=O)(O)O)C(OP(=O)(O)O)C(OP(=O)(O)O)C1OP(=O)(OP(=O)(O)O)O
CACTVS 3.370O[P](O)(=O)O[CH]1[CH](O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH](O[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]1O[P](O)(O)=O
OpenEye OEToolkits 1.7.2C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
OpenEye OEToolkits 1.7.2[C@H]1([C@H](C([C@H]([C@@H](C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
CACTVS 3.370O[P](O)(=O)O[C@H]1[C@@H](O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@@H](O[P](O)(=O)O[P](O)(O)=O)[C@H](O[P](O)(O)=O)[C@H]1O[P](O)(O)=O
FormulaC6 H19 O27 P7
Name(1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate;
1D-myo-inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate
ChEMBLCHEMBL1241856
DrugBank
ZINCZINC000085552707
PDB chain6pcl Chain A Residue 201 [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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PDB6pcl Vip1 is a kinase and pyrophosphatase switch that regulates inositol diphosphate signaling.
Resolution1.3 Å
Binding residue
(original residue number in PDB)		R10 K18 R20 S39 S40 I47 G50 G51 E66 E70 R89 R115 K133
Binding residue
(residue number reindexed from 1)		R3 K11 R13 S32 S33 I40 G43 G44 E59 E63 R82 R108 K126
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.1.10: endopolyphosphatase.
3.6.1.52: diphosphoinositol-polyphosphate diphosphatase.
3.6.1.59: 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase.
3.6.1.61: diadenosine hexaphosphate hydrolase (ATP-forming).
3.6.1.62: 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase.
Gene Ontology
Molecular Function
GO:0016462 pyrophosphatase activity
GO:0016787 hydrolase activity

View graph for
Molecular Function
External links
PDB RCSB:6pcl, PDBe:6pcl, PDBj:6pcl
PDBsum6pcl
PubMed32303658
UniProtO95989|NUDT3_HUMAN Diphosphoinositol polyphosphate phosphohydrolase 1 (Gene Name=NUDT3)

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