Structure of PDB 6vcl Chain B Binding Site BS03

Receptor Information
>6vcl Chain B (length=160) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMIDDDGYRPNVGIVICNRQGQVMWARRFGQHSWQFPQGGINPGESAEQA
MYRELFEEVGLSRKDVRILASTRNWLRYKLPKRLVRWDTKPVCIGQKQKW
FLLQLVSGDAEINMQTSSTPEFDGWRWVSYWYPVRQVVSFKRDVYRRVMK
EFASVVMSLA
Ligand information
Ligand ID0O2
InChIInChI=1S/C10H18N5O20P5/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(32-39(26,27)33-36(18,19)20)3(31-9)1-30-38(24,25)35-40(28,29)34-37(21,22)23/h2-3,5-6,9,16H,1H2,(H,24,25)(H,26,27)(H,28,29)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKeyKCPMACXZAITQAX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3OP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O[P](O)(=O)O[P](O)(O)=O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(=O)O[P](O)(O)=O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H18 N5 O20 P5
Nameguanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)
ChEMBL
DrugBank
ZINCZINC000083923877
PDB chain6vcl Chain B Residue 209 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6vcl Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.
Resolution2.06 Å
Binding residue
(original residue number in PDB)		R8 R27 S32 Q37 Y77 Q95 V137 K140
Binding residue
(residue number reindexed from 1)		R9 R28 S33 Q38 Y78 Q96 V138 K141
Annotation score1
Binding affinityMOAD: ic50=54.4uM
Enzymatic activity
Enzyme Commision number 3.6.1.-
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0005515 protein binding
GO:0016462 pyrophosphatase activity
GO:0016787 hydrolase activity
GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
GO:0034353 mRNA 5'-diphosphatase activity
GO:0110153 RNA NAD-cap (NMN-forming) hydrolase activity
Biological Process
GO:0006402 mRNA catabolic process
GO:0008033 tRNA processing
GO:0050779 RNA destabilization
GO:0110154 RNA decapping
GO:0110155 NAD-cap decapping
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6vcl, PDBe:6vcl, PDBj:6vcl
PDBsum6vcl
PubMed31960065
UniProtP0A776|RPPH_ECOLI RNA pyrophosphohydrolase (Gene Name=rppH)

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