Structure of PDB 4ohx Chain A Binding Site BS01

Receptor Information
>4ohx Chain A (length=399) Species: 6239 (Caenorhabditis elegans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ENVQEFVLKEDCELRFAAGDDSDVCLELVKGYAEIFGTELLLNKKYTFPA
KSRVAAFTWKGATIELVGTTESAYVAESTPMVIYLNIHAAMEEVRKKREE
QAAKAKGPRLLLVGPTDVGKTTVSRILCNYSVRQGRTPIFVELDVGQNSV
SVPGTVAAVLVQKTADVIDGFERNQPIVFNFGHTSPSANLSLYEALFKEM
ATTLNAQIQENDEAKIGGMIINTCGWVDGEGYKCIVKAASAFEVDVVIVL
DHERLYSDLSKELPEFVRLTHVPKSGGVEQRTGQIRSKMRGENVHRYFYG
TRANNLYPFTFDVSFDDVTLCKIGHETKLVIMEPSADIKHHLFAFSRSTK
ADENVLKSPVFGFCLVTEVDLEKRTMSILCPQRTIPSKVLVFSDITHLD
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-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)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[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)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain4ohx Chain A Residue 501 [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]
PDB4ohx RNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1.
Resolution1.98 Å
Binding residue
(original residue number in PDB)		A58 D124 V125 G126 K127 T128 T129 G284 R288
Binding residue
(residue number reindexed from 1)		A55 D117 V118 G119 K120 T121 T122 G277 R281
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0051731 polynucleotide 5'-hydroxyl-kinase activity
GO:0051736 ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity
Biological Process
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation
GO:0006396 RNA processing
GO:0006397 mRNA processing
GO:0031124 mRNA 3'-end processing
Cellular Component
GO:0005634 nucleus
GO:0005849 mRNA cleavage factor complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ohx, PDBe:4ohx, PDBj:4ohx
PDBsum4ohx
PubMed24813946
UniProtP52874|CLP1_CAEEL Protein clpf-1 (Gene Name=clpf-1)

[Back to BioLiP]