Structure of PDB 5ldk Chain B Binding Site BS01

Receptor Information
>5ldk Chain B (length=172) Species: 469008 (Escherichia coli BL21(DE3)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEPQRLFFAIDLPAEIREQIIHWRAKHFPPEAGRPVAADNLHLTLAFLGE
VSAEKEKALSLLAGRIRQPGFTLTLDDAGQWLRSRVVWLGMRQPPRGLIQ
LANMLRSQAARSGCFRPFHPHITLLRDASEAVTIPPPGFNWSYAVTEFTL
YASSFARGRTRYTPLKRWALTQ
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
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)OP(=O)(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)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain5ldk Chain B 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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PDB5ldk Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase.
Resolution2.099 Å
Binding residue
(original residue number in PDB)		F8 H43 F48 S157
Binding residue
(residue number reindexed from 1)		F7 H42 F47 S153
Annotation score1
Binding affinityMOAD: Ka=15000M^-1
PDBbind-CN: -logKd/Ki=4.17,Kd=67uM
Enzymatic activity
Enzyme Commision number 3.1.4.58: RNA 2',3'-cyclic 3'-phosphodiesterase.
Gene Ontology
Molecular Function
GO:0004113 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity
GO:0005524 ATP binding
GO:0008081 phosphoric diester hydrolase activity
GO:0008664 RNA 2',3'-cyclic 3'-phosphodiesterase activity
GO:0016787 hydrolase activity
GO:0016874 ligase activity

View graph for
Molecular Function
External links
PDB RCSB:5ldk, PDBe:5ldk, PDBj:5ldk
PDBsum5ldk
PubMed28141848
UniProtA0A140NFI1

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