Structure of PDB 5ldo Chain A Binding Site BS01

Receptor Information
>5ldo Chain A (length=174) Species: 469008 (Escherichia coli BL21(DE3)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EPQRLFFAIDLPAEIREQIIHWRAKHFPPEAGRPVAADNLHLTLAFLGEV
SAEKEKALSLLAGRIRQPGFTLTLDDAGQWLRSRVVWLGMRQPPRGLIQL
ANMLRSQAARSGCFQSNRPFHPHITLLRDASEAVTIPPPGFNWSYAVTEF
TLYASSFARGRTRYTPLKRWALTQ
Ligand information
Ligand ID3AM
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(17)7(4(1-16)21-10)22-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyLNQVTSROQXJCDD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OC3C(OC(n2cnc1c(ncnc12)N)C3O)CO
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O[P](O)(O)=O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O[P](O)(O)=O)[CH]3O
FormulaC10 H14 N5 O7 P
Name[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate;
3'-AMP
ChEMBLCHEMBL576739
DrugBank
ZINCZINC000001631259
PDB chain5ldo 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

[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]
PDB5ldo Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase.
Resolution2.752 Å
Binding residue
(original residue number in PDB)		F8 H43 T45 F48 F116 H125 T127 R130
Binding residue
(residue number reindexed from 1)		F6 H41 T43 F46 F114 H123 T125 R128
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.75,Kd=177uM
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:5ldo, PDBe:5ldo, PDBj:5ldo
PDBsum5ldo
PubMed28141848
UniProtA0A140NFI1

[Back to BioLiP]