Structure of PDB 5ldq Chain A Binding Site BS01

Receptor Information
>5ldq Chain A (length=175) 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
LANMLRSQAARSGCFQSNRPFHPHITLLRDASEAVTIPPPGFNWSYAVTE
FTLYASSFARGRTRYTPLKRWALTQ
Ligand information
Ligand IDNAP
InChIInChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyXJLXINKUBYWONI-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O17 P3
NameNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
ChEMBLCHEMBL295069
DrugBankDB03461
ZINC
PDB chain5ldq 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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PDB5ldq Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		R6 F8 H43 T45 F48 H125 T127 R130 S157 S158 Y166
Binding residue
(residue number reindexed from 1)		R5 F7 H42 T44 F47 H124 T126 R129 S156 S157 Y165
Annotation score1
Binding affinityMOAD: Kd=40uM
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:5ldq, PDBe:5ldq, PDBj:5ldq
PDBsum5ldq
PubMed28141848
UniProtA0A140NFI1

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