Structure of PDB 3ru3 Chain A Binding Site BS02

Receptor Information
>3ru3 Chain A (length=489) Species: 243274 (Thermotoga maritima MSB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKEIDELTIKEYGVDSRILMERAGISVVLAMEEELGNLSDYRFLVLCGGG
NNGGDGFVVARNLLGVVKDVLVVFLGKKKTPDCEYNYGLYKKFGGKVVEQ
FEPSILNEFDVVVDAIFGTGLRGEITGEYAEIINLVNKSGKVVVSVDVPS
GIDSNTGKVLRTAVKADLTVTFGVPKIGHILFPGRDLTGKLKVANIGHPV
HLINSINRYVITREMVRSLLPERPRDSHKGTYGKVLIIAGSRLYSGAPVL
SGMGSLKVGTGLVKLAVPFPQNLIATSRFPELISVPIDTEKGFFSLQNLQ
ECLELSKDVDVVAIGPGLGNNEHVREFVNEFLKTLEKPAVIDADAINVLD
TSVLKERKSPAVLTPHPGEMARLVKKTVGDVKYNYELAEEFAKENDCVLV
LKSATTIVTDGEKTLFNITGNTGLSKGGSGDVLTGMIAGFIAQGLSPLEA
STVSVYLHGFAAELFEQDERGLTASELLRLIPEAIRRLK
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/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/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-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)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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)C1=CN(C=CC1)[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 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain3ru3 Chain A Residue 493 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ru3 Identification of unknown protein function using metabolite cocktail screening.
Resolution2.605 Å
Binding residue
(original residue number in PDB)		G50 N51 N52 D55 F117 G118 T119 G120 R122 E124 Y129 D147
Binding residue
(residue number reindexed from 1)		G50 N51 N52 D55 F117 G118 T119 G120 R122 E124 Y129 D147
Annotation score4
Enzymatic activity
Enzyme Commision number 4.2.1.136: ADP-dependent NAD(P)H-hydrate dehydratase.
5.1.99.6: NAD(P)H-hydrate epimerase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016829 lyase activity
GO:0016836 hydro-lyase activity
GO:0016853 isomerase activity
GO:0046872 metal ion binding
GO:0052855 ADP-dependent NAD(P)H-hydrate dehydratase activity
GO:0052856 NAD(P)HX epimerase activity
Biological Process
GO:0046496 nicotinamide nucleotide metabolic process
GO:0110051 metabolite repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3ru3, PDBe:3ru3, PDBj:3ru3
PDBsum3ru3
PubMed22940582
UniProtQ9X024|NNR_THEMA Bifunctional NAD(P)H-hydrate repair enzyme Nnr (Gene Name=nnr)

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