Structure of PDB 3rs8 Chain A Binding Site BS04

Receptor Information
>3rs8 Chain A (length=490) Species: 243274 (Thermotoga maritima MSB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMKEIDELTIKEYGVDSRILMERAGISVVLAMEEELGNLSDYRFLVLCGG
GNNGGDGFVVARNLLGVVKDVLVVFLGKKKTPDCEYNYGLYKKFGGKVVE
QFEPSILNEFDVVVDAIFGTGLRGEITGEYAEIINLVNKSGKVVVSVDVP
SGIDSNTGKVLRTAVKADLTVTFGVPKIGHILFPGRDLTGKLKVANIGHP
VHLINSINRYVITREMVRSLLPERPRDSHKGTYGKVLIIAGSRLYSGAPV
LSGMGSLKVGTGLVKLAVPFPQNLIATSRFPELISVPIDTEKGFFSLQNL
QECLELSKDVDVVAIGPGLGNNEHVREFVNEFLKTLEKPAVIDADAINVL
DTSVLKERKSPAVLTPHPGEMARLVKKTVGDVKYNYELAEEFAKENDCVL
VLKSATTIVTDGEKTLFNITGNTGLSKGGSGDVLTGMIAGFIAQGLSPLE
ASTVSVYLHGFAAELFEQDERGLTASELLRLIPEAIRRLK
Ligand information
Ligand IDAPR
InChIInChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1
InChIKeySRNWOUGRCWSEMX-KEOHHSTQSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)OP(=O)(O)OCC4OC(O)C(O)C4O
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)O)O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
FormulaC15 H23 N5 O14 P2
NameADENOSINE-5-DIPHOSPHORIBOSE
ChEMBLCHEMBL1231026
DrugBank
ZINCZINC000017654550
PDB chain3rs8 Chain A Residue 495 [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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PDB3rs8 Identification of unknown protein function using metabolite cocktail screening.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y244 H366 P367 G368 R372 V378 K382
Binding residue
(residue number reindexed from 1)		Y245 H367 P368 G369 R373 V379 K383
Annotation score4
Binding affinityMOAD: Kd=5.1uM
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:3rs8, PDBe:3rs8, PDBj:3rs8
PDBsum3rs8
PubMed22940582
UniProtQ9X024|NNR_THEMA Bifunctional NAD(P)H-hydrate repair enzyme Nnr (Gene Name=nnr)

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