Home Research COVID-19 Services Publications People Teaching Job Opening News Forum Lab Only
Online Services

●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●DeepFoldRNA ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DAMpred

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

BioLiP

Structure of PDB 5dhr Chain B Binding Site BS02

Receptor Information
>5dhr Chain B (length=262) Species: 169963 (Listeria monocytogenes EGD-e) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKYMITSKGDEKSDLLRLNMIAGFGEYDMEYDDVEPEIVISIGGDGTFLS
AFHQYEERLDEIAFIGIHTGHLGFYADWRPAEADKLVKLLAKGEYQKVSY
PLLKTTVKYKEATYLALNESTVKSSGPFVVDVVINDIHFERFRGDGLCMS
TPSGTTAYNKSLGGALMHPSIEAMQLTEMASINNRVYRTIGSPLVFPKHH
VVSLQPVNDKDFQISVDHLSILHRDVQEIRYEVSAKKIHFARFRSFPFWR
RVHDSFIEDLEH
Ligand information
Ligand ID5AJ
InChIInChI=1S/C21H23N11O4S/c22-18-15-19(26-9-25-18)32(20-17(35)16(34)12(36-20)7-27-31-23)21(30-15)37-8-14(33)24-6-5-13-28-10-3-1-2-4-11(10)29-13/h1-4,9,12,16-17,20,34-35H,5-8H2,(H,24,33)(H,28,29)(H2,22,25,26)/t12-,16-,17-,20-/m1/s1
InChIKeyQNDDYPVSXWRDOZ-QQRWZLOUSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1nc2c(c(n1)N)nc(n2C3OC(C/N=[N+]=[N-])C(O)C3O)SCC(NCCc5nc4ccccc4n5)=O
OpenEye OEToolkits 1.9.2c1ccc2c(c1)[nH]c(n2)CCNC(=O)CSc3nc4c(ncnc4n3C5C(C(C(O5)CN=[N+]=[N-])O)O)N
OpenEye OEToolkits 1.9.2c1ccc2c(c1)[nH]c(n2)CCNC(=O)CSc3nc4c(ncnc4n3[C@H]5[C@@H]([C@@H]([C@H](O5)CN=[N+]=[N-])O)O)N
CACTVS 3.385Nc1ncnc2n([CH]3O[CH](CN=[N+]=[N-])[CH](O)[CH]3O)c(SCC(=O)NCCc4[nH]c5ccccc5n4)nc12
CACTVS 3.385Nc1ncnc2n([C@@H]3O[C@H](CN=[N+]=[N-])[C@@H](O)[C@H]3O)c(SCC(=O)NCCc4[nH]c5ccccc5n4)nc12
FormulaC21 H23 N11 O4 S
Name5'-azido-8-[(2-{[2-(1H-benzimidazol-2-yl)ethyl]amino}-2-oxoethyl)sulfanyl]-5'-deoxyadenosine
ChEMBLCHEMBL3883775
DrugBank
ZINCZINC000584904853
PDB chain5dhr Chain D Residue 301 [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]
PDB5dhr 8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode.
Resolution2.31 Å
Binding residue
(original residue number in PDB)		R148 G149
Binding residue
(residue number reindexed from 1)		R143 G144
Annotation score1
Binding affinityMOAD: Ki=23uM
Enzymatic activity
Enzyme Commision number 2.7.1.23: NAD(+) kinase.
Gene Ontology
Molecular Function
GO:0003951 NAD+ kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0046872 metal ion binding
GO:0051287 NAD binding
Biological Process
GO:0006741 NADP biosynthetic process
GO:0016310 phosphorylation
GO:0019674 NAD metabolic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5dhr, PDBe:5dhr, PDBj:5dhr
PDBsum5dhr
PubMed27783975
UniProtQ8Y8D7|NADK1_LISMO NAD kinase 1 (Gene Name=nadK1)

[Back to BioLiP]

zhanglabzhanggroup.org | +65-6601-1241 | Computing 1, 13 Computing Drive, Singapore 117417