Structure of PDB 6fl4 Chain B Binding Site BS03

Receptor Information
>6fl4 Chain B (length=138) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AIPRVAVVVFILNGNSILLGRRRSSIGNSTFALPGGHLEFGESFEECAAR
EVMEETGLKIEKMKLLTVTNNVFKEAPTPSHYVSVSIRAVLVDPSQEPKN
MEPEKCEGWDWYDWENLPKPLFWPLEKLFGSGFNPFTH
Ligand information
Ligand ID8DG
InChIInChI=1S/C10H16N5O14P3/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(27-5)2-26-31(22,23)29-32(24,25)28-30(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1
InChIKeyBUZOGVVQWCXXDP-VPENINKCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C3=C(C(=O)NC(=N3)N)NC2=O)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
CACTVS 3.341NC1=NC2=C(NC(=O)N2[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3)C(=O)N1
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(N2C(=O)NC1=C2N=C(N)NC1=O)CC3O
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C3=C(C(=O)NC(=N3)N)NC2=O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341NC1=NC2=C(NC(=O)N2[C@H]3C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3)C(=O)N1
FormulaC10 H16 N5 O14 P3
Name8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000040165388
PDB chain6fl4 Chain B Residue 203 [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]
PDB6fl4 Crystal Structure and Substrate Specificity of the 8-oxo-dGTP Hydrolase NUDT1 from Arabidopsis thaliana.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		V13 R27 A37 L38 G40 G41 H42 E56 Y87 S89 F127 P129
Binding residue
(residue number reindexed from 1)		V8 R22 A32 L33 G35 G36 H37 E51 Y82 S84 F122 P124
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.1.22: NAD(+) diphosphatase.
3.6.1.55: 8-oxo-dGTP diphosphatase.
3.6.1.67: dihydroneopterin triphosphate diphosphatase.
Gene Ontology
Molecular Function
GO:0000210 NAD+ diphosphatase activity
GO:0008413 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity
GO:0016787 hydrolase activity
GO:0019177 dihydroneopterin triphosphate pyrophosphohydrolase activity
GO:0035529 NADH pyrophosphatase activity
GO:0035539 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity
GO:0046872 metal ion binding
Biological Process
GO:0006974 DNA damage response
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6fl4, PDBe:6fl4, PDBj:6fl4
PDBsum6fl4
PubMed30614695
UniProtQ9CA40|NUDT1_ARATH Nudix hydrolase 1 (Gene Name=NUDT1)

[Back to BioLiP]