Structure of PDB 6fl4 Chain A Binding Site BS03

Receptor Information
>6fl4 Chain A (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 A Residue 203 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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 L38 G40 G41 H42 E56 F78 Y87 S89 K110 F127
Binding residue
(residue number reindexed from 1)		V8 R22 L33 G35 G36 H37 E51 F73 Y82 S84 K105 F122
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

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

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