Structure of PDB 5ghj Chain A Binding Site BS01

Receptor Information
>5ghj Chain A (length=156) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGAR
RELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDE
MRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTL
REVDTV
Ligand information
Ligand ID6U4
InChIInChI=1S/C10H16N5O13P3/c11-8-7-9(14-10(17)13-8)15(3-12-7)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
InChIKeyUOACBPRDWRDEHJ-KVQBGUIXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5C1C(C(OC1N2C=NC3=C(NC(=O)N=C32)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.385NC1=C2N=CN([C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3)C2=NC(=O)N1
OpenEye OEToolkits 2.0.5C1[C@@H]([C@H](O[C@H]1N2C=NC3=C(NC(=O)N=C32)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.385NC1=C2N=CN([CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3)C2=NC(=O)N1
FormulaC10 H16 N5 O13 P3
Name[[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate;
2-oxo-dATP
ChEMBL
DrugBank
ZINCZINC000038662361
PDB chain5ghj Chain A Residue 201 [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]
PDB5ghj Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism for Its Broad Substrate Specificity
Resolution1.2 Å
Binding residue
(original residue number in PDB)		Y7 T8 N33 G36 G37 K38 F72 W117 D119 D120
Binding residue
(residue number reindexed from 1)		Y7 T8 N33 G36 G37 K38 F72 W117 D119 D120
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.1.-
3.6.1.56: 2-hydroxy-dATP diphosphatase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008413 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity
GO:0008828 dATP diphosphatase activity
GO:0016787 hydrolase activity
GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
GO:0030515 snoRNA binding
GO:0035539 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity
GO:0046872 metal ion binding
GO:0047693 ATP diphosphatase activity
GO:0106377 2-hydroxy-ATP hydrolase activity
GO:0106378 2-hydroxy-dATP hydrolase activity
GO:0106431 N6-methyl-(d)ATP hydrolase activity
GO:0106433 O6-methyl-dGTP hydrolase activity
GO:0140933 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity
Biological Process
GO:0006152 purine nucleoside catabolic process
GO:0006281 DNA repair
GO:0006979 response to oxidative stress
GO:0008584 male gonad development
GO:0042262 DNA protection
GO:0046686 response to cadmium ion
Cellular Component
GO:0001669 acrosomal vesicle
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005829 cytosol
GO:0031965 nuclear membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ghj, PDBe:5ghj, PDBj:5ghj
PDBsum5ghj
PubMed28035004
UniProtP36639|8ODP_HUMAN Oxidized purine nucleoside triphosphate hydrolase (Gene Name=NUDT1)

[Back to BioLiP]