Structure of PDB 6m65 Chain A Binding Site BS01

Receptor Information
>6m65 Chain A (length=290) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HTVRAAGAVLWRDATVEVAVIHRPRYDDWSLPKGKLDQGETEPVAAAREI
HEETGHTAVLGRRLGRVTYPIPQGTKRVWYWAAKSTGGDFSPNDEVDKLV
WLPVDAAMDQLQYPDDRKVLRRFVKRPVDTKTVLVVRHGTAGRRSRYKGD
DRKRPLDKRGRAQAEALVAQLMAFGATTLYAADRVRCHQTIEPLAQELDQ
LIHNEPLLTEEAYAADHKAARKRLLEIAGRPGNPVICTQGKVIPGLIEWW
CERAKVRPETTGNRKGSTWVLSLSDGELVGADYLSPPDEK
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain6m65 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6m65 Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1.
Resolution1.44 Å
Binding residue
(original residue number in PDB)		R55 Y58 K65 Y101 K108 Y145
Binding residue
(residue number reindexed from 1)		R23 Y26 K33 Y69 K76 Y113
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.1.58: 8-oxo-dGDP phosphatase.
3.6.1.61: diadenosine hexaphosphate hydrolase (ATP-forming).
3.6.1.69: 8-oxo-(d)GTP phosphatase.
Gene Ontology
Molecular Function
GO:0008413 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity
GO:0016787 hydrolase activity
GO:0044715 8-oxo-dGDP phosphatase activity
GO:0044716 8-oxo-GDP phosphatase activity
GO:0046872 metal ion binding
Biological Process
GO:0006260 DNA replication
GO:0006281 DNA repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6m65, PDBe:6m65, PDBj:6m65
PDBsum6m65
PubMed33021500
UniProtA0QUZ2|MUTT1_MYCS2 8-oxo-(d)GTP phosphatase (Gene Name=mutT1)

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