Structure of PDB 1del Chain A Binding Site BS02

Receptor Information
>1del Chain A (length=241) Species: 10665 (Tequatrovirus T4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKLIFLSGVKRSGKDTTADFIMSNYSAVKYQLAGPIKDALAYAWGVFAAN
TDYPCLTRKEFEGIDYDRETNLNLTKLEVITIMEQAFCYLNGKSPIKGVF
VFDDEGKESVNFVAFNKITDVINNIEDQWSVRRLMQALGTDLIVNNFDRM
YWVKLFALDYLDKFNSGYDYYIVPDTRQDHEMDAARAMGATVIHVVRPGQ
KSNDTHITEAGLPIRDGDLVITNDGSLEELFSKIKNTLKVL
Ligand information
Ligand IDDGP
InChIInChI=1S/C10H14N5O7P/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(22-6)2-21-23(18,19)20/h3-6,16H,1-2H2,(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
InChIKeyLTFMZDNNPPEQNG-KVQBGUIXSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3
OpenEye OEToolkits 1.7.0c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.7.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H14 N5 O7 P
Name2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL477487
DrugBankDB04457
ZINCZINC000001730395
PDB chain1del Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1del Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		K37 R132 G139 T140 W152 R177 E181 E209
Binding residue
(residue number reindexed from 1)		K37 R132 G139 T140 W152 R177 E181 E209
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D15 R68 H206
Catalytic site (residue number reindexed from 1) D15 R68 H206
Enzyme Commision number 2.7.4.13: (deoxy)nucleoside-phosphate kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0047507 (deoxy)nucleoside-phosphate kinase activity
Biological Process
GO:0016310 phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1del, PDBe:1del, PDBj:1del
PDBsum1del
PubMed8670851
UniProtP04531|DNMK_BPT4 Deoxynucleotide monophosphate kinase (Gene Name=1)

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