Structure of PDB 1dek Chain B Binding Site BS02

Receptor Information
>1dek Chain B (length=231) Species: 10665 (Tequatrovirus T4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKLIFLSGVKRSGKDTTADFIMSNYSAVKYQLAGPIKDALAYAWGVFAAN
TDYPCLTRKEFEGIDYDRETNLNLTKLEVITIMEQAFCYLNGKSPIKGVF
VFDDEGKESVNFVAFNKITDVINNIEDQWSVRRLMQALGTDLIVNNFDRM
YWVKLFALDYLDKFNSGYDYYIVPDTRQDHEMDAARAMGATVIHVVRPGA
GLPIRDGDLVITNDGSLEELFSKIKNTLKVL
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 chain1dek Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1dek Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L32 K37 R68 R132 M135 G139 T140 D175 E181
Binding residue
(residue number reindexed from 1)		L32 K37 R68 R132 M135 G139 T140 D175 E181
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D15 R68
Catalytic site (residue number reindexed from 1) D15 R68
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
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Biological Process
External links
PDB RCSB:1dek, PDBe:1dek, PDBj:1dek
PDBsum1dek
PubMed8670851
UniProtP04531|DNMK_BPT4 Deoxynucleotide monophosphate kinase (Gene Name=1)

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