Structure of PDB 5yyd Chain F Binding Site BS03

Receptor Information
>5yyd Chain F (length=342) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPAR
KFGVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEP
LSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLA
KIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRT
CGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTM
AEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTT
QEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDP
Ligand information
Ligand IDTTW
InChIInChI=1S/C10H18N3O13P3/c1-5-3-13(10(16)11-9(5)15)8-2-6(14)7(25-8)4-24-29(22,23)26-28(20,21)12-27(17,18)19/h3,6-8,14H,2,4H2,1H3,(H,22,23)(H,11,15,16)(H4,12,17,18,19,20,21)/t6-,7+,8+/m0/s1
InChIKeyRTOWUXJWTDSUGC-XLPZGREQSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)O2)C(=O)NC1=O
CACTVS 3.385CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)O2)C(=O)NC1=O
OpenEye OEToolkits 2.0.6CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O
OpenEye OEToolkits 2.0.6CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O
ACDLabs 12.01O=C1C(=CN(C(N1)=O)C2CC(C(O2)COP(OP(NP(=O)(O)O)(O)=O)(O)=O)O)C
FormulaC10 H18 N3 O13 P3
Name5'-O-[hydroxy{[hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]thymidine
ChEMBL
DrugBank
ZINC
PDB chain5yyd Chain F Residue 900 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5yyd Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction
Resolution2.05 Å
Binding residue
(original residue number in PDB)		D8 M9 D10 C11 F12 F13 S42 T43 R49 D103 K157
Binding residue
(residue number reindexed from 1)		D9 M10 D11 C12 F13 F14 S43 T44 R50 D104 K158
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0005515 protein binding
GO:0008296 3'-5'-DNA exonuclease activity
GO:0046872 metal ion binding
Biological Process
GO:0000731 DNA synthesis involved in DNA repair
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006281 DNA repair
GO:0006974 DNA damage response
GO:0009432 SOS response
GO:0042276 error-prone translesion synthesis
GO:0070987 error-free translesion synthesis
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5yyd, PDBe:5yyd, PDBj:5yyd
PDBsum5yyd
PubMed29850882
UniProtQ47155|DPO4_ECOLI DNA polymerase IV (Gene Name=dinB)

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