Structure of PDB 6juq Chain A Binding Site BS04

Receptor Information
>6juq Chain A (length=341) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRKIIHVDMDCFAAAVEMRDNPALRDIPIAIGGSRERRGVISCANYPARK
FGVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPL
SLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAK
IASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRTC
GDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTMA
EDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQ
EHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDP
Ligand information
Ligand ID2TM
InChIInChI=1S/C10H18N3O13P3/c11-6-1-2-13(10(16)12-6)9-8(15)7(14)5(25-9)3-24-27(17,18)4-28(19,20)26-29(21,22)23/h1-2,5,7-9,14-15H,3-4H2,(H,17,18)(H,19,20)(H2,11,12,16)(H2,21,22,23)/t5-,7-,8-,9-/m1/s1
InChIKeySTGUOVSTMBLHFT-ZOQUXTDFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O
CACTVS 3.385NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
CACTVS 3.385NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
FormulaC10 H18 N3 O13 P3
Name5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine;
CMPcPP
ChEMBL
DrugBank
ZINCZINC000098208273
PDB chain6juq Chain A Residue 401 [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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PDB6juq A polar filter in DNA polymerases prevents ribonucleotide incorporation.
Resolution2.74 Å
Binding residue
(original residue number in PDB)		D8 M9 D10 C11 F12 A13 S42 C43 R49 D103 K157
Binding residue
(residue number reindexed from 1)		D8 M9 D10 C11 F12 A13 S42 C43 R49 D103 K157
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
View graph for
Cellular Component
External links
PDB RCSB:6juq, PDBe:6juq, PDBj:6juq
PDBsum6juq
PubMed31544946
UniProtQ47155|DPO4_ECOLI DNA polymerase IV (Gene Name=dinB)

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