Structure of PDB 6jum Chain A Binding Site BS04

Receptor Information
>6jum Chain A (length=347) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTKWVLHVDLDQFLASVELRRRPDLRGQPVIVGGSGDPSEPRKVVTTASY
EAREFGVHAGMPLRAAARRCPDATFLPSDPAAYDEASEQVMGLLRDLGHP
LEVWGWDEAYLGADLPDESDPVEVAERIRTVVAAETGLSCSVGISDNKQR
AKVATGFAKPAGIYVLTEANWMTVMGDRPPDALWGVGPKTTKKLAAMGIT
TVADLAVTDPSVLTTAFGPSTGLWLLLLAKGGGDTEVSSEPWVPRSRSHV
VTFPQDLTERREMDSAVRDLALQTLAEIVEQGRIVTRVAVTVRTSTFYTR
TKIRKLPAPSTDAGQIVDTALAVLDQFELDRPVRLLGVRLELAMDDV
Ligand information
Ligand ID0KX
InChIInChI=1S/C9H17N4O12P3/c10-7-1-2-13(9(15)11-7)8-3-5(14)6(24-8)4-23-26(16,17)12-27(18,19)25-28(20,21)22/h1-2,5-6,8,14H,3-4H2,(H2,10,11,15)(H2,20,21,22)(H3,12,16,17,18,19)/t5-,6+,8+/m0/s1
InChIKeySTYMTWKSQLVXJN-SHYZEUOFSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2
CACTVS 3.370NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2
OpenEye OEToolkits 1.7.6C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O
OpenEye OEToolkits 1.7.6C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
FormulaC9 H17 N4 O12 P3
Name2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine
ChEMBL
DrugBank
ZINCZINC000032016790
PDB chain6jum 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6jum A polar filter in DNA polymerases prevents ribonucleotide incorporation.
Resolution1.78 Å
Binding residue
(original residue number in PDB)		D9 L10 D11 Q12 F13 T46 T47 Y50 R53 A59 D107 K159
Binding residue
(residue number reindexed from 1)		D9 L10 D11 Q12 F13 T46 T47 Y50 R53 A59 D107 K159
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:0046872 metal ion binding
Biological Process
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
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6jum, PDBe:6jum, PDBj:6jum
PDBsum6jum
PubMed31544946
UniProtA0QR77

[Back to BioLiP]