Structure of PDB 4qwd Chain A Binding Site BS03

Receptor Information
>4qwd Chain A (length=341) Species: 273057 (Saccharolobus solfataricus P2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEA
RKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIE
IASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVF
AKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGIN
KLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVT
MKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGR
TFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI
Ligand information
Ligand ID3TT
InChIInChI=1S/C8H15N4O11P3S/c9-5-1-2-12(8(13)10-5)6-4-27-7(22-6)3-21-26(19,20)23-25(17,18)11-24(14,15)16/h1-2,6-7H,3-4H2,(H,19,20)(H2,9,10,13)(H4,11,14,15,16,17,18)/t6-,7+/m0/s1
InChIKeyKGYPGPIERPVYLF-NKWVEPMBSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NC1=NC(=O)N(C=C1)[CH]2CS[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)O2
OpenEye OEToolkits 1.7.6C1C(OC(S1)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)N2C=CC(=NC2=O)N
CACTVS 3.370NC1=NC(=O)N(C=C1)[C@@H]2CS[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)O2
OpenEye OEToolkits 1.7.6C1[C@H](O[C@H](S1)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)N2C=CC(=NC2=O)N
FormulaC8 H15 N4 O11 P3 S
Name[[[[(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid
ChEMBL
DrugBank
ZINCZINC000098208468
PDB chain4qwd Chain A Residue 701 [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]
PDB4qwd Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		D7 F8 D9 Y10 F11 Y12 A44 T45 R51 A57 D105 K159
Binding residue
(residue number reindexed from 1)		D7 F8 D9 Y10 F11 Y12 A44 T45 R51 A57 D105 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:0042276 error-prone translesion synthesis
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4qwd, PDBe:4qwd, PDBj:4qwd
PDBsum4qwd
PubMed25104018
UniProtQ97W02|DPO4_SACS2 DNA polymerase IV (Gene Name=dbh)

[Back to BioLiP]