Structure of PDB 4qwc Chain A Binding Site BS05

Receptor Information
>4qwc Chain A (length=342) 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
TFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIE
Ligand information
Ligand IDLTP
InChIInChI=1S/C9H15N3O10P2/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(21-8)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m1/s1
InChIKeyFTDHDKPUHBLBTL-CHKWXVPMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)O)O
OpenEye OEToolkits 1.7.6C1[C@H]([C@@H](O[C@@H]1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)O)O
CACTVS 3.370NC1=NC(=O)N(C=C1)[C@@H]2C[C@@H](O)[C@H](CO[P](O)(=O)O[P](O)(O)=O)O2
CACTVS 3.370NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O
FormulaC9 H15 N3 O10 P2
Name4-amino-1-{2-deoxy-5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one
ChEMBL
DrugBank
ZINCZINC000013435046
PDB chain4qwc Chain A Residue 405 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4qwc Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		Y10 Y12 A44 T45 R51 A57 D105 K159
Binding residue
(residue number reindexed from 1)		Y10 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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4qwc, PDBe:4qwc, PDBj:4qwc
PDBsum4qwc
PubMed25104018
UniProtQ97W02|DPO4_SACS2 DNA polymerase IV (Gene Name=dbh)

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