Structure of PDB 8dr5 Chain E Binding Site BS03

Receptor Information
>8dr5 Chain E (length=352) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKT
RCMALLESIFGPGVYRLKIDVRQFVTASNRKLELNVVSSPYHLEITPSDM
GNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTKDAQ
AALRRTMEKYSKNIRLIMVCDSMSPIIAPIKSRCLLIRCPAPSDSEISTI
LSDVVTNERIQLETKDILKRIAQASNGNLRVSLLMLESMALNNELALKSS
SPIIKPDWIIVIHKLTRKIVKERSVNSLIECRAVLYDLLAHCIPANIILK
ELTFSLLDVETLNTTNKSSIIEYSSVFDERLSLGNKAIFHLEGFIAKVMC
CL
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain8dr5 Chain E Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8dr5 Multistep loading of a DNA sliding clamp onto DNA by replication factor C.
Resolution2.76 Å
Binding residue
(original residue number in PDB)		V5 R9 P10 S17 H18 G46 G48 K49 K50 T51 R52 I201 L230 R231
Binding residue
(residue number reindexed from 1)		V4 R8 P9 S16 H17 G45 G47 K48 K49 T50 R51 I200 L229 R230
Annotation score3
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003689 DNA clamp loader activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0000077 DNA damage checkpoint signaling
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006271 DNA strand elongation involved in DNA replication
GO:0006272 leading strand elongation
GO:0006281 DNA repair
GO:0007062 sister chromatid cohesion
GO:0007064 mitotic sister chromatid cohesion
GO:0090618 DNA clamp unloading
Cellular Component
GO:0005634 nucleus
GO:0005663 DNA replication factor C complex
GO:0031389 Rad17 RFC-like complex
GO:0031390 Ctf18 RFC-like complex
GO:0031391 Elg1 RFC-like complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8dr5, PDBe:8dr5, PDBj:8dr5
PDBsum8dr5
PubMed35939393
UniProtP38251|RFC5_YEAST Replication factor C subunit 5 (Gene Name=RFC5)

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