Structure of PDB 8b9b Chain 5 Binding Site BS02

Receptor Information
>8b9b Chain 5 (length=533) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DDDNTEIIKSFKNFILEFRLDSQFIYRDQLRNNILVKNYSLTVNMEHLIG
YNEDIYKKLSDEPSDIIPLFETAITQVAKRISILSLPTFQLILNSNANQI
PLRDLDSEHVSKIVRLSGIIISTSVLSSRATYLSIMCRNCRHTTSITINN
FNVSLPRSCLSNCGPDPYIIIHESSKFIDQQFLKLQEIPELVPVGEMPRN
LTMTCDRYLTNKVIPGTRVTIVGIYSIYNSGVAIRTPYIKILGIQSMFTE
EEEEEFLQLSRNPKLYEILTNSIAPSIFGNEDIKKAIVCLLMGGSKKILP
DGMRLRGDINVLLLAKSQLLKFVEKVSPIAVYTSGKGSSAAGLTASVQRR
EFYLEGGAMVLADGGVVCIDEFDKMRDEDRVAIHEAMEQQTISIAKAGIT
TVLNSRTSVLAAANTTILSRFDMIFIVKDDHNEERDISIANHVINIHTEI
SIEKMKRYITYCRLKCAPRLSPQAAEKLSSNFVTIRKQLLINPITIRQLE
AIIRITESLAKLELSPIAQERHVDEAIRLFQAS
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain8b9b Chain 3 Residue 1500 [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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PDB8b9b How Pol alpha-primase is targeted to replisomes to prime eukaryotic DNA replication.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		E498 R651 E654
Binding residue
(residue number reindexed from 1)		E388 R497 E500
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.4.12: DNA helicase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003688 DNA replication origin binding
GO:0003697 single-stranded DNA binding
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0017116 single-stranded DNA helicase activity
GO:0043138 3'-5' DNA helicase activity
Biological Process
GO:0000727 double-strand break repair via break-induced replication
GO:0006260 DNA replication
GO:0006267 pre-replicative complex assembly involved in nuclear cell cycle DNA replication
GO:0006268 DNA unwinding involved in DNA replication
GO:0006270 DNA replication initiation
GO:0006279 premeiotic DNA replication
GO:0006368 transcription elongation by RNA polymerase II
GO:0030174 regulation of DNA-templated DNA replication initiation
GO:0031507 heterochromatin formation
GO:0031509 subtelomeric heterochromatin formation
GO:0032508 DNA duplex unwinding
GO:0033260 nuclear DNA replication
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005656 nuclear pre-replicative complex
GO:0005737 cytoplasm
GO:0031261 DNA replication preinitiation complex
GO:0031298 replication fork protection complex
GO:0042555 MCM complex
GO:0043596 nuclear replication fork
GO:0071162 CMG complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8b9b, PDBe:8b9b, PDBj:8b9b
PDBsum8b9b
PubMed37506699
UniProtP29496|MCM5_YEAST Minichromosome maintenance protein 5 (Gene Name=MCM5)

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