Structure of PDB 6r5e Chain E Binding Site BS04

Receptor Information
>6r5e Chain E (length=382) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDI
YIRYQSFNNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQE
KELVFDIDMTDYDDVRRCCSSADICPKCWTLMTMAIRIIDRALKEDFGFK
HRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGQDVKKKVH
LSEKIHPFIRKSINIIKKYFEEYALVNQDILENKESWDKILALVPETIHD
ELQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIMLQYCFP
RLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFI
CRELDAIDYKKTSLAPYVKVFEHFLENLDKSR
Ligand information
Ligand IDJSQ
InChIInChI=1S/C10H15FN5O13P3/c11-10-14-7(12)4-8(15-10)16(2-13-4)9-6(18)5(17)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,17-18H,1H2,(H,22,23)(H,24,25)(H2,12,14,15)(H2,19,20,21)/t3-,5-,6-,9-/m1/s1
InChIKeyPIOKUWLZUXUBCO-UUOKFMHZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1nc(F)nc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 2.0.7c1nc2c(nc(nc2n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)F)N
OpenEye OEToolkits 2.0.7c1nc2c(nc(nc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)F)N
CACTVS 3.385Nc1nc(F)nc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H15 F N5 O13 P3
Name2-fluoro-ATP
ChEMBL
DrugBank
ZINC
PDB chain6r5e Chain E Residue 504 [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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PDB6r5e Structural Basis for Inhibition of Human Primase by Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		Y54 K77 D79 D109 D111 S160 R162 R163 H166 H315 L316 L317 K318 H324
Binding residue
(residue number reindexed from 1)		Y51 K74 D76 D106 D108 S157 R159 R160 H163 H312 L313 L314 K315 H321
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.102: DNA primase AEP.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003896 DNA primase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0032553 ribonucleotide binding
GO:0046872 metal ion binding
Biological Process
GO:0006260 DNA replication
GO:0006269 DNA replication, synthesis of primer
GO:0006270 DNA replication initiation
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005654 nucleoplasm
GO:0005658 alpha DNA polymerase:primase complex
GO:0016020 membrane
GO:1990077 primosome complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6r5e, PDBe:6r5e, PDBj:6r5e
PDBsum6r5e
PubMed31479243
UniProtP49642|PRI1_HUMAN DNA primase small subunit (Gene Name=PRIM1)

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