Structure of PDB 6r5d Chain A Binding Site BS04

Receptor Information
>6r5d Chain A (length=384) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDIY
IRYQSFNNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEK
ELVFDIDMTDYDDVRRCCSSADICPKCWTLMTMAIRIIDRALKEDFGFKH
RLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGQDVKKKVHL
SEKIHPFIRKSINIIKKYFEEYALVNQDILENKESWDKILALVPETIHDE
LQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIMLQYCFPR
LDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFIC
RELDAITRDYKKTSLAPYVKVFEHFLENLDKSRK
Ligand information
Ligand IDDTP
InChIInChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
InChIKeySUYVUBYJARFZHO-RRKCRQDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
FormulaC10 H16 N5 O12 P3
Name2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL335538
DrugBankDB03222
ZINCZINC000008215662
PDB chain6r5d Chain A 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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PDB6r5d Structural Basis for Inhibition of Human Primase by Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		D109 D111 S160 R162 R163 H166 L316 L317 K318 H324
Binding residue
(residue number reindexed from 1)		D105 D107 S156 R158 R159 H162 L312 L313 K314 H320
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6r5d, PDBe:6r5d, PDBj:6r5d
PDBsum6r5d
PubMed31479243
UniProtP49642|PRI1_HUMAN DNA primase small subunit (Gene Name=PRIM1)

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