Structure of PDB 6r4t Chain D Binding Site BS03

Receptor Information
>6r4t Chain D (length=385) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETFDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKD
DIYIRYQSFNNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQA
QEKELVFDIDMTDYDDVRRCCSSADICPKCWTLMTMAIRIIDRALKEDFG
FKHRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGQDVKKK
VHLSEKIHPFIRKSINIIKKYFEEYALVNQDILENKESWDKILALVPETI
HDELQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIMLQYC
FPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTIS
FICRELDAIDYKKTSLAPYVKVFEHFLENLDKSRK
Ligand information
Ligand IDHEJ
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7+,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-UHTZMRCNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
OpenEye OEToolkits 2.0.6c1nc(c2c(n1)n(cn2)[C@H]3[C@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.385Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01Nc1ncnc2c1ncn2C3OC(COP(O)(=O)OP(O)(=O)OP(O)(=O)O)C(O)C3O
CACTVS 3.385Nc1ncnc2n(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 H16 N5 O13 P3
Name9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine;
Vidarabine-TRIPHOSPHATE
ChEMBLCHEMBL4441501
DrugBank
ZINCZINC000011726744
PDB chain6r4t Chain D Residue 503 [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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PDB6r4t Structural Basis for Inhibition of Human Primase by Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		Y54 D79 D111 S160 R162 R163 H166 K318 H324
Binding residue
(residue number reindexed from 1)		Y53 D78 D110 S159 R161 R162 H165 K317 H323
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:6r4t, PDBe:6r4t, PDBj:6r4t
PDBsum6r4t
PubMed31479243
UniProtP49642|PRI1_HUMAN DNA primase small subunit (Gene Name=PRIM1)

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