Structure of PDB 4lil Chain A Binding Site BS03

Receptor Information
>4lil Chain A (length=370) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PTELPELLKLYYRRLFPYSQYYRWLNYIKNYFQHREFSFTLKDDIYIRYQ
SFNNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVF
DIDMTDYDDVRRCCSDICPKCWTLMTMAIRIIDRALKEDFGFKHRLWVYS
GRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKKKKVHLSEKIHPFIRKS
INIIKKYFEEYALVNQDILENKESWDKILALVPETIHDELQQSFQKSHNS
LQRWEHLKKVASRYQNNIKNDKYGPWLEWEIMLQYCFPRLDINVSKGINH
LLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFICRELDATRDYKK
TSLAPYVKVFEHFLENLDKS
Ligand information
Ligand IDUTP
InChIInChI=1S/C9H15N2O15P3/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyPGAVKCOVUIYSFO-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H15 N2 O15 P3
NameURIDINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL336296
DrugBankDB04005
ZINCZINC000003861755
PDB chain4lil Chain A Residue 504 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4lil Insights into Eukaryotic Primer Synthesis from Structures of the p48 Subunit of Human DNA Primase.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		S160 R162 R163 H166 K318
Binding residue
(residue number reindexed from 1)		S150 R152 R153 H156 K303
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.90,Kd=12.5uM
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:4lil, PDBe:4lil, PDBj:4lil
PDBsum4lil
PubMed24239947
UniProtP49642|PRI1_HUMAN DNA primase small subunit (Gene Name=PRIM1)

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