Structure of PDB 4ebd Chain A Binding Site BS03

Receptor Information
>4ebd Chain A (length=376) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSRVIVHVDLDCFYAQVEMISNPELKDKPLGVQQKYLVVTCNYEARKLGV
KKLMNVRDAKEKCPQLVLVNGEDLTRYREMSYKVTELLEEFSPVVERLGF
DENFVDLTEMVEKRLQQLQSDELSAVTVSGHVYNNQSINLLDVLHIRLLV
GSQIAAEMREAMYNQLGLTGCAGVASNKLLAKLVSGVFKPNQQTVLLPES
CQHLIHSLNHIKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGI
SVAQRIQKLSFGEDNSPVILSGPPQSFSEEDSFKKCSSEVEAKNKIEELL
ASLLNRVCQDRKPHTVRLIIRRYGRESRQCPIPSHVIQKDVMTPMVDILM
KLFRNMVNVKMPFHLTLLSVCFCNLK
Ligand information
Ligand ID0OJ
InChIInChI=1S/C12H18N5O11P3/c13-10-9-11(15-4-14-10)17(5-16-9)12-1-7(12)6(8(18)2-12)3-26-30(22,23)28-31(24,25)27-29(19,20)21/h4-8,18H,1-3H2,(H,22,23)(H,24,25)(H2,13,14,15)(H2,19,20,21)/t6-,7-,8-,12-/m0/s1
InChIKeyDNBZILMJAUSGHT-QZOVBDONSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C34CC3C(C(C4)O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@]34C[C@H]3[C@@H]([C@H](C4)O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C]34C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH]3C4
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@]34C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H]3C4
FormulaC12 H18 N5 O11 P3
NameSouth-methanocarba-2'-deoxyadenosine triphosphate
ChEMBL
DrugBank
ZINCZINC000033505563
PDB chain4ebd Chain A Residue 501 [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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PDB4ebd A Nucleotide-Analogue-Induced Gain of Function Corrects the Error-Prone Nature of Human DNA Polymerase iota.
Resolution2.571 Å
Binding residue
(original residue number in PDB)		C37 Y39 V64 T65 Y68 R71 K77 L78 D126 K214
Binding residue
(residue number reindexed from 1)		C12 Y14 V39 T40 Y43 R46 K52 L53 D101 K189
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0003684 damaged DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:0006281 DNA repair

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:4ebd, PDBe:4ebd, PDBj:4ebd
PDBsum4ebd
PubMed22632140
UniProtQ9UNA4|POLI_HUMAN DNA polymerase iota (Gene Name=POLI)

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