Structure of PDB 3h4d Chain A Binding Site BS05

Receptor Information
>3h4d Chain A (length=373) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASSRVIVHVDLDCFYAQVEMISNPELKDKPLGVQQKYLVVTCNYEARKLG
VKKLMNVRDAKEKCPQLVLVNGEDLTRYREMSYKVTELLEEFSPVVERLG
FDENFVDLTEMVEKRLQQLQSDELSAVTVSGHVYNNQSINLLDVLHIRLL
VGSQIAAEMREAMYNQLGLTGCAGVASNKLLAKLVSGVFKPNQQTVLLPE
SCQHLIHSLNHIKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELG
ISVAQRIQKLSFGEDNSPVILSGPPQSFSEEDSFKKCSSEVEAKNKIEEL
LASLLNRVCQDGRKPHTVRLIIRRYSSEKHYGRESRQCPIPSHVIQVMTP
MVDILMKLFRNMTLLSVCFCNLK
Ligand information
Ligand IDDGT
InChIInChI=1S/C10H16N5O13P3/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
InChIKeyHAAZLUGHYHWQIW-KVQBGUIXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[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(n2cnc1c2N=C(N)NC1=O)CC3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H16 N5 O13 P3
Name2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL477486
DrugBankDB02181
ZINCZINC000008215755
PDB chain3h4d Chain T Residue 875 [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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PDB3h4d Replication across template T/U by human DNA polymerase-iota.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		L35 D36 C37 F38 Y39 T65 Y68 R71 K77 D126 K214
Binding residue
(residue number reindexed from 1)		L11 D12 C13 F14 Y15 T41 Y44 R47 K53 D102 K190
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:3h4d, PDBe:3h4d, PDBj:3h4d
PDBsum3h4d
PubMed19604477
UniProtQ9UNA4|POLI_HUMAN DNA polymerase iota (Gene Name=POLI)

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