Structure of PDB 7m4k Chain A Binding Site BS05

Receptor Information
>7m4k Chain A (length=310) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEAC
SIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQ
MWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQ
KAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDS
LRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLY
FTGSAHFNRSMRALAKTKGMSLSEHALSTAVPGRVLPTPTEKDVFRLLGL
PYREPAERDW
Ligand information
Ligand IDYQS
InChIInChI=1S/C10H17N2O13P3S/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(23-8)4-22-28(21,29)25-27(19,20)24-26(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,29)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+,28-/m0/s1
InChIKeyPXHHTOSRELKWOE-ISVKTPMGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(OP(=O)(O)OP(=O)(O)O)S)O
OpenEye OEToolkits 2.0.7CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@](=O)(OP(=O)(O)OP(=O)(O)O)S)O
CACTVS 3.385CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](S)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
CACTVS 3.385CC1=CN([CH]2C[CH](O)[CH](CO[P](S)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H17 N2 O13 P3 S
Name[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain7m4k Chain A Residue 612 [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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PDB7m4k Watching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints.
Resolution1.719 Å
Binding residue
(original residue number in PDB)
R386 G416 S417 R420 G426 D427 D429 Y505 T507 G508 A510 N513
Binding residue
(residue number reindexed from 1)
R136 G166 S167 R170 G176 D177 D179 Y250 T252 G253 A255 N258
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
4.2.99.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0016779 nucleotidyltransferase activity
GO:0034061 DNA polymerase activity
Biological Process
GO:0006281 DNA repair

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:7m4k, PDBe:7m4k, PDBj:7m4k
PDBsum7m4k
PubMed35680862
UniProtQ9UGP5|DPOLL_HUMAN DNA polymerase lambda (Gene Name=POLL)

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