Structure of PDB 7m0e Chain D Binding Site BS06

Receptor Information
>7m0e Chain D (length=325) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WVCAQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKS
FHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELF
SNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMP
REEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGR
SHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRR
LDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAGRV
LPTPTEKDVFRLLGLPYREPAERDW
Ligand information
Ligand IDDUP
InChIInChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1
InChIKeyXZLLMTSKYYYJLH-SHYZEUOFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[C@H]1C[C@@H](O[C@@H]1CO[P@](O)(=O)N[P@](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341O[CH]1C[CH](O[CH]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
FormulaC9 H16 N3 O13 P3
Name2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
ChEMBLCHEMBL1232397
DrugBankDB01965
ZINC
PDB chain7m0e Chain D Residue 603 [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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PDB7m0e Analysis of diverse double-strand break synapsis with Pol lambda reveals basis for unique substrate specificity in nonhomologous end-joining.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		R386 G416 S417 R420 C425 G426 D427 D429 Y505 T507 G508 A510
Binding residue
(residue number reindexed from 1)		R148 G178 S179 R182 C187 G188 D189 D191 Y267 T269 G270 A272
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:7m0e, PDBe:7m0e, PDBj:7m0e
PDBsum7m0e
PubMed35778389
UniProtQ9UGP5|DPOLL_HUMAN DNA polymerase lambda (Gene Name=POLL)

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