Structure of PDB 4k4i Chain M Binding Site BS04

Receptor Information
>4k4i Chain M (length=329) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQE
ACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKT
AQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQT
VQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLL
DSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSE
FACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPG
RVLPTPTEKDVFRLLGLPYREPAERDWLE
Ligand information
Ligand ID1RY
InChIInChI=1S/C8H13FN3O12P3S/c9-4-1-12(8(13)11-7(4)10)5-3-28-6(22-5)2-21-26(17,18)24-27(19,20)23-25(14,15)16/h1,5-6H,2-3H2,(H,17,18)(H,19,20)(H2,10,11,13)(H2,14,15,16)/t5-,6+/m0/s1
InChIKeyWIEOLFZNMKSGEX-NTSWFWBYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NC1=NC(=O)N(C=C1F)[CH]2CS[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
OpenEye OEToolkits 1.7.6C1[C@H](O[C@H](S1)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=C(C(=NC2=O)N)F
CACTVS 3.370NC1=NC(=O)N(C=C1F)[C@@H]2CS[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
OpenEye OEToolkits 1.7.6C1C(OC(S1)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N2C=C(C(=NC2=O)N)F
FormulaC8 H13 F N3 O12 P3 S
Name[[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
ChEMBLCHEMBL341421
DrugBank
ZINC
PDB chain4k4i Chain M Residue 601 [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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PDB4k4i Structural basis for the binding and incorporation of nucleotide analogs with L-stereochemistry by human DNA polymerase lambda.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		R386 S417 G426 Y505 S509 A510 N513 R517
Binding residue
(residue number reindexed from 1)		R138 S169 G178 Y257 S261 A262 N265 R269
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D427 D429 D490
Catalytic site (residue number reindexed from 1) D179 D181 D242
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:4k4i, PDBe:4k4i, PDBj:4k4i
PDBsum4k4i
PubMed25015085
UniProtQ9UGP5|DPOLL_HUMAN DNA polymerase lambda (Gene Name=POLL)

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