Structure of PDB 4k4i Chain A Binding Site BS04

Receptor Information
>4k4i Chain A (length=333) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEA
CSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTA
QMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTV
QKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLD
SLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEF
ACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGR
VLPTPTEKDVFRLLGLPYREPAERDWLEHHHHH
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 A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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 G416 S417 R420 C425 G426 D427 D429 Y505 F506 A510 N513
Binding residue
(residue number reindexed from 1)		R137 G167 S168 R171 C176 G177 D178 D180 Y256 F257 A261 N264
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D427 D429 D490
Catalytic site (residue number reindexed from 1) D178 D180 D241
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

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Molecular Function
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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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