Structure of PDB 4k4g Chain E Binding Site BS04

Receptor Information
>4k4g Chain E (length=323) 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
DSLRQEGFLTDDLVSQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACAL
LYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPT
PTEKDVFRLLGLPYREPAERDWL
Ligand information
Ligand ID1S0
InChIInChI=1S/C9H16N3O13P3/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(23-8)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,21)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m1/s1
InChIKeyRGWHQCVHVJXOKC-CHKWXVPMSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O
OpenEye OEToolkits 1.7.6C1[C@H]([C@@H](O[C@@H]1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
OpenEye OEToolkits 1.7.6C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.370NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
CACTVS 3.370NC1=NC(=O)N(C=C1)[C@@H]2C[C@@H](O)[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
FormulaC9 H16 N3 O13 P3
Name4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one
ChEMBL
DrugBank
ZINCZINC000013435054
PDB chain4k4g Chain E Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4k4g Structural basis for the binding and incorporation of nucleotide analogs with L-stereochemistry by human DNA polymerase lambda.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		R386 S417 R420 G426 D427 D429 Y505 F506 A510 N513
Binding residue
(residue number reindexed from 1)		R138 S169 R172 G178 D179 D181 Y252 F253 A257 N260
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D427 D429 D490
Catalytic site (residue number reindexed from 1) D179 D181 D237
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:4k4g, PDBe:4k4g, PDBj:4k4g
PDBsum4k4g
PubMed25015085
UniProtQ9UGP5|DPOLL_HUMAN DNA polymerase lambda (Gene Name=POLL)

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