Structure of PDB 5dga Chain A Binding Site BS03

Receptor Information
>5dga Chain A (length=428) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIA
VSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEV
MEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEG
LPQGPTVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAI
ERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRK
IRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRG
IEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTK
DRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIK
NCNTSGIQTEWSPPLTMLFLCATKFSAS
Ligand information
Ligand ID1FZ
InChIInChI=1S/C10H18N3O13P3/c1-5-3-13(10(16)11-9(5)15)8-2-6(14)7(25-8)4-24-27(17,18)12-28(19,20)26-29(21,22)23/h3,6-8,14H,2,4H2,1H3,(H,11,15,16)(H2,21,22,23)(H3,12,17,18,19,20)/t6-,7+,8+/m0/s1
InChIKeyYRKUYVYMPXAOAT-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 1.7.6CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
CACTVS 3.370CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H18 N3 O13 P3
Name5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine
ChEMBL
DrugBank
ZINCZINC000013455017
PDB chain5dga Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5dga Structural and Kinetic Analysis of Miscoding Opposite the DNA Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion DNA Polymerase eta.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D13 M14 D15 C16 F17 F18 I48 Y52 R55 R61 D115 K231
Binding residue
(residue number reindexed from 1)		D14 M15 D16 C17 F18 F19 I49 Y53 R56 R62 D116 K227
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0003684 damaged DNA binding
Biological Process
GO:0006281 DNA repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5dga, PDBe:5dga, PDBj:5dga
PDBsum5dga
PubMed27226627
UniProtQ9Y253|POLH_HUMAN DNA polymerase eta (Gene Name=POLH)

[Back to BioLiP]