Structure of PDB 6s1n Chain A Binding Site BS04

Receptor Information
>6s1n Chain A (length=1010) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RWLRPTPPALDPQTEPLIFQQLEIDHYVGPAQPVSVPVLRAFGVTDEGFS
VCCHIHGFAPYFYTPAPPGFGPEHMGDLQRELNLAISRDSRGGRELTGPA
VLAVELCSRESMFGYHGHGPSPFLRITVALPRLVAPARRLLEQGIRVAGL
GTPSFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYALRLKEKATQCQL
EADVLWSDVVSHPPEGPWQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQ
ICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIR
IMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVAGLCSNIRDSSF
QSKQTGRRDTKVVSMVGRVQMDMLQVLLREYKLRSYTLNAVSFHFLGEHS
IITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVP
LSYLLSRGQQVKVVSQLLRQAMHEGLLMPVVKSEGGEDYTGATVIEPLKG
YYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGLTEDQFIRTPT
GDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLA
LKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKYTVE
NGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRL
EFEKVYFPYLLISKKRYAGLLFSSRPDAHDRMDCKGLEAVRRDNCPLVAN
LVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAAS
DYAGKQAHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDP
LFVLEHSLPIDTQYYLEQQLAKPLLRIFEPILGEGRAEAVLLRGDHTRCK
TVLGLLAFAKRRNCCIGCRTVLSHQGAVCEFCQPRESELYQKEVSHLNAL
EERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMRKKVRKDLEDQEQLLR
RFGPPGPEAW
Ligand information
Ligand IDTTP
InChIInChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyNHVNXKFIZYSCEB-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H17 N2 O14 P3
NameTHYMIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL363559
DrugBankDB02452
ZINCZINC000008215959
PDB chain6s1n Chain T Residue 101 [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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PDB6s1n Structure of the processive human Pol delta holoenzyme.
Resolution4.86 Å
Binding residue
(original residue number in PDB)		S605 L606 Y607 R667 K694 N698
Binding residue
(residue number reindexed from 1)		S513 L514 Y515 R575 K602 N606
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
3.1.11.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003684 damaged DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0004527 exonuclease activity
GO:0005515 protein binding
GO:0008296 3'-5'-DNA exonuclease activity
GO:0008408 3'-5' exonuclease activity
GO:0019899 enzyme binding
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0000731 DNA synthesis involved in DNA repair
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006281 DNA repair
GO:0006287 base-excision repair, gap-filling
GO:0006297 nucleotide-excision repair, DNA gap filling
GO:0009411 response to UV
GO:0034644 cellular response to UV
GO:0045004 DNA replication proofreading
GO:0055089 fatty acid homeostasis
GO:0070987 error-free translesion synthesis
GO:0071897 DNA biosynthetic process
Cellular Component
GO:0000109 nucleotide-excision repair complex
GO:0000781 chromosome, telomeric region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0016235 aggresome
GO:0043625 delta DNA polymerase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6s1n, PDBe:6s1n, PDBj:6s1n
PDBsum6s1n
PubMed32111820
UniProtP28340|DPOD1_HUMAN DNA polymerase delta catalytic subunit (Gene Name=POLD1)

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