Structure of PDB 7n2m Chain A Binding Site BS03

Receptor Information
>7n2m Chain A (length=865) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EQVFHFYWLDAYEDQYNQPGVVFLFGKVWIESAETHVSCCVMVKNIERTL
YFLPREMKIDLNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKSKPVEK
NYAFEIPDVPEKSEYLEVKYSAEMPQLPQDLKGETFSHVFGTNTSSLELF
LMNRKIKGPCWLEVKSPQLLNQPVSWCKAEAMALKPDLVNVIKDVSPPPL
VVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQSHFCVVS
KPKDCIFPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGH
NIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGFGERNATCGRMIC
DVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYL
LEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFL
LLHAFYENNYIVPDKQIRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYP
SIIQEFNICFTTVQRVEQIPELPDPSLEMGILPREIRKLVERRKQVKQLM
KQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYK
GREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEV
NKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYVTKQELKGLDI
VRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVP
VSQFEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVI
CQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDG
IDAVLIATWLGLDPT
Ligand information
Ligand IDDCP
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+/m0/s1
InChIKeyRGWHQCVHVJXOKC-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341NC1=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
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2
FormulaC9 H16 N3 O13 P3
Name2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL560403
DrugBankDB03258
ZINCZINC000008215945
PDB chain7n2m Chain A Residue 1301 [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]
PDB7n2m Structural and functional insight into mismatch extension by human DNA polymerase alpha.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		D860 F861 N862 S863 L864 Y865 R922 K950 N954 Y957 D1004
Binding residue
(residue number reindexed from 1)		D494 F495 N496 S497 L498 Y499 R543 K571 N575 Y578 D625
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:1902975 mitotic DNA replication initiation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7n2m, PDBe:7n2m, PDBj:7n2m
PDBsum7n2m
PubMed35467978
UniProtP09884|DPOLA_HUMAN DNA polymerase alpha catalytic subunit (Gene Name=POLA1)

[Back to BioLiP]