Structure of PDB 8e23 Chain D Binding Site BS03

Receptor Information
>8e23 Chain D (length=603) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSESLSIIDVASDQNLFQTFIKEWRCKKRFSISLACEKIRKTGFPIKGCD
DTLVVGLAVCWGGRDAYYFSLQKESLDPSLTLKDRMWYLQSCLRKEKECS
VVIYDFIQSYKILLLSCGISLEQSYEDPKVACWLLDPDSQEPTLHSIVTS
FLPHELPLLEGMEIQSLGLNAGSEHSGRYRASVESILIFNSMNQLNSLLQ
KENLQDVFRKVEMPSQYCLALLELNGIGECESQKHIMQAKLDAIETQAYQ
LAHSFSFTSSDDIAEVLFLELKLPPFSTSKDVLNKLKALHPLPGLILEWR
RITNAITKVVFPLQREKCLNPFLMERIYPVSQSHTATGRITFTEPNIQNV
PRDFEIISMRHAFPGGSILAADYSQLELRILAHLSHDRRLIQVLNTGADV
FRSIEWKMIEPESVGDDLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAA
CYIDSFKSRYTGINQFMTETVKNCKRDGFVQTILGRRRYLPGIKDNNPYR
KAHAERQAINTIVQGSAADIVKIATVNIQKQLETTFKSHGHREGCPIRFI
LQLHDELLYEVAEEDVVQQIVKNEMESAVKLSVKLKVKVKIGASWGELKD
FDV
Ligand information
Ligand IDDG3
InChIInChI=1S/C10H16N5O12P3/c11-10-13-8-7(9(16)14-10)12-4-15(8)6-2-1-5(25-6)3-24-29(20,21)27-30(22,23)26-28(17,18)19/h4-6H,1-3H2,(H,20,21)(H,22,23)(H2,17,18,19)(H3,11,13,14,16)/t5-,6+/m0/s1
InChIKeyHDRRAMINWIWTNU-NTSWFWBYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@H]3CC[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3CC[C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc2c(n1C3CCC(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N=C(NC2=O)N
FormulaC10 H16 N5 O12 P3
Name2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL54224
DrugBank
ZINCZINC000013516810
PDB chain8e23 Chain D Residue 2601 [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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PDB8e23 Identification of RP-6685 , an Orally Bioavailable Compound that Inhibits the DNA Polymerase Activity of Pol theta.
Resolution2.59 Å
Binding residue
(original residue number in PDB)		Q2333 E2335 R2379 Q2380 Y2387 D2540
Binding residue
(residue number reindexed from 1)		Q375 E377 R419 Q420 Y427 D555
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.49: RNA-directed DNA polymerase.
2.7.7.7: DNA-directed DNA polymerase.
3.6.4.12: DNA helicase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8e23, PDBe:8e23, PDBj:8e23
PDBsum8e23
PubMed36126059
UniProtO75417|DPOLQ_HUMAN DNA polymerase theta (Gene Name=POLQ)

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