Structure of PDB 7zx0 Chain DDD Binding Site BS04

Receptor Information
>7zx0 Chain DDD (length=633) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLSIIDVASDQNLFQTFIKEWRCKKRFSISLACEKIDDGFPIKGCDDTLV
VGLAVCWGGRDAYYFSLQKVPPSLDPSLTLKDRMWYLQSCLRKESDKECS
VVIYDFIQSYKILLLSCGISLEQSYEDPKVACWLLDPDSQEPTLHSIVTS
FLPHELPLLEGMETSQGIQSLGLNAGSEHSGRYRASVESILIFNSMNQLN
SLLQKENLQDVFRKVEMPSQYCLALLELNGIGFSTAECESQKHIMQAKLD
AIETQAYQLAGHSFSFTSSDDIAEVLFLELKLPPFSTSKDVLNKLKALHP
LPGLILEWRRITNAITKVVFPLQREKCLNPFLGMERIYPVSQSHTATGRI
TFTEPNIQNVPRDFEIKMGGMPFSISMRHAFVPFPGGSILAADYSQLELR
ILAHLSHDRRLIQVLNTGADVFRSIAAEWKMIEPESVGDDLRQQAKQICY
GIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYTGINQFMTETVKNCKRD
GFVQTILGRRRYLPGIKDNNPYRKAHAERQAINTIVQGSAADIVKIATVN
IQKQLETFHSTFKSHGHRECPIRGGFFILQLHDELLYEVAEEDVVQVAQI
VKNEMESAVKLSVKLKVKVKIGASWGELKDFDV
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 chain7zx0 Chain DDD Residue 2602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7zx0 Discovery, Characterization, and Structure-Based Optimization of Small-Molecule In Vitro and In Vivo Probes for Human DNA Polymerase Theta.
Resolution2.99 Å
Binding residue
(original residue number in PDB)		R2241 D2330 E2335 F2359 R2379 K2383 Y2387 Y2391 D2540
Binding residue
(residue number reindexed from 1)		R349 D393 E398 F422 R442 K446 Y450 Y454 D583
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:7zx0, PDBe:7zx0, PDBj:7zx0
PDBsum7zx0
PubMed36200480
UniProtO75417|DPOLQ_HUMAN DNA polymerase theta (Gene Name=POLQ)

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