Structure of PDB 4x0q Chain B Binding Site BS05

Receptor Information
>4x0q Chain B (length=625) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLSIIDVASDQNLFQTFIKEWRCKKRFSISLACEKIRDDTLVVGLAVCWG
GRDAYYFSLLDPSLTLKDRMWYLQSCLRKESDKECSVVIYDFIQSYKILL
LSCGISLEQSYEDPKVACWLLDPDSQEPTLHSIVTSFLPHELPLLEGMET
SQGIQSLGLNAGSEHSGRYRASVESILIFNSMNQLNSLLQKENLQDVFRK
VEMPSQYCLALLELNGIGFSTAECESQKHIMQAKLDAIETQAYQLAGHSF
SFTSSDDIAEVLFLELKLPPQFSTSKDVLNKLKALHPLPGLILEWRRITN
AITKVVFPLQREKCLNPFLGMERIYPVSQSHTATGRITFTEPNIQNVPRD
FEIKMGMPFSISMRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLIQV
LNTGADVFRSIAAEWKMIEPESVGDDLRQQAKQICYGIIYGMGAKSLGEQ
MGIKENDAACYIDSFKSRYTGINQFMTETVKNCKRDGFVQTILGRRRYLP
GIKDNNPYRKAHAERQAINTIVQGSAADIVKIATVNIQKQLETFHSTFKS
HGHREGMLQSDCPIRGGFFILQLHDELLYEVAEEDVVQVAQIVKNEMESA
VKLSVKLKVKVKIGASWGELKDFDV
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 chain4x0q Chain B Residue 2604 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4x0q Human DNA polymerase theta grasps the primer terminus to mediate DNA repair.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		E2335 R2379 K2383 Q2384 Y2387 Y2391 D2540
Binding residue
(residue number reindexed from 1)		E384 R428 K432 Q433 Y436 Y440 D575
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:4x0q, PDBe:4x0q, PDBj:4x0q
PDBsum4x0q
PubMed25775267
UniProtO75417|DPOLQ_HUMAN DNA polymerase theta (Gene Name=POLQ)

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