Structure of PDB 8gd7 Chain A Binding Site BS04

Receptor Information

>8gd7 Chain A (length=631) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

LSIIDVASDQNLFQTFIKEWRCKKRFSISLACEKIRSGDDTLVVGLAVCW
GGRDAYYFSLGLDPSLTLKDRMWYLQSCLRKESDKECSVVIYDFIQSYKI
LLLSCGISLEQSYEDPKVACWLLDPDSQEPTLHSIVTSFLPHELPLLEGM
ETSQGIQSLGLNAGSEHSGRYRASVESILIFNSMNQLNSLLQKENLQDVF
RKVEMPSQYCLALLELNGIGFSTAECESQKHIMQAKLDAIETQAYQLAGH
SFSFTSSDDIAEVLFLELKLPPGGQFSTSKDVLNKLKALHPLPGLILEWR
RITNAITKVVFPLQREKCLNPFLGMERIYPVSQSHTATGRITFTEPNIQN
VPRDFEIKMGGSGGMPFSISMRHAFVPFPGGSILAADYSQLELRILAHLS
HDRRLIQVLNTGADVFRSIAAEWKMIEPESVGDDLRQQAKQICYGIIYGM
GAKSLGEQMGIKENDAACYIDSFKSRYTGINQFMTETVKNCKRDGFVQTI
LGRRRYLPGIKDNNPYRKAHAERQAINTIVQGSAADIVKIATVNIQKQLE
TFHSTFKSHGHREGMLQCPIRGGFFILQLHDELLYEVAEEDVVQVAQIVK
NEMESAVKLSVKLKVKVKIGASWGELKDFDV

Ligand information

Ligand ID

DG3

InChI

InChI=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

InChIKey

HDRRAMINWIWTNU-NTSWFWBYSA-N

SMILES

Software	SMILES
CACTVS 3.341	NC1=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 1.5.0	c1nc2c(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 3.341	NC1=Nc2n(cnc2C(=O)N1)[CH]3CC[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0	c1nc2c(n1C3CCC(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)N=C(NC2=O)N

Formula

C10 H16 N5 O12 P3

Name

2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE

PDB chain

8gd7 Chain A Residue 2602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	8gd7 Discovery of a small-molecule inhibitor that traps Pol theta on DNA and synergizes with PARP inhibitors.
Resolution	3.24 Å
Binding residue (original residue number in PDB)	Q2333 E2335 F2359 R2379 K2383 Y2387 Y2391 D2540
Binding residue (residue number reindexed from 1)	Q390 E392 F416 R436 K440 Y444 Y448 D581
Annotation score	2

External links

PDB	RCSB:8gd7, PDBe:8gd7, PDBj:8gd7
PDBsum	8gd7
PubMed	38580648
UniProt	O75417\|DPOLQ_HUMAN DNA polymerase theta (Gene Name=POLQ)

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