Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T33492 | Target Info | |||
| Target Name | Tyrosyl-DNA phosphodiesterase 1 (TDP1) | ||||
| Synonyms | Tyr-DNA phosphodiesterase 1 | ||||
| Target Type | Patented-recorded Target | ||||
| Gene Name | TDP1 | ||||
| Biochemical Class | Phosphoric diester hydrolase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | 1,2,4-Benzenetricarboxylic acid | Ligand Info | |||
| Canonical SMILES | C1=CC(=C(C=C1C(=O)O)C(=O)O)C(=O)O | ||||
| InChI | 1S/C9H6O6/c10-7(11)4-1-2-5(8(12)13)6(3-4)9(14)15/h1-3H,(H,10,11)(H,12,13)(H,14,15) | ||||
| InChIKey | ARCGXLSVLAOJQL-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 10708 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 6DHU Crystal structure of Tdp1 catalytic domain in complex with Zenobia fragment ZT0911 from cocktail soak | ||||||
| Method | X-ray diffraction | Resolution | 1.63 Å | Mutation | No | [1] |
| PDB Sequence |
NPFQFYLTRV
171 SGVKPKYNSG181 ALHIKDILSP191 LFGTLVSSAQ201 FNYCFDVDWL211 VKQYPPEFRK 221 KPILLVHGDK231 REAKAHLHAQ241 AKPYENISLC251 QAKLDIAFGT261 HHTKMMLLLY 271 EEGLRVVIHT281 SNLIHADWHQ291 KTQGIWLSPL301 YPRIADGTHK311 SGESPTHFKA 321 DLISYLMAYN331 APSLKEWIDV341 IHKHDLSETN351 VYLIGSTPGR361 FQGSQKDNWG 371 HFRLKKLLKD381 HASSMPNAES391 WPVVGQFSSV401 GSLGADESKW411 LCSEFKESML 421 TLGKESSSVP436 LYLIYPSVEN446 VRTSLEGYPA456 GGSLPYSIQT466 AEKQNWLHSY 476 FHKWSAETSG486 RSNAMPHIKT496 YMRPSPDFSK506 IAWFLVTSAN516 LSKAAWGALE 526 KNGTQLMIRS536 YELGVLFLPS546 AFGLDSFKVK556 QKFFAGMATF570 PVPYDLPPEL 580 YGSKDRPWIW590 NIPYVKAPDT600 HGNMWVP
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| PDB ID: 6DIE Crystal structure of Tdp1 catalytic domain in complex with Zenobia fragment benzene-1,2,4-tricarboxylic acid from single soak | ||||||
| Method | X-ray diffraction | Resolution | 1.78 Å | Mutation | No | [1] |
| PDB Sequence |
NPFQFYLTRV
171 SGVKPKYNSG181 ALHIKDILSP191 LFGTLVSSAQ201 FNYCFDVDWL211 VKQYPPEFRK 221 KPILLVHGDK231 REAKAHLHAQ241 AKPYENISLC251 QAKLDIAFGT261 HHTKMMLLLY 271 EEGLRVVIHT281 SNLIHADWHQ291 KTQGIWLSPL301 YPRIADGTHK311 SGESPTHFKA 321 DLISYLMAYN331 APSLKEWIDV341 IHKHDLSETN351 VYLIGSTPGR361 FQGSQKDNWG 371 HFRLKKLLKD381 HASSMPNAES391 WPVVGQFSSV401 GSLGADESKW411 LCSEFKESML 421 TLGKESSSVP436 LYLIYPSVEN446 VRTSLEGYPA456 GGSLPYSIQT466 AEKQNWLHSY 476 FHKWSAETSG486 RSNAMPHIKT496 YMRPSPDFSK506 IAWFLVTSAN516 LSKAAWGALE 526 KNGTQLMIRS536 YELGVLFLPS546 AFGLDSFKVK556 QKFFAPMATF570 PVPYDLPPEL 580 YGSKDRPWIW590 NIPYVKAPDT600 HGNMWVP
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening. Nucleic Acids Res. 2019 Nov 4;47(19):10134-10150. | ||||
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