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 | Spermine | Ligand Info | |||
| Canonical SMILES | C(CCNCCCN)CNCCCN | ||||
| InChI | 1S/C10H26N4/c11-5-3-9-13-7-1-2-8-14-10-4-6-12/h13-14H,1-12H2 | ||||
| InChIKey | PFNFFQXMRSDOHW-UHFFFAOYSA-N | ||||
| PubChem Compound ID | 1103 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 1RFF Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT. | ||||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | Yes | [1] |
| PDB Sequence |
NPFQFYLTRV
171 SGVKPKYNSG181 ALHIKDILSP191 LFGTLVSSAQ201 FNYCFDVDWL211 VKQYPPEFRK 221 KPILLVHGDK231 REAKAHLHAQ241 AKPYENISLC251 QAKLDIAFGT261 HHTKMMLLLY 271 EEGLRVVIHT281 SNLIHADWHQ291 KTQGIWLSPL301 YPRIADGTHK311 SGESPTHFKA 321 NLISYLTAYN331 APSLKEWIDV341 IHKHDLSETN351 VYLIGSTPGR361 FQGSQKDNWG 371 HFRLKKLLKD381 HASSMSWPVV395 GQFSSVGSLG405 ADESKWLCSE415 FKESMLTLGV 435 PLYLIYPSVE445 NVRTSLEGYP455 AGGSLPYSIQ465 TAEKQNWLHS475 YFHKWSAETS 485 GRSNAMPHIK495 TYMRPSPDFS505 KIAWFLVTSA515 NLSKAAWGAL525 EKNGTQLMIR 535 SYELGVLFLP545 SALGLDSFKV555 KQKFATFPVP573 YDLPPELYGS583 KDRPWIWNIP 593 YVKAPDTHGN603 MWVPS
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| PDB ID: 1RGT Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTC | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [1] |
| PDB Sequence |
NPFQFYLTRV
171 SGVKPKYNSG181 ALHIKDILSP191 LFGTLVSSAQ201 FNYCFDVDWL211 VKQYPPEFRK 221 KPILLVHGDK231 REAKAHLHAQ241 AKPYENISLC251 QAKLDIAFGT261 HHTKMMLLLY 271 EEGLRVVIHT281 SNLIHADWHQ291 KTQGIWLSPL301 YPRIADGTHK311 SGESPTHFKA 321 NLISYLTAYN331 APSLKEWIDV341 IHKHDLSETN351 VYLIGSTPGR361 FQGSQKDNWG 371 HFRLKKLLKD381 HASSMSWPVV395 GQFSSVGSLG405 ADESKWLCSE415 FKESMLTLGV 435 PLYLIYPSVE445 NVRTSLEGYP455 AGGSLPYSIQ465 TAEKQNWLHS475 YFHKWSAETS 485 GRSNAMPHIK495 TYMRPSPDFS505 KIAWFLVTSA515 NLSKAAWGAL525 EKNGTQLMIR 535 SYELGVLFLP545 SALGLDSFKV555 KQKFTFPVPY574 DLPPELYGSK584 DRPWIWNIPY 594 VKAPDTHGNM604 WVPS
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| PDB ID: 1RG1 Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTT | ||||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | Yes | [1] |
| PDB Sequence |
NPFQFYLTRV
171 SGVKPKYNSG181 ALHIKDILSP191 LFGTLVSSAQ201 FNYCFDVDWL211 VKQYPPEFRK 221 KPILLVHGDK231 REAKAHLHAQ241 AKPYENISLC251 QAKLDIAFGT261 HHTKMMLLLY 271 EEGLRVVIHT281 SNLIHADWHQ291 KTQGIWLSPL301 YPRIADGTHK311 SGESPTHFKA 321 NLISYLTAYN331 APSLKEWIDV341 IHKHDLSETN351 VYLIGSTPGR361 FQGSQKDNWG 371 HFRLKKLLKD381 HASSMSWPVV395 GQFSSVGSLG405 ADESKWLCSE415 FKESMLTLGV 435 PLYLIYPSVE445 NVRTSLEGYP455 AGGSLPYSIQ465 TAEKQNWLHS475 YFHKWSAETS 485 GRSNAMPHIK495 TYMRPSPDFS505 KIAWFLVTSA515 NLSKAAWGAL525 EKNGTQLMIR 535 SYELGVLFLP545 SALGLDSFKV555 KQKFTFPVPY574 DLPPELYGSK584 DRPWIWNIPY 594 VKAPDTHGNM604 WVPS
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| PDB ID: 1RG2 Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTA | ||||||
| Method | X-ray diffraction | Resolution | 2.10 Å | Mutation | Yes | [1] |
| PDB Sequence |
NPFQFYLTRV
171 SGVKPKYNSG181 ALHIKDILSP191 LFGTLVSSAQ201 FNYCFDVDWL211 VKQYPPEFRK 221 KPILLVHGDK231 REAKAHLHAQ241 AKPYENISLC251 QAKLDIAFGT261 HHTKMMLLLY 271 EEGLRVVIHT281 SNLIHADWHQ291 KTQGIWLSPL301 YPRIADGTHK311 SGESPTHFKA 321 NLISYLTAYN331 APSLKEWIDV341 IHKHDLSETN351 VYLIGSTPGR361 FQGSQKDNWG 371 HFRLKKLLKD381 HASSMSWPVV395 GQFSSVGSLG405 ADESKWLCSE415 FKESMLTLGV 435 PLYLIYPSVE445 NVRTSLEGYP455 AGGSLPYSIQ465 TAEKQNWLHS475 YFHKWSAETS 485 GRSNAMPHIK495 TYMRPSPDFS505 KIAWFLVTSA515 NLSKAAWGAL525 EKNGTQLMIR 535 SYELGVLFLP545 SALGLDSFKV555 KQKFATFPVP573 YDLPPELYGS583 KDRPWIWNIP 593 YVKAPDTHGN603 MWVPS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SPM or .SPM2 or .SPM3 or :3SPM;style chemicals stick;color identity;select .A:590 or .A:591 or .A:604 or .A:605 or .A:606 or .A:607 or .A:608; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| PDB ID: 1RFI Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC | ||||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | Yes | [1] |
| PDB Sequence |
NPFQFYLTRV
171 SGVKPKYNSG181 ALHIKDILSP191 LFGTLVSSAQ201 FNYCFDVDWL211 VKQYPPEFRK 221 KPILLVHGDK231 REAKAHLHAQ241 AKPYENISLC251 QAKLDIAFGT261 HHTKMMLLLY 271 EEGLRVVIHT281 SNLIHADWHQ291 KTQGIWLSPL301 YPRIADGTHK311 SGESPTHFKA 321 NLISYLTAYN331 APSLKEWIDV341 IHKHDLSETN351 VYLIGSTPGR361 FQGSQKDNWG 371 HFRLKKLLKD381 HASSMSWPVV395 GQFSSVGSLG405 ADESKWLCSE415 FKESMLTLGV 435 PLYLIYPSVE445 NVRTSLEGYP455 AGGSLPYSIQ465 TAEKQNWLHS475 YFHKWSAETS 485 GRSNAMPHIK495 TYMRPSPDFS505 KIAWFLVTSA515 NLSKAAWGAL525 EKNGTQLMIR 535 SYELGVLFLP545 SALGLDSFKV555 KQKFATFPVP573 YDLPPELYGS583 KDRPWIWNIP 593 YVKAPDTHGN603 MWVPS
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SPM or .SPM2 or .SPM3 or :3SPM;style chemicals stick;color identity;select .A:590 or .A:591 or .A:604 or .A:605 or .A:606 or .A:607 or .A:608; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| PDB ID: 1RGU The crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTG | ||||||
| Method | X-ray diffraction | Resolution | 2.22 Å | Mutation | Yes | [1] |
| PDB Sequence |
NPFQFYLTRV
171 SGVKPKYNSG181 ALHIKDILSP191 LFGTLVSSAQ201 FNYCFDVDWL211 VKQYPPEFRK 221 KPILLVHGDK231 REAKAHLHAQ241 AKPYENISLC251 QAKLDIAFGT261 HHTKMMLLLY 271 EEGLRVVIHT281 SNLIHADWHQ291 KTQGIWLSPL301 YPRIADGTHK311 SGESPTHFKA 321 NLISYLTAYN331 APSLKEWIDV341 IHKHDLSETN351 VYLIGSTPGR361 FQGSQKDNWG 371 HFRLKKLLKD381 HASSMSWPVV395 GQFSSVGSLG405 ADESKWLCSE415 FKESMLTLGV 435 PLYLIYPSVE445 NVRTSLEGYP455 AGGSLPYSIQ465 TAEKQNWLHS475 YFHKWSAETS 485 GRSNAMPHIK495 TYMRPSPDFS505 KIAWFLVTSA515 NLSKAAWGAL525 EKNGTQLMIR 535 SYELGVLFLP545 SALGLDSFKV555 KQKFATFPVP573 YDLPPELYGS583 KDRPWIWNIP 593 YVKAPDTHGN603 MWVPS
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SPM or .SPM2 or .SPM3 or :3SPM;style chemicals stick;color identity;select .A:590 or .A:591 or .A:604 or .A:605 or .A:606 or .A:607 or .A:608; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| PDB ID: 1RH0 Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine and trinucleotide GTT | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | Yes | [1] |
| PDB Sequence |
NPFQFYLTRV
171 SGVKPKYNSG181 ALHIKDILSP191 LFGTLVSSAQ201 FNYCFDVDWL211 VKQYPPEFRK 221 KPILLVHGDK231 REAKAHLHAQ241 AKPYENISLC251 QAKLDIAFGT261 HHTKMMLLLY 271 EEGLRVVIHT281 SNLIHADWHQ291 KTQGIWLSPL301 YPRIADGTHK311 SGESPTHFKA 321 NLISYLTAYN331 APSLKEWIDV341 IHKHDLSETN351 VYLIGSTPGR361 FQGSQKDNWG 371 HFRLKKLLKD381 HASSMSWPVV395 GQFSSVGSLG405 ADESKWLCSE415 FKESMLTLGV 435 PLYLIYPSVE445 NVRTSLEGYP455 AGGSLPYSIQ465 TAEKQNWLHS475 YFHKWSAETS 485 GRSNAMPHIK495 TYMRPSPDFS505 KIAWFLVTSA515 NLSKAAWGAL525 EKNGTQLMIR 535 SYELGVLFLP545 SALGLDSFKV555 KQKFATFPVP573 YDLPPELYGS583 KDRPWIWNIP 593 YVKAPDTHGN603 MWVPS
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SPM or .SPM2 or .SPM3 or :3SPM;style chemicals stick;color identity;select .A:604 or .A:605 or .A:606 or .A:607 or .A:608; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes. J Med Chem. 2004 Feb 12;47(4):829-37. | ||||
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