Binding Site Information of Target
| 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 | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Spermine | Ligand Info | |||||
| Structure Description | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT. | PDB:1RFF | ||||
| 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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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Octopamine | Ligand Info | |||||
| Structure Description | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTC | PDB:1RGT | ||||
| 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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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (+)-Octopamine | Ligand Info | |||||
| Structure Description | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTC | PDB:1RGT | ||||
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .OTS or .OTS2 or .OTS3 or :3OTS;style chemicals stick;color identity;select .A:204 or .A:205 or .A:263 or .A:283 or .A:399 or .A:458 or .A:459 or .A:460 or .A:461 or .A:493 or .A:495; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: Tungstate | Ligand Info | |||||
| Structure Description | Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Tungstate Complex | PDB:1MU7 | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | Yes | [2] |
| 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 HAAESWPVVG396 QFSSVGSLGA406 DESKWLCSEF416 KESMLTLGSV 435 PLYLIYPSVE445 NVRTSLEGYP455 AGGSLPYSIQ465 TAEKQNWLHS475 YFHKWSAETS 485 GRSNAMPHIK495 TYMRPSPDFS505 KIAWFLVTSA515 NLSKAAWGAL525 ETQLMIRSYE 538 LGVLFLPSAL548 GLDSFKVKQK558 FATFPVPYDL576 PPELYGSKDR586 PWIWNIPYVK 596 APDTHGNMWV606 PS
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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 .WO4 or .WO42 or .WO43 or :3WO4;style chemicals stick;color identity;select .A:204 or .A:263 or .A:265 or .A:281 or .A:283 or .A:399 or .A:459 or .A:493 or .A:495 or .A:514 or .A:516; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-Fluorophthalic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with compound XZ575 | PDB:6N0D | ||||
| Method | X-ray diffraction | Resolution | 1.45 Å | Mutation | No | [3] |
| 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 TLGKESSVPL437 YLIYPSVENV447 RTSLEGYPAG457 GSLPYSIQTA467 EKQNWLHSYF 477 HKWSAETSGR487 SNAMPHIKTY497 MRPSPDFSKI507 AWFLVTSANL517 SKAAWGALEK 527 NGTQLMIRSY537 ELGVLFLPSA547 FGLDSFKVKQ557 KFFAPMATFP571 VPYDLPPELY 581 GSKDRPWIWN591 IPYVKAPDTH601 GNMWVP
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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 .K8J or .K8J2 or .K8J3 or :3K8J;style chemicals stick;color identity;select .A:204 or .A:261 or .A:263 or .A:265 or .A:283 or .A:399 or .A:400 or .A:459 or .A:461 or .A:493 or .A:495 or .A:514 or .A:516; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-Methylphthalic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with compound XZ574 | PDB:6N0N | ||||
| Method | X-ray diffraction | Resolution | 1.48 Å | Mutation | No | [4] |
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .KAY or .KAY2 or .KAY3 or :3KAY;style chemicals stick;color identity;select .A:204 or .A:261 or .A:263 or .A:265 or .A:283 or .A:399 or .A:400 or .A:459 or .A:461 or .A:493 or .A:495 or .A:514 or .A:516; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-{[2-(2-Hydroxyphenyl)imidazo[1,2-a]pyridin-3-yl]amino}benzene-1,2-dicarboxylic acid | Ligand Info | |||||
| Structure Description | Structure of Tdp1 catalytic domain in complex with inhibitor XZ635p | PDB:6W7J | ||||
| Method | X-ray diffraction | Resolution | 1.49 Å | Mutation | No | [5] |
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TGM or .TGM2 or .TGM3 or :3TGM;style chemicals stick;color identity;select .A:204 or .A:261 or .A:263 or .A:265 or .A:283 or .A:399 or .A:400 or .A:458 or .A:459 or .A:461 or .A:493 or .A:495 or .A:514 or .A:516 or .A:590; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-[(4-Carboxybutanoyl)amino]benzene-1,2-dicarboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with compound XZ578 | PDB:6N19 | ||||
| Method | X-ray diffraction | Resolution | 1.50 Å | Mutation | No | [6] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
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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 .K8V or .K8V2 or .K8V3 or :3K8V;style chemicals stick;color identity;select .A:204 or .A:261 or .A:263 or .A:265 or .A:283 or .A:399 or .A:400 or .A:401 or .A:402 or .A:403 or .A:459 or .A:461 or .A:493 or .A:495 or .A:514 or .A:516 or .A:518 or .A:520; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-(Methylamino)benzene-1,2-dicarboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with compound XZ572 | PDB:6N0R | ||||
| Method | X-ray diffraction | Resolution | 1.54 Å | Mutation | No | [7] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
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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 .K8D or .K8D2 or .K8D3 or :3K8D;style chemicals stick;color identity;select .A:204 or .A:261 or .A:263 or .A:265 or .A:283 or .A:399 or .A:400 or .A:459 or .A:461 or .A:493 or .A:495 or .A:514 or .A:516; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 1,2,4-Benzenetricarboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with Zenobia fragment ZT0911 from cocktail soak | PDB:6DHU | ||||
| Method | X-ray diffraction | Resolution | 1.63 Å | Mutation | No | [6] |
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GHM or .GHM2 or .GHM3 or :3GHM;style chemicals stick;color identity;select .A:204 or .A:263 or .A:265 or .A:283 or .A:288 or .A:399 or .A:400 or .A:459 or .A:461 or .A:493 or .A:495 or .A:514 or .A:516; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 4-[(3-Carboxypropanoyl)amino]benzene-1,2-dicarboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with compound XZ577 | PDB:6N17 | ||||
| Method | X-ray diffraction | Resolution | 1.64 Å | Mutation | No | [6] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
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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 .K8Y or .K8Y2 or .K8Y3 or :3K8Y;style chemicals stick;color identity;select .A:204 or .A:261 or .A:263 or .A:265 or .A:283 or .A:399 or .A:400 or .A:401 or .A:402 or .A:459 or .A:461 or .A:493 or .A:495 or .A:514 or .A:516 or .A:518; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-oxo-8-Phenyl-1,4-dihydroquinoline-3-carboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with compound XZ520 | PDB:6MYZ | ||||
| Method | X-ray diffraction | Resolution | 1.66 Å | Mutation | No | [8] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
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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 .K7D or .K7D2 or .K7D3 or :3K7D;style chemicals stick;color identity;select .A:204 or .A:263 or .A:265 or .A:283 or .A:288 or .A:458 or .A:459 or .A:461 or .A:493 or .A:495 or .A:516 or .A:590; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-Hydroxyquinoline-3,8-dicarboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with compound XZ502 | PDB:6DJF | ||||
| Method | X-ray diffraction | Resolution | 1.67 Å | Mutation | No | [6] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
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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 .GNV or .GNV2 or .GNV3 or :3GNV;style chemicals stick;color identity;select .A:204 or .A:263 or .A:265 or .A:281 or .A:283 or .A:458 or .A:459 or .A:460 or .A:461 or .A:493 or .A:495 or .A:590; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 4-[(2-Phenylimidazo[1,2-a]pyridin-3-yl)amino]benzene-1,2-dicarboxylic acid | Ligand Info | |||||
| Structure Description | Structure of Tdp1 catalytic domain in complex with inhibitor XZ634p | PDB:6W7K | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [9] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
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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 .TG7 or .TG72 or .TG73 or :3TG7;style chemicals stick;color identity;select .A:204 or .A:259 or .A:261 or .A:263 or .A:265 or .A:283 or .A:288 or .A:399 or .A:400 or .A:458 or .A:459 or .A:461 or .A:493 or .A:495 or .A:514 or .A:516 or .A:590; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-Hydroxy-8-(propan-2-yl)quinoline-3-carboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with Sigma Aldrich compound CDS010292 | PDB:6DJE | ||||
| Method | X-ray diffraction | Resolution | 1.71 Å | Mutation | No | [6] |
| 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 TLGKESSVPL437 YLIYPSVENV447 RTSLEGYPAG457 GSLPYSIQTA467 EKQNWLHSYF 477 HKWSAETSGR487 SNAMPHIKTY497 MRPSPDFSKI507 AWFLVTSANL517 SKAAWGALEK 527 NGTQLMIRSY537 ELGVLFLPSA547 FGLDSFKVKQ557 KFFAGMATFP571 VPYDLPPELY 581 GSKDRPWIWN591 IPYVKAPDTH601 GNMWVP
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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 .GNY or .GNY2 or .GNY3 or :3GNY;style chemicals stick;color identity;select .A:204 or .A:263 or .A:265 or .A:281 or .A:283 or .A:458 or .A:459 or .A:461 or .A:493 or .A:495 or .A:516 or .A:590; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-Aminophthalic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with compound XZ532 | PDB:6DJJ | ||||
| Method | X-ray diffraction | Resolution | 1.74 Å | Mutation | No | [6] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
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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 .GM7 or .GM72 or .GM73 or :3GM7;style chemicals stick;color identity;select .A:204 or .A:261 or .A:263 or .A:265 or .A:283 or .A:399 or .A:400 or .A:459 or .A:461 or .A:493 or .A:495 or .A:514 or .A:516; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-Hydroxyphthalic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with compound XZ522 | PDB:6DJI | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [6] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
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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 .GOG or .GOG2 or .GOG3 or :3GOG;style chemicals stick;color identity;select .A:204 or .A:261 or .A:263 or .A:265 or .A:283 or .A:399 or .A:400 or .A:459 or .A:461 or .A:493 or .A:495 or .A:514 or .A:516; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 4-Hydroxyphthalic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with Sigma Aldrich compound PH004941 | PDB:6DIH | ||||
| Method | X-ray diffraction | Resolution | 1.78 Å | Mutation | No | [6] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
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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 .GJS or .GJS2 or .GJS3 or :3GJS;style chemicals stick;color identity;select .A:204 or .A:263 or .A:265 or .A:283 or .A:399 or .A:400 or .A:459 or .A:461 or .A:493 or .A:495 or .A:514 or .A:516; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 4-Oxo-1,4-dihydroquinoline-3-carboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with Zenobia fragment ZT1982 (single soak) | PDB:6DJD | ||||
| Method | X-ray diffraction | Resolution | 1.78 Å | Mutation | No | [6] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
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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 .GJP or .GJP2 or .GJP3 or :3GJP;style chemicals stick;color identity;select .A:204 or .A:263 or .A:265 or .A:283 or .A:458 or .A:459 or .A:460 or .A:461 or .A:493 or .A:495 or .A:516 or .A:590; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 3[N-Morpholino]propane sulfonic acid | Ligand Info | |||||
| Structure Description | Structure of Tdp1 catalytic domain in complex with inhibitor XZ633p | PDB:6W4R | ||||
| Method | X-ray diffraction | Resolution | 1.82 Å | Mutation | No | [10] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
|
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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 .MPO or .MPO2 or .MPO3 or :3MPO;style chemicals stick;color identity;select .A:261 or .A:263 or .A:400 or .A:401 or .A:402 or .A:461 or .A:462 or .A:463 or .A:466 or .A:516 or .A:518 or .A:520 or .A:521 or .A:538 or .A:590; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 4-{[2-(2-Hydroxyphenyl)imidazo[1,2-a]pyrazin-3-yl]amino}benzene-1,2-dicarboxylic acid | Ligand Info | |||||
| Structure Description | Structure of Tdp1 catalytic domain in complex with inhibitor XZ633p | PDB:6W4R | ||||
| Method | X-ray diffraction | Resolution | 1.82 Å | Mutation | No | [10] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
|
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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 .SZV or .SZV2 or .SZV3 or :3SZV;style chemicals stick;color identity;select .A:204 or .A:261 or .A:263 or .A:265 or .A:283 or .A:399 or .A:400 or .A:458 or .A:459 or .A:461 or .A:493 or .A:495 or .A:514 or .A:516 or .A:590; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 4-[(2-Phenylimidazo[1,2-a]pyrazin-3-yl)amino]benzene-1,2-dicarboxylic acid | Ligand Info | |||||
| Structure Description | Structure of Tdp1 catalytic domain in complex with inhibitor XZ632p | PDB:6W7L | ||||
| Method | X-ray diffraction | Resolution | 1.86 Å | Mutation | No | [9] |
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TGV or .TGV2 or .TGV3 or :3TGV;style chemicals stick;color identity;select .A:204 or .A:261 or .A:263 or .A:265 or .A:283 or .A:399 or .A:400 or .A:458 or .A:459 or .A:461 or .A:493 or .A:495 or .A:514 or .A:516 or .A:590; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 4-Oxo-8-sulfo-1,4-dihydroquinoline-3-carboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with compound XZ503 | PDB:6DJG | ||||
| Method | X-ray diffraction | Resolution | 1.88 Å | Mutation | No | [6] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
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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 .GNJ or .GNJ2 or .GNJ3 or :3GNJ;style chemicals stick;color identity;select .A:204 or .A:263 or .A:265 or .A:281 or .A:283 or .A:288 or .A:458 or .A:459 or .A:460 or .A:461 or .A:493 or .A:495 or .A:590; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 8-Bromo-4-hydroxyquinoline-3-carboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with compound XZ515 | PDB:6DJH | ||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | No | [6] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
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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 .GNM or .GNM2 or .GNM3 or :3GNM;style chemicals stick;color identity;select .A:204 or .A:263 or .A:265 or .A:281 or .A:283 or .A:288 or .A:458 or .A:459 or .A:460 or .A:461 or .A:493 or .A:495 or .A:590; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 4-Nitrophthalic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with compound XZ523 | PDB:6N0O | ||||
| Method | X-ray diffraction | Resolution | 1.94 Å | Mutation | No | [11] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
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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 .K8G or .K8G2 or .K8G3 or :3K8G;style chemicals stick;color identity;select .A:204 or .A:261 or .A:263 or .A:265 or .A:283 or .A:288 or .A:399 or .A:400 or .A:459 or .A:461 or .A:493 or .A:495 or .A:514 or .A:516; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 5-Hydroxypyrazine-2,3-dicarboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with compound XZ530 | PDB:6MZ0 | ||||
| Method | X-ray diffraction | Resolution | 1.97 Å | Mutation | No | [12] |
| 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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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .K7A or .K7A2 or .K7A3 or :3K7A;style chemicals stick;color identity;select .A:204 or .A:263 or .A:265 or .A:281 or .A:283 or .A:288 or .A:399 or .A:458 or .A:459 or .A:461 or .A:493 or .A:495 or .A:516; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 4-Hydroxy-8-nitroquinoline-3-carboxylic acid | Ligand Info | |||||
| Structure Description | Crystal structure of Tdp1 catalytic domain in complex with compound XZ519 | PDB:6MJ5 | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [6] |
| 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 QKFFAGPMAT569 FPVPYDLPPE 579 LYGSKDRPWI589 WNIPYVKAPD599 THGNMWVP
|
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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 .JTA or .JTA2 or .JTA3 or :3JTA;style chemicals stick;color identity;select .A:204 or .A:263 or .A:265 or .A:281 or .A:283 or .A:288 or .A:458 or .A:459 or .A:460 or .A:461 or .A:493 or .A:495 or .A:590; 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. | ||||
| REF 2 | Insights into substrate binding and catalytic mechanism of human tyrosyl-DNA phosphodiesterase (Tdp1) from vanadate and tungstate-inhibited structures. J Mol Biol. 2002 Dec 13;324(5):917-32. | ||||
| REF 3 | Crystal structure of Tdp1 catalytic domain in complex with compound XZ575 | ||||
| REF 4 | Crystal structure of Tdp1 catalytic domain | ||||
| REF 5 | Tdp1 catalytic domain | ||||
| REF 6 | 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. | ||||
| REF 7 | Crystal structure of Tdp1 catalytic domain | ||||
| REF 8 | Structure of Tdp1 catalytic domain in complex with compound XZ520 | ||||
| REF 9 | Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites. doi:10.1039/D0SC05411A. | ||||
| REF 10 | Tdp1 catalytic domain | ||||
| REF 11 | Crystal structure of Tdp1 catalytic domain | ||||
| REF 12 | Structure of Tdp1 catalytic domain in complex with compound XZ530 | ||||
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