Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T28052 | Target Info | |||
| Target Name | Lysine-specific demethylase 5A (KDM5A) | ||||
| Synonyms | Retinoblastoma-binding protein 2; RBP2; RBBP2; RBBP-2; Jumonji/ARID domain-containing protein 1A; JARID1A; Histone demethylase JARID1A | ||||
| Target Type | Patented-recorded Target | ||||
| Gene Name | KDM5A | ||||
| Biochemical Class | Paired donor oxygen oxidoreductase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Alpha-ketoglutaric acid | Ligand Info | |||||
| Structure Description | A High Resolution Structure of a Linked KDM5A Jmj Domain with Alpha-Ketoglutarate | PDB:5IVB | ||||
| Method | X-ray diffraction | Resolution | 1.39 Å | Mutation | No | [1] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMTEQAVREY361 TLQSFGEMAD371 NFKSDYFNMP381 VHMVPTELVE 391 KEFWRLVSSI401 EEDVIVEYGA411 DISSKDFGSG421 FPVKDGRRKI431 LPEEEEYALS 441 GWNLNNMPVL451 EKVPWLYVGM475 CFSSFCWHIE485 DHWSYSINYL495 HWGEPKTWYG 505 VPSHAAEQLE515 EVMRELAPEL525 FESQPDLLHQ535 LVTIMNPNVL545 MEHGVPVYRT 555 NQCAGEFVVT565 FPRAYHSGFN575 QGYNFAEAVN585 FCT
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: GSK-J1 | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR GSK-J1 | PDB:6DQ4 | ||||
| Method | X-ray diffraction | Resolution | 1.39 Å | Mutation | No | [2] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMTRPREAF352 GFEQAVREYT362 LQSFGEMADN372 FKSDYFNMPV 382 HMVPTELVEK392 EFWRLVSSIE402 EDVIVEYGAD412 ISSKDFGSGF422 PVKDGRRKIL 432 PEEEEYALSG442 WNLNNMPVLE452 QSVLAHINVM466 KVPWLYVGMC476 FSSFCWHIED 486 HWSYSINYLH496 WGEPKTWYGV506 PSHAAEQLEE516 VMRELAPELF526 ESQPDLLHQL 536 VTIMNPNVLM546 EHGVPVYRTN556 QCAGEFVVTF566 PRAYHSGFNQ576 GYNFAEAVNF 586 CT
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| Ligand Name: 6EP | Ligand Info | |||||
| Structure Description | Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-chloro-2-methylbenzyl)oxy)-1H-pyrazol-1-yl)isonicotinic acid] | PDB:5IW0 | ||||
| Method | X-ray diffraction | Resolution | 1.63 Å | Mutation | No | [1] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMREAFGFEQ356 AVREYTLQSF366 GEMADNFKSD376 YFNMPVHMVP 386 TELVEKEFWR396 LVSSIEEDVI406 VEYGADISSK416 DFGSGFPVKD426 GRRKILPEEE 436 EYALSGWNLN446 NMPVLEQSVL456 AHINKVPWLY472 VGMCFSSFCW482 HIEDHWSYSI 492 NYLHWGEPKT502 WYGVPSHAAE512 QLEEVMRELA522 PELFESQPDL532 LHQLVTIMNP 542 NVLMEHGVPV552 YRTNQCAGEF562 VVTFPRAYHS572 GFNQGYNFAE582 AVNFCT |
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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 .6EP or .6EP2 or .6EP3 or :36EP;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:472 or .A:479 or .A:480 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:571 or .A:581; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: KDOAM25 | Ligand Info | |||||
| Structure Description | Linked KDM5A Jmj Domain Bound to the Inhibitor 2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinamid | PDB:5IWF | ||||
| Method | X-ray diffraction | Resolution | 2.29 Å | Mutation | No | [1] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMGFEQAVR359 EYTLQSFGEM369 ADNFKSDYFN379 MPVHMVPTEL 389 VEKEFWRLVS399 SIEEDVIVEY409 GADISSKDFG419 SGFPVKDGRR429 KILPEEEEYA 439 LSGWNLNNMP449 VLEQSVKVPW470 LYVGMCFSSF480 CWHIEDHWSY490 SINYLHWGEP 500 KTWYGVPSHA510 AEQLEEVMRE520 LAPELFESQP530 DLLHQLVTIM540 NPNVLMEHGV 550 PVYRTNQCAG560 EFVVTFPRAY570 HSGFNQGYNF580 AEAVNFCT
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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 .LQT or .LQT2 or .LQT3 or :3LQT;style chemicals stick;color identity;select .A:409 or .A:412 or .A:470 or .A:472 or .A:480 or .A:483 or .A:485 or .A:486 or .A:493 or .A:501 or .A:503 or .A:571 or .A:581 or .A:583 or .A:584 or .A:585; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: [(3s)-3-(4-Bromo-1h-Pyrazol-1-Yl)pyrrolidin-1-Yl][3-(Propan-2-Yl)-1h-Pyrazol-5-Yl]methanone | Ligand Info | |||||
| Structure Description | Crystal structure of pyrrolidine amide inhibitor [(3S)-3-(4-bromo-1H-pyrazol-1-yl)pyrrolidin-1-yl][3-(propan-2-yl)-1H-pyrazol-5-yl]methanone (compound 35) in complex with KDM5A | PDB:5V9P | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | No | [3] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMTRVRLDFL91 DQLAKFWELQ101 GSTLKIPVVE111 RKILDLYALS 121 KIVASKGGFE131 MVTKEKKWSK141 VGSRLGYLPG151 KGTGSLLKSH161 YERILYPYEL 171 FQSGVSLMGV181 QMYTLQSFGE368 MADNFKSDYF378 NMPVHMVPTE388 LVEKEFWRLV 398 SSIEEDVIVE408 YGADISSKDF418 GSGFPVKDGR428 RKILPEEEEY438 ALSGWNLNNM 448 PVLEQSVLAH458 INVDISGMKV468 PWLYVGMCFS478 SFCWHIEDHW488 SYSINYLHWG 498 EPKTWYGVPS508 HAAEQLEEVM518 RELAPELFES528 QPDLLHQLVT538 IMNPNVLMEH 548 GVPVYRTNQC558 AGEFVVTFPR568 AYHSGFNQGY578 NFAEAVNFCT588 ADWLPIGRQC 598 VNHYRRLRRH608 CVFSHEELIF618 KMAADPECLD628 VGLAAMVCKE638 LTLMTEEETR 648 LRESVVQMGV658 LMSEEEVFEL668 VPDDERQCSA678 CRTTCFLSAL688 TCSCNPERLV 698 CLYHPTDLCP708 CPMQKKCLRY718 RYPLEDLPSL728 LYGVKVRAQS738 YDTWVSVMLE 768 DAEDRKYPEN778 DLFRKLR
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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 .90S or .90S2 or .90S3 or :390S;style chemicals stick;color identity;select .A:409 or .A:411 or .A:466 or .A:470 or .A:472 or .A:479 or .A:480 or .A:483 or .A:485 or .A:491 or .A:493 or .A:501 or .A:503 or .A:565 or .A:571 or .A:575 or .A:581 or .A:583 or .A:584 or .A:585; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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TYR409
4.127
ALA411
3.535
MET466
4.403
TRP470
2.963
TYR472
2.692
SER479
4.408
PHE480
2.754
HIS483
2.241
GLU485
1.973
SER491
2.995
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| Ligand Name: 6-Isopropyl-7-oxo-5-phenyl-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile | Ligand Info | |||||
| Structure Description | Structure of histone lysine demethylase KDM5A in complex with selective inhibitor | PDB:5CEH | ||||
| Method | X-ray diffraction | Resolution | 3.14 Å | Mutation | No | [4] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMTRVRLDFL91 DQLAKFWELQ101 GSTLKIPVVE111 RKILDLYALS 121 KIVASKGGFE131 MVTKEKKWSK141 VGSRLGYLPG151 KGTGSLLKSH161 YERILYPYEL 171 FQSGVSLMGV181 QMYTLQSFGE368 MADNFKSDYF378 NMPVHMVPTE388 LVEKEFWRLV 398 SSIEEDVIVE408 YGADISSKDF418 GSGFPVKDGR428 RKILPEEEEY438 ALSGWNLNNM 448 PVLEQSVLAH458 INVDISGMKV468 PWLYVGMCFS478 SFCWHIEDHW488 SYSINYLHWG 498 EPKTWYGVPS508 HAAEQLEEVM518 RELAPELFES528 QPDLLHQLVT538 IMNPNVLMEH 548 GVPVYRTNQC558 AGEFVVTFPR568 AYHSGFNQGY578 NFAEAVNFCT588 ADWLPIGRQC 598 VNHYRRLRRH608 CVFSHEELIF618 KMAADPECLD628 VGLAAMVCKE638 LTLMTEEETR 648 LRESVVQMGV658 LMSEEEVFEL668 VPDDERQCSA678 CRTTCFLSAL688 TCSCNPERLV 698 CLYHPTDLCP708 CPMQKKCLRY718 RYPLEDLPSL728 LYGVKVRAQS738 YDTWVSVMLE 768 DAEDRKYPEN778 DLFRKLR
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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 .50P or .50P2 or .50P3 or :350P;style chemicals stick;color identity;select .A:73 or .A:409 or .A:410 or .A:411 or .A:472 or .A:473 or .A:478 or .A:479 or .A:480 or .A:481 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:571 or .A:575; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-ethyl-4-hydroxy-2-oxo-1H-1,7-naphthyridine-3-carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of KDM5A in complex with a naphthyridone inhibitor | PDB:5K4L | ||||
| Method | X-ray diffraction | Resolution | 3.18 Å | Mutation | No | [5] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMTRVRLDFL91 DQLAKFWELQ101 GSTLKIPVVE111 RKILDLYALS 121 KIVASKGGFE131 MVTKEKKWSK141 VGSRLGYLPG151 KGTGSLLKSH161 YERILYPYEL 171 FQSGVSLMGV181 QMYTLQSFGE368 MADNFKSDYF378 NMPVHMVPTE388 LVEKEFWRLV 398 SSIEEDVIVE408 YGADISSKDF418 GSGFPVKDGR428 RKILPEEEEY438 ALSGWNLNNM 448 PVLEQSVLAH458 INVDISGMKV468 PWLYVGMCFS478 SFCWHIEDHW488 SYSINYLHWG 498 EPKTWYGVPS508 HAAEQLEEVM518 RELAPELFES528 QPDLLHQLVT538 IMNPNVLMEH 548 GVPVYRTNQC558 AGEFVVTFPR568 AYHSGFNQGY578 NFAEAVNFCT588 ADWLPIGRQC 598 VNHYRRLRRH608 CVFSHEELIF618 KMAADPECLD628 VGLAAMVCKE638 LTLMTEEETR 648 LRESVVQMGV658 LMSEEEVFEL668 VPDDERQCSA678 CRTTCFLSAL688 TCSCNPERLV 698 CLYHPTDLCP708 CPMQKKCLRY718 RYPLEDLPSL728 LYGVKVRAQS738 YDTWVSVMLE 768 DAEDRKYPEN778 DLFRKLR
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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 .6QN or .6QN2 or .6QN3 or :36QN;style chemicals stick;color identity;select .A:75 or .A:409 or .A:410 or .A:411 or .A:472 or .A:473 or .A:474 or .A:475 or .A:478 or .A:479 or .A:480 or .A:483 or .A:485 or .A:491 or .A:493 or .A:501 or .A:503 or .A:565 or .A:571 or .A:574 or .A:575 or .A:581; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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GLN75
4.053
TYR409
2.686
GLY410
3.173
ALA411
3.390
TYR472
2.478
VAL473
3.161
GLY474
3.029
MET475
3.973
SER478
2.374
SER479
3.135
PHE480
2.747
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| Ligand Name: 2-[(S)-(2-chlorophenyl){2-[(2R)-1-methylpyrrolidin-2-yl]ethoxy}methyl]-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(1-methylpyrrolidin-2-yl)ethoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid(Compound 46) | PDB:6BGY | ||||
| Method | X-ray diffraction | Resolution | 1.22 Å | Mutation | No | [6] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMREYTLQS365 FGEMADNFKS375 DYFNMPVHMV385 PTELVEKEFW 395 RLVSSIEEDV405 IVEYGADISS415 KDFGSGFPVK425 DGRRKILPEE435 EEYALSGWNL 445 NNMPVLEQSV455 LAHINKVPWL471 YVGMCFSSFC481 WHIEDHWSYS491 INYLHWGEPK 501 TWYGVPSHAA511 EQLEEVMREL521 APELFESQPD531 LLHQLVTIMN541 PNVLMEHGVP 551 VYRTNQCAGE561 FVVTFPRAYH571 SGFNQGYNFA581 EAVNFCT
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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 .DLJ or .DLJ2 or .DLJ3 or :3DLJ;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:484 or .A:485 or .A:486 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:571 or .A:581; 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-{[(4-Chlorophenyl)acetyl]amino}pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Linked KDM5A Jmj Domain Bound to the Inhibitor N16 [3-(2-(4-chlorophenyl)acetamido)isonicotinic acid] | PDB:5IVY | ||||
| Method | X-ray diffraction | Resolution | 1.45 Å | Mutation | No | [1] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMTQAVREYT362 LQSFGEMADN372 FKSDYFNMPV382 HMVPTELVEK 392 EFWRLVSSIE402 EDVIVEYGAD412 ISSKDFGSGF422 PVKDGRRKIL432 PEEEEYALSG 442 WNLNNMPVLE452 QSVLAHINKV468 PWLYVGMCFS478 SFCWHIEDHW488 SYSINYLHWG 498 EPKTWYGVPS508 HAAEQLEEVM518 RELAPELFES528 QPDLLHQLVT538 IMNPNVLMEH 548 GVPVYRTNQC558 AGEFVVTFPR568 AYHSGFNQGY578 NFAEAVNFCT588 |
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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 .6EO or .6EO2 or .6EO3 or :36EO;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:472 or .A:479 or .A:480 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:536 or .A:571; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Kdm5A-IN-1 | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (R)-N-(1-(3-isopropyl-1H-pyrazole-5-carbonyl)pyrrolidin-3-yl)cyclopropanecarboxamide (Compound N54) | PDB:6BH2 | ||||
| Method | X-ray diffraction | Resolution | 1.45 Å | Mutation | No | [6] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMFGFEREY361 TLQSFGEMAD371 NFKSDYFNMP381 VHMVPTELVE 391 KEFWRLVSSI401 EEDVIVEYGA411 DISSKDFGSG421 FPVKDGRRKI431 LPEEEEYALS 441 GWNLNNMPVL451 EQMKVPWLYV473 GMCFSSFCWH483 IEDHWSYSIN493 YLHWGEPKTW 503 YGVPSHAAEQ513 LEEVMRELAP523 ELFESQPDLL533 HQLVTIMNPN543 VLMEHGVPVY 553 RTNQCAGEFV563 VTFPRAYHSG573 FNQGYNFAEA583 VNFCT
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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 .90V or .90V2 or .90V3 or :390V;style chemicals stick;color identity;select .A:409 or .A:410 or .A:411 or .A:470 or .A:472 or .A:473 or .A:478 or .A:479 or .A:480 or .A:483 or .A:485 or .A:491 or .A:493 or .A:501 or .A:503 or .A:571 or .A:575 or .A:581 or .A:583 or .A:584 or .A:585; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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TYR409
3.492
GLY410
4.101
ALA411
4.523
TRP470
3.891
TYR472
2.986
VAL473
4.794
SER478
4.092
SER479
3.594
PHE480
3.368
HIS483
3.111
GLU485
2.877
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 2-[(R)-(2-chlorophenyl){2-[(2S)-1-methylpyrrolidin-2-yl]ethoxy}methyl]thieno[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N49 i.e. 2-((2-chlorophenyl)(2-(1-methylpyrrolidin-2-yl)ethoxy)methyl)thieno[3,2-b]pyridine-7-carboxylic acid | PDB:6DQ8 | ||||
| Method | X-ray diffraction | Resolution | 1.46 Å | Mutation | No | [2] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMTAFGFEQ356 AVREYTLQSF366 GEMADNFKSD376 YFNMPVHMVP 386 TELVEKEFWR396 LVSSIEEDVI406 VEYGADISSK416 DFGSGFPVKD426 GRRKILPEEE 436 EYALSGWNLN446 NMPVLEQSVL456 KVPWLYVGMC476 FSSFCWHIED486 HWSYSINYLH 496 WGEPKTWYGV506 PSHAAEQLEE516 VMRELAPELF526 ESQPDLLHQL536 VTIMNPNVLM 546 EHGVPVYRTN556 QCAGEFVVTF566 PRAYHSGFNQ576 GYNFAEAVNF586 CT |
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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 .H6S or .H6S2 or .H6S3 or :3H6S;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:470 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:571 or .A:581; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-[(S)-(2-chlorophenyl){2-[(2S)-1-methylpyrrolidin-2-yl]ethoxy}methyl]thieno[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N49 i.e. 2-((2-chlorophenyl)(2-(1-methylpyrrolidin-2-yl)ethoxy)methyl)thieno[3,2-b]pyridine-7-carboxylic acid | PDB:6DQ8 | ||||
| Method | X-ray diffraction | Resolution | 1.46 Å | Mutation | No | [2] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMTAFGFEQ356 AVREYTLQSF366 GEMADNFKSD376 YFNMPVHMVP 386 TELVEKEFWR396 LVSSIEEDVI406 VEYGADISSK416 DFGSGFPVKD426 GRRKILPEEE 436 EYALSGWNLN446 NMPVLEQSVL456 KVPWLYVGMC476 FSSFCWHIED486 HWSYSINYLH 496 WGEPKTWYGV506 PSHAAEQLEE516 VMRELAPELF526 ESQPDLLHQL536 VTIMNPNVLM 546 EHGVPVYRTN556 QCAGEFVVTF566 PRAYHSGFNQ576 GYNFAEAVNF586 CT |
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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 .H6T or .H6T2 or .H6T3 or :3H6T;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:484 or .A:485 or .A:486 or .A:493 or .A:501 or .A:503 or .A:535 or .A:571 or .A:581; 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-({1-[2-(4,4-Difluoropiperidin-1-Yl)ethyl]-5-Fluoro-1h-Indazol-3-Yl}amino)pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4-difluoropiperidin-1-yl)ethyl]-5-fluoro-1H-indazol-3-yl}amino)pyridine-4-carboxylic acid] | PDB:5IVJ | ||||
| Method | X-ray diffraction | Resolution | 1.57 Å | Mutation | No | [1] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMGFEQAVRE360 YTLQSFGEMA370 DNFKSDYFNM380 PVHMVPTELV 390 EKEFWRLVSS400 IEEDVIVEYG410 ADISSKDFGS420 GFPVKDGRRK430 ILPEEEEYAL 440 SGWNLNNMPV450 LEQSKVPWLY472 VGMCFSSFCW482 HIEDHWSYSI492 NYLHWGEPKT 502 WYGVPSHAAE512 QLEEVMRELA522 PELFESQPDL532 LHQLVTIMNP542 NVLMEHGVPV 552 YRTNQCAGEF562 VVTFPRAYHS572 GFNQGYNFAE582 AVNFCT
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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 .6ED or .6ED2 or .6ED3 or :36ED;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:472 or .A:479 or .A:480 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:532 or .A:535 or .A:536 or .A:571 or .A:581; 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-Phenylethyl)carbamoyl][2,2'-Bipyridine]-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Linked KDM5A Jmj Domain Bound to the Inhibitor N3 (4'-[(2-phenylethyl)carbamoyl][2,2'-bipyridine]-4-carboxylic acid) | PDB:5IVC | ||||
| Method | X-ray diffraction | Resolution | 1.57 Å | Mutation | No | [1] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMRPREAFGF354 EQAVREYTLQ364 SFGEMADNFK374 SDYFNMPVHM 384 VPTELVEKEF394 WRLVSSIEED404 VIVEYGADIS414 SKDFGSGFPV424 KDGRRKILPE 434 EEEYALSGWN444 LNNMPVLEQS454 VLAHINKVPW470 LYVGMCFSSF480 CWHIEDHWSY 490 SINYLHWGEP500 KTWYGVPSHA510 AEQLEEVMRE520 LAPELFESQP530 DLLHQLVTIM 540 NPNVLMEHGV550 PVYRTNQCAG560 EFVVTFPRAY570 HSGFNQGYNF580 AEAVNFCT |
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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 .6E7 or .6E72 or .6E73 or :36E7;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:472 or .A:479 or .A:480 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:536 or .A:571; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-{(S)-(2-chlorophenyl)[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1l2-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N40) | PDB:6BGV | ||||
| Method | X-ray diffraction | Resolution | 1.59 Å | Mutation | No | [6] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMTPREAFG353 FEQAVREYTL363 QSFGEMADNF373 KSDYFNMPVH 383 MVPTELVEKE393 FWRLVSSIEE403 DVIVEYGADI413 SSKDFGSGFP423 VKDGRRKILP 433 EEEEYALSGW443 NLNNMPVLEQ453 SVLAHINKVP469 WLYVGMCFSS479 FCWHIEDHWS 489 YSINYLHWGE499 PKTWYGVPSH509 AAEQLEEVMR519 ELAPELFESQ529 PDLLHQLVTI 539 MNPNVLMEHG549 VPVYRTNQCA559 GEFVVTFPRA569 YHSGFNQGYN579 FAEAVNFCT |
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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 .DQG or .DQG2 or .DQG3 or :3DQG;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:470 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:571 or .A:581; 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-[[6-(4-Ethenylsulfonyl-1,4-diazepan-1-yl)-2-pyridin-2-ylpyrimidin-4-yl]amino]propanoic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N44 i.e. 3-((2-(pyridin-2-yl)-6-(4-(vinylsulfonyl)-1,4-diazepan-1-yl)pyrimidin-4-yl)amino)propanoic acid | PDB:6DQ6 | ||||
| Method | X-ray diffraction | Resolution | 1.59 Å | Mutation | No | [2] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMTRREYTLQ364 SFGEMADNFK374 SDYFNMPVHM384 VPTELVEKEF 394 WRLVSSIEED404 VIVEYGADIS414 SKDFGSGFPV424 KDGRRKILPE434 EEEYALSGWN 444 LNNMPVLEQS454 VLAHINKVPW470 LYVGMCFSSF480 CWHIEDHWSY490 SINYLHWGEP 500 KTWYGVPSHA510 AEQLEEVMRE520 LAPELFESQP530 DLLHQLVTIM540 NPNVLMEHGV 550 PVYRTNQCAG560 EFVVTFPRAY570 HSGFNQGYNF580 AEAVNFCT
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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 .H6J or .H6J2 or .H6J3 or :3H6J;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:484 or .A:485 or .A:486 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:571 or .A:581; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-{(S)-(2-chlorophenyl)[2-(4,4-difluoropiperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(4,4-difluoropiperidin-1-yl)ethoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid(Compound N41) | PDB:6BGW | ||||
| Method | X-ray diffraction | Resolution | 1.64 Å | Mutation | No | [6] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMTPREAFG353 FEQAVREYTL363 QSFGEMADNF373 KSDYFNMPVH 383 MVPTELVEKE393 FWRLVSSIEE403 DVIVEYGADI413 SSKDFGSGFP423 VKDGRRKILP 433 EEEEYALSGW443 NLNNMPVLEQ453 SVLAHINKVP469 WLYVGMCFSS479 FCWHIEDHWS 489 YSINYLHWGE499 PKTWYGVPSH509 AAEQLEEVMR519 ELAPELFESQ529 PDLLHQLVTI 539 MNPNVLMEHG549 VPVYRTNQCA559 GEFVVTFPRA569 YHSGFNQGYN579 FAEAVNFCT |
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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 .DKS or .DKS2 or .DKS3 or :3DKS;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:470 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:571 or .A:581; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-{(S)-(2-chlorophenyl)[3-(piperidin-1-yl)propoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(3-(piperidin-1-yl)propoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N48) | PDB:6BH5 | ||||
| Method | X-ray diffraction | Resolution | 1.65 Å | Mutation | No | [6] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMTREYTLQS365 FGEMADNFKS375 DYFNMPVHMV385 PTELVEKEFW 395 RLVSSIEEDV405 IVEYGADISS415 KDFGSGFPVK425 DGRRKILPEE435 EEYALSGWNL 445 NNMPVLEQSV455 KVPWLYVGMC476 FSSFCWHIED486 HWSYSINYLH496 WGEPKTWYGV 506 PSHAAEQLEE516 VMRELAPELF526 ESQPDLLHQL536 VTIMNPNVLM546 EHGVPVYRTN 556 QCAGEFVVTF566 PRAYHSGFNQ576 GYNFAEAVNF586 CT
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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 .DNY or .DNY2 or .DNY3 or :3DNY;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:484 or .A:485 or .A:486 or .A:493 or .A:501 or .A:503 or .A:532 or .A:535 or .A:536 or .A:571 or .A:581; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-[(R)-(2-chlorophenyl)(propoxy)methyl]-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(propoxy)methyl)-1H-pyrrolo[3,2-b]pyridine (Compound N9) | PDB:6BGU | ||||
| Method | X-ray diffraction | Resolution | 1.68 Å | Mutation | No | [6] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMTPREAFG353 FEQAVREYTL363 QSFGEMADNF373 KSDYFNMPVH 383 MVPTELVEKE393 FWRLVSSIEE403 DVIVEYGADI413 SSKDFGSGFP423 VKDGRRKILP 433 EEEEYALSGW443 NLNNMPVLEQ453 SVLAHINKVP469 WLYVGMCFSS479 FCWHIEDHWS 489 YSINYLHWGE499 PKTWYGVPSH509 AAEQLEEVMR519 ELAPELFESQ529 PDLLHQLVTI 539 MNPNVLMEHG549 VPVYRTNQCA559 GEFVVTFPRA569 YHSGFNQGYN579 FAEAVNFCT |
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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 .DKP or .DKP2 or .DKP3 or :3DKP;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:472 or .A:479 or .A:480 or .A:481 or .A:482 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:571 or .A:581; 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-(1-Methyl-1h-Imidazol-4-Yl)-2-(4,4,4-Trifluorobutoxy)pyrido[3,4-D]pyrimidin-4-Ol | Ligand Info | |||||
| Structure Description | Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-methyl-1H-imidazol-4-yl)-2-(4,4,4-trifluorobutoxy)pyrido[3,4-d]pyrimidin-4-ol | PDB:5IVF | ||||
| Method | X-ray diffraction | Resolution | 1.68 Å | Mutation | No | [1] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMRPREAFGF354 EQAVREYTLQ364 SFGEMADNFK374 SDYFNMPVHM 384 VPTELVEKEF394 WRLVSSIEED404 VIVEYGADIS414 SKDFGSGFPV424 KDGRRKILPE 434 EEEYALSGWN444 LNNMPVLEQS454 VLAHINKVPW470 LYVGMCFSSF480 CWHIEDHWSY 490 SINYLHWGEP500 KTWYGVPSHA510 AEQLEEVMRE520 LAPELFESQP530 DLLHQLVTIM 540 NPNVLMEHGV550 PVYRTNQCAG560 EFVVTFPRAY570 HSGFNQGYNF580 AEAVNFCT |
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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 .6EB or .6EB2 or .6EB3 or :36EB;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:472 or .A:479 or .A:480 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:571; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-(5-phenyl-4-{(R)-phenyl[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrazol-1-yl)pyridine-4-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N67 i.e. 2-(5-phenyl-4-(phenyl(2-(piperidin-1-yl)ethoxy)methyl)-1H-pyrazol-1-yl)isonicotinic acid | PDB:6DQE | ||||
| Method | X-ray diffraction | Resolution | 1.69 Å | Mutation | No | [7] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMREYTLQS365 FGEMADNFKS375 DYFNMPVHMV385 PTELVEKEFW 395 RLVSSIEEDV405 IVEYGADISS415 KDFGSGFPVK425 DGRRKILPEE435 EEYALSGWNL 445 NNMPVLEQSV455 LAKVPWLYVG474 MCFSSFCWHI484 EDHWSYSINY494 LHWGEPKTWY 504 GVPSHAAEQL514 EEVMRELAPE524 LFESQPDLLH534 QLVTIMNPNV544 LMEHGVPVYR 554 TNQCAGEFVV564 TFPRAYHSGF574 NQGYNFAEAV584 NFCT
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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 .H6A or .H6A2 or .H6A3 or :3H6A;style chemicals stick;color identity;select .A:73 or .A:409 or .A:411 or .A:412 or .A:470 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:571 or .A:581; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-{(S)-(2-chlorophenyl)[2-(1-methyl-1H-imidazol-2-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(1-methyl-1H-imidazol-2-yl)ethoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N47) | PDB:6BGZ | ||||
| Method | X-ray diffraction | Resolution | 1.69 Å | Mutation | No | [6] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMAVREYTL363 QSFGEMADNF373 KSDYFNMPVH383 MVPTELVEKE 393 FWRLVSSIEE403 DVIVEYGADI413 SSKDFGSGFP423 VKDGRRKILP433 EEEEYALSGW 443 NLNNMPVLEQ453 SKVPWLYVGM475 CFSSFCWHIE485 DHWSYSINYL495 HWGEPKTWYG 505 VPSHAAEQLE515 EVMRELAPEL525 FESQPDLLHQ535 LVTIMNPNVL545 MEHGVPVYRT 555 NQCAGEFVVT565 FPRAYHSGFN575 QGYNFAEAVN585 FCT
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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 .DNV or .DNV2 or .DNV3 or :3DNV;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:484 or .A:485 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:571 or .A:581; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-{1-[2-(piperidin-1-yl)ethyl]-1H-benzimidazol-2-yl}thieno[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N68 i.e. 2-(1-(2-(piperidin-1-yl)ethyl)-1H-benzo[d]imidazol-2-yl)thieno[3,2-b]pyridine-7-carboxylic acid | PDB:6DQF | ||||
| Method | X-ray diffraction | Resolution | 1.69 Å | Mutation | No | [8] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMFEQREYT362 LQSFGEMADN372 FKSDYFNMPV382 HMVPTELVEK 392 EFWRLVSSIE402 EDVIVEYGAD412 ISSKDFGSGF422 PVKDGRRKIL432 PEEEEYALSG 442 WNLNNMPVLE452 QSKVPWLYVG474 MCFSSFCWHI484 EDHWSYSINY494 LHWGEPKTWY 504 GVPSHAAEQL514 EEVMRELAPE524 LFESQPDLLH534 QLVTIMNPNV544 LMEHGVPVYR 554 TNQCAGEFVV564 TFPRAYHSGF574 NQGYNFAEAV584 NFCT
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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 .H61 or .H612 or .H613 or :3H61;style chemicals stick;color identity;select .A:73 or .A:409 or .A:411 or .A:412 or .A:470 or .A:472 or .A:480 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:536 or .A:571 or .A:581; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-{[(2-{[(E)-2-(Dimethylamino)ethenyl](Ethyl)amino}-2-Oxoethyl)amino]methyl}pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Linked KDM5A Jmj Domain Bound to the Inhibitor C49 (2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid) | PDB:5ISL | ||||
| Method | X-ray diffraction | Resolution | 1.69 Å | Mutation | No | [1] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMTRPREAFG353 FEQAVREYTL363 QSFGEMADNF373 KSDYFNMPVH 383 MVPTELVEKE393 FWRLVSSIEE403 DVIVEYGADI413 SSKDFGSGFP423 VKDGRRKILP 433 EEEEYALSGW443 NLNNMPVLEQ453 SVLMKVPWLY472 VGMCFSSFCW482 HIEDHWSYSI 492 NYLHWGEPKT502 WYGVPSHAAE512 QLEEVMRELA522 PELFESQPDL532 LHQLVTIMNP 542 NVLMEHGVPV552 YRTNQCAGEF562 VVTFPRAYHS572 GFNQGYNFAE582 AVNFCT |
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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 .MMK or .MMK2 or .MMK3 or :3MMK;style chemicals stick;color identity;select .A:409 or .A:412 or .A:470 or .A:472 or .A:480 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:571 or .A:581 or .A:583 or .A:584 or .A:585; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-{(3S)-1-[5-(propan-2-yl)-1H-pyrazole-3-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (S)-N-(1-(3-isopropyl-1H-pyrazole-5-carbonyl)pyrrolidin-3-yl)cyclopropanecarboxamide (Compound N55) | PDB:6BH3 | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [6] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMTFGFEQA357 VREYTLQSFG367 EMADNFKSDY377 FNMPVHMVPT 387 ELVEKEFWRL397 VSSIEEDVIV407 EYGADISSKD417 FGSGFPVKDG427 RRKILPEEEE 437 YALSGWNLNN447 MPVLEQSVLM466 KVPWLYVGMC476 FSSFCWHIED486 HWSYSINYLH 496 WGEPKTWYGV506 PSHAAEQLEE516 VMRELAPELF526 ESQPDLLHQL536 VTIMNPNVLM 546 EHGVPVYRTN556 QCAGEFVVTF566 PRAYHSGFNQ576 GYNFAEAVNF586 CT |
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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 .DQJ or .DQJ2 or .DQJ3 or :3DQJ;style chemicals stick;color identity;select .A:409 or .A:410 or .A:411 or .A:412 or .A:470 or .A:472 or .A:478 or .A:479 or .A:480 or .A:483 or .A:485 or .A:491 or .A:493 or .A:501 or .A:503 or .A:571 or .A:575 or .A:583 or .A:584 or .A:585; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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TYR409
3.524
GLY410
4.797
ALA411
4.609
ASP412
4.873
TRP470
3.902
TYR472
2.966
SER478
4.100
SER479
3.486
PHE480
3.436
HIS483
3.209
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| Ligand Name: 2-[(R)-2-piperidin-1-ylethoxy-[3-(prop-2-enoylamino)phenyl]methyl]thieno[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | Linked KDM5A JMJ Domain Bound to the Covalent Inhibitor N69 i.e. [2-((3-acrylamidophenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2-b]pyridine-7-carboxylic acid] | PDB:6DQ9 | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [2] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMGFEQAVR359 EYTLQSFGEM369 ADNFKSDYFN379 MPVHMVPTEL 389 VEKEFWRLVS399 SIEEDVIVEY409 GADISSKDFG419 SGFPVKDGRR429 KILPEEEEYA 439 LSGWNLNNMP449 VLEQSVLKVP469 WLYVGMCFSS479 FCWHIEDHWS489 YSINYLHWGE 499 PKTWYGVPSH509 AAEQLEEVMR519 ELAPELFESQ529 PDLLHQLVTI539 MNPNVLMEHG 549 VPVYRTNQCA559 GEFVVTFPRA569 YHSGFNQGYN579 FAEAVNFCT
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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 .H74 or .H742 or .H743 or :3H74;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:470 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:485 or .A:486 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:537 or .A:538 or .A:539 or .A:571 or .A:581 or .A:585; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ARG73
3.746
GLN75
3.829
TYR409
2.422
ALA411
4.147
ASP412
2.878
TRP470
4.330
TYR472
3.516
SER479
3.780
PHE480
3.276
CYS481
1.803
HIS483
3.227
GLU485
4.449
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| Ligand Name: 2-[4-{[2-(dimethylamino)ethyl](ethyl)carbamoyl}-5-(4-methoxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N50 i.e. 2-(4-((2-(dimethylamino)ethyl)(ethyl)carbamoyl)-5-(4-methoxyphenyl)-1H-pyrazol-1-yl)isonicotinic acid | PDB:6DQC | ||||
| Method | X-ray diffraction | Resolution | 1.75 Å | Mutation | No | [9] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMTPREAFG353 FEQAVREYTL363 QSFGEMADNF373 KSDYFNMPVH 383 MVPTELVEKE393 FWRLVSSIEE403 DVIVEYGADI413 SSKDFGSGFP423 VKDGRRKILP 433 EEEEYALSGW443 NLNNMPVLEQ453 SVLAHINVMK467 VPWLYVGMCF477 SSFCWHIEDH 487 WSYSINYLHW497 GEPKTWYGVP507 SHAAEQLEEV517 MRELAPELFE527 SQPDLLHQLV 537 TIMNPNVLME547 HGVPVYRTNQ557 CAGEFVVTFP567 RAYHSGFNQG577 YNFAEAVNFC 587 T
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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 .H5Y or .H5Y2 or .H5Y3 or :3H5Y;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:472 or .A:479 or .A:480 or .A:483 or .A:484 or .A:485 or .A:486 or .A:493 or .A:501 or .A:503 or .A:535 or .A:571; 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-Methyl-7-Oxo-6-(Propan-2-Yl)-4,7-Dihydropyrazolo[1,5-A]pyrimidine-3-Carbonitrile | Ligand Info | |||||
| Structure Description | Linked KDM5A Jmj Domain Bound to the Inhibitor N8 ( 5-methyl-7-oxo-6-(propan-2-yl)-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile) | PDB:5IVE | ||||
| Method | X-ray diffraction | Resolution | 1.78 Å | Mutation | No | [1] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMTPREAFG353 FEQAVREYTL363 QSFGEMADNF373 KSDYFNMPVH 383 MVPTELVEKE393 FWRLVSSIEE403 DVIVEYGADI413 SSKDFGSGFP423 VKDGRRKILP 433 EEEEYALSGW443 NLNNMPVLEQ453 SVLKVPWLYV473 GMCFSSFCWH483 IEDHWSYSIN 493 YLHWGEPKTW503 YGVPSHAAEQ513 LEEVMRELAP523 ELFESQPDLL533 HQLVTIMNPN 543 VLMEHGVPVY553 RTNQCAGEFV563 VTFPRAYHSG573 FNQGYNFAEA583 VNFCT |
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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 .6E8 or .6E82 or .6E83 or :36E8;style chemicals stick;color identity;select .A:409 or .A:410 or .A:411 or .A:472 or .A:473 or .A:474 or .A:478 or .A:479 or .A:480 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:571 or .A:575; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: 2-{(R)-(3-{[(2E)-4-(dimethylamino)but-2-enoyl]amino}phenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN FORMING COVALENT BOND TO INHIBITOR N71 i.e. 2-((3-(4-(dimethylamino)but-2-enamido)phenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2-b]pyridine-7-carboxylic acid | PDB:6DQB | ||||
| Method | X-ray diffraction | Resolution | 1.79 Å | Mutation | No | [2] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMAVREYTL363 QSFGEMADNF373 KSDYFNMPVH383 MVPTELVEKE 393 FWRLVSSIEE403 DVIVEYGADI413 SSKDFGSGFP423 VKDGRRKILP433 EEEEYALSGW 443 NLNNMPVLEQ453 SVLKVPWLYV473 GMCFSSFCWH483 IEDHWSYSIN493 YLHWGEPKTW 503 YGVPSHAAEQ513 LEEVMRELAP523 ELFESQPDLL533 HQLVTIMNPN543 VLMEHGVPVY 553 RTNQCAGEFV563 VTFPRAYHSG573 FNQGYNFAEA583 VNFCT
|
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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 .H77 or .H772 or .H773 or :3H77;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:470 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:571 or .A:581; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-{(R)-(3-{[4-(dimethylamino)butanoyl]amino}phenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN FORMING COVALENT BOND TO INHIBITOR N71 i.e. 2-((3-(4-(dimethylamino)but-2-enamido)phenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2-b]pyridine-7-carboxylic acid | PDB:6DQB | ||||
| Method | X-ray diffraction | Resolution | 1.79 Å | Mutation | No | [2] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMAVREYTL363 QSFGEMADNF373 KSDYFNMPVH383 MVPTELVEKE 393 FWRLVSSIEE403 DVIVEYGADI413 SSKDFGSGFP423 VKDGRRKILP433 EEEEYALSGW 443 NLNNMPVLEQ453 SVLKVPWLYV473 GMCFSSFCWH483 IEDHWSYSIN493 YLHWGEPKTW 503 YGVPSHAAEQ513 LEEVMRELAP523 ELFESQPDLL533 HQLVTIMNPN543 VLMEHGVPVY 553 RTNQCAGEFV563 VTFPRAYHSG573 FNQGYNFAEA583 VNFCT
|
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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 .HZV or .HZV2 or .HZV3 or :3HZV;style chemicals stick;color identity;select .A:73 or .A:75 or .A:76 or .A:77 or .A:79 or .A:409 or .A:411 or .A:412 or .A:470 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:539 or .A:571 or .A:581; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG73
3.399
GLN75
3.679
ARG76
3.598
LEU77
4.518
GLU79
3.380
TYR409
2.356
ALA411
3.365
ASP412
3.084
TRP470
3.265
TYR472
3.555
SER479
3.070
PHE480
3.348
|
|||||
| Ligand Name: 2-{(S)-(3-{[(2E)-4-(dimethylamino)but-2-enoyl]amino}phenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN FORMING COVALENT BOND TO INHIBITOR N71 i.e. 2-((3-(4-(dimethylamino)but-2-enamido)phenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2-b]pyridine-7-carboxylic acid | PDB:6DQB | ||||
| Method | X-ray diffraction | Resolution | 1.79 Å | Mutation | No | [2] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMAVREYTL363 QSFGEMADNF373 KSDYFNMPVH383 MVPTELVEKE 393 FWRLVSSIEE403 DVIVEYGADI413 SSKDFGSGFP423 VKDGRRKILP433 EEEEYALSGW 443 NLNNMPVLEQ453 SVLKVPWLYV473 GMCFSSFCWH483 IEDHWSYSIN493 YLHWGEPKTW 503 YGVPSHAAEQ513 LEEVMRELAP523 ELFESQPDLL533 HQLVTIMNPN543 VLMEHGVPVY 553 RTNQCAGEFV563 VTFPRAYHSG573 FNQGYNFAEA583 VNFCT
|
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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 .HZM or .HZM2 or .HZM3 or :3HZM;style chemicals stick;color identity;select .A:73 or .A:75 or .A:76 or .A:77 or .A:79 or .A:409 or .A:411 or .A:412 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:537 or .A:539 or .A:571 or .A:581; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG73
3.389
GLN75
3.674
ARG76
3.584
LEU77
4.509
GLU79
3.387
TYR409
2.351
ALA411
3.341
ASP412
3.415
TYR472
3.593
SER479
3.075
PHE480
3.332
CYS481
1.911
|
|||||
| Ligand Name: 3-[(1-Methyl-1h-Pyrrolo[2,3-B]pyridin-3-Yl)amino]pyridine-4-Carboxylic Acid | Ligand Info | |||||
| Structure Description | Linked KDM5A Jmj Domain Bound to the Inhibitor N12 [3-((1-methyl-1H-pyrrolo[2,3-b]pyridin-3-yl)amino)isonicotinic acid] | PDB:5IVV | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [1] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMAFGFEQAV358 REYTLQSFGE368 MADNFKSDYF378 NMPVHMVPTE 388 LVEKEFWRLV398 SSIEEDVIVE408 YGADISSKDF418 GSGFPVKDGR428 RKILPEEEEY 438 ALSGWNLNNM448 PVLEQSVLKV468 PWLYVGMCFS478 SFCWHIEDHW488 SYSINYLHWG 498 EPKTWYGVPS508 HAAEQLEEVM518 RELAPELFES528 QPDLLHQLVT538 IMNPNVLMEH 548 GVPVYRTNQC558 AGEFVVTFPR568 AYHSGFNQGY578 NFAEAVNFCT588 |
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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 .6EN or .6EN2 or .6EN3 or :36EN;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:472 or .A:479 or .A:480 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:571 or .A:581; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 3-[[6-[4-(2-Hydroxyacetyl)-1,4-diazepan-1-yl]-2-pyridin-2-ylpyrimidin-4-yl]amino]propanoic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE POTENTIAL HYDROLYSIS PRODUCT OF INHIBITOR N45 i.e. 3-((6-(4-(2-cyano-3-methylbut-2-enoyl)-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoic acid | PDB:6DQ7 | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [10] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMTVREYTL363 QSFGEMADNF373 KSDYFNMPVH383 MVPTELVEKE 393 FWRLVSSIEE403 DVIVEYGADI413 SSKDFGSGFP423 VKDGRRKILP433 EEEEYALSGW 443 NLNNMPVLEQ453 SVKVPWLYVG474 MCFSSFCWHI484 EDHWSYSINY494 LHWGEPKTWY 504 GVPSHAAEQL514 EEVMRELAPE524 LFESQPDLLH534 QLVTIMNPNV544 LMEHGVPVYR 554 TNQCAGEFVV564 TFPRAYHSGF574 NQGYNFAEAV584 NFCT
|
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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 .H6M or .H6M2 or .H6M3 or :3H6M;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:484 or .A:485 or .A:486 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:571 or .A:575 or .A:581; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG73
3.458
GLN75
3.978
TYR409
2.279
ALA411
3.485
ASP412
3.327
TYR472
3.659
SER479
3.510
PHE480
3.324
CYS481
2.962
HIS483
3.163
ILE484
4.248
|
|||||
| Ligand Name: 2-{(S)-(2-chlorophenyl)[(4,4-difluorocyclohexyl)methoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)((4,4-difluorocyclohexyl)methoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid(Compound N42) | PDB:6BGX | ||||
| Method | X-ray diffraction | Resolution | 1.88 Å | Mutation | No | [6] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMRPREAFGF354 EQAVREYTLQ364 SFGEMADNFK374 SDYFNMPVHM 384 VPTELVEKEF394 WRLVSSIEED404 VIVEYGADIS414 SKDFGSGFPV424 KDGRRKILPE 434 EEEYALSGWN444 LNNMPVLEQS454 VLAHINKVPW470 LYVGMCFSSF480 CWHIEDHWSY 490 SINYLHWGEP500 KTWYGVPSHA510 AEQLEEVMRE520 LAPELFESQP530 DLLHQLVTIM 540 NPNVLMEHGV550 PVYRTNQCAG560 EFVVTFPRAY570 HSGFNQGYNF580 AEAVNFCT |
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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 .DKV or .DKV2 or .DKV3 or :3DKV;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:484 or .A:485 or .A:486 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:571 or .A:581 or .A:585; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG73
3.603
GLN75
4.107
TYR409
2.438
ALA411
3.374
ASP412
3.573
TYR472
3.389
SER479
3.573
PHE480
3.219
CYS481
3.395
HIS483
3.200
ILE484
4.157
|
|||||
| Ligand Name: 2-{(R)-(3-aminophenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | Linked KDM5A JMJ Domain Bound to Inhibitor N70 i.e.[2-((3-aminophenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2-b]pyridine-7-carboxylic acid] | PDB:6DQA | ||||
| Method | X-ray diffraction | Resolution | 1.89 Å | Mutation | No | [2] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMFEQAVRE360 YTLQSFGEMA370 DNFKSDYFNM380 PVHMVPTELV 390 EKEFWRLVSS400 IEEDVIVEYG410 ADISSKDFGS420 GFPVKDGRRK430 ILPEEEEYAL 440 SGWNLNNMPV450 LEQSVKVPWL471 YVGMCFSSFC481 WHIEDHWSYS491 INYLHWGEPK 501 TWYGVPSHAA511 EQLEEVMREL521 APELFESQPD531 LLHQLVTIMN541 PNVLMEHGVP 551 VYRTNQCAGE561 FVVTFPRAYH571 SGFNQGYNFA581 EAVNFCT
|
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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 .H6V or .H6V2 or .H6V3 or :3H6V;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:470 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:571 or .A:581; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: N-[6-(4-acryloyl-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl]-beta-alanine | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N43 i.e. 3-((6-(4-acryloyl-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoic acid | PDB:6DQ5 | ||||
| Method | X-ray diffraction | Resolution | 1.89 Å | Mutation | No | [2] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMTVREYTLQ364 SFGEMADNFK374 SDYFNMPVHM384 VPTELVEKEF 394 WRLVSSIEED404 VIVEYGADIS414 SKDFGSGFPV424 KDGRRKILPE434 EEEYALSGWN 444 LNNMPVLEQS454 VLAHINVKVP469 WLYVGMCFSS479 FCWHIEDHWS489 YSINYLHWGE 499 PKTWYGVPSH509 AAEQLEEVMR519 ELAPELFESQ529 PDLLHQLVTI539 MNPNVLMEHG 549 VPVYRTNQCA559 GEFVVTFPRA569 YHSGFNQGYN579 FAEAVNFC
|
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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 .H6G or .H6G2 or .H6G3 or :3H6G;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:484 or .A:485 or .A:486 or .A:493 or .A:501 or .A:503 or .A:535 or .A:536 or .A:571 or .A:581; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-[5-([1,1'-biphenyl]-3-yl)-4-{(1S)-1-[2-(piperidin-1-yl)ethoxy]ethyl}-1H-pyrazol-1-yl]pyridine-4-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N53 i.e. 2-(5-([1,1'-biphenyl]-3-yl)-4-(1-(2-(piperidin-1-yl)ethoxy)ethyl)-1H-pyrazol-1-yl)isonicotinic acid | PDB:6DQD | ||||
| Method | X-ray diffraction | Resolution | 1.99 Å | Mutation | No | [11] |
| PDB Sequence |
EFVPPPECPV
21 FEPSWEEFTD31 PLSFIGRIRP41 LAEKTGICKI51 RPPKDWQPPF61 ACEVKSFRFT 71 PRVQRLNELE81 AMREAFGFEQ356 AVREYTLQSF366 GEMADNFKSD376 YFNMPVHMVP 386 TELVEKEFWR396 LVSSIEEDVI406 VEYGADISSK416 DFGSGFPVKD426 GRRKILPEEE 436 EYALSGWNLN446 NMPVLEQSVL456 AHINKVPWLY472 VGMCFSSFCW482 HIEDHWSYSI 492 NYLHWGEPKT502 WYGVPSHAAE512 QLEEVMRELA522 PELFESQPDL532 LHQLVTIMNP 542 NVLMEHGVPV552 YRTNQCAGEF562 VVTFPRAYHS572 GFNQGYNFAE582 AVNFCT |
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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 .H67 or .H672 or .H673 or :3H67;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:470 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:484 or .A:485 or .A:493 or .A:501 or .A:503 or .A:535 or .A:571 or .A:581; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: 2-{(R)-(2-chlorophenyl)[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (R)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1l2-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N51) | PDB:6BH0 | ||||
| Method | X-ray diffraction | Resolution | 1.99 Å | Mutation | No | [6] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMTGFEQAV358 REYTLQSFGE368 MADNFKSDYF378 NMPVHMVPTE 388 LVEKEFWRLV398 SSIEEDVIVE408 YGADISSKDF418 GSGFPVKILP433 EEEEYALSGW 443 NLNNMPVLEK467 VPWLYVGMCF477 SSFCWHIEDH487 WSYSINYLHW497 GEPKTWYGVP 507 SHAAEQLEEV517 MRELAPELFE527 SQPDLLHQLV537 TIMNPNVLME547 HGVPVYRTNQ 557 CAGEFVVTFP567 RAYHSGFNQG577 YNFAEAVNFC587 T
|
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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 .DO1 or .DO12 or .DO13 or :3DO1;style chemicals stick;color identity;select .A:73 or .A:75 or .A:409 or .A:411 or .A:412 or .A:470 or .A:472 or .A:479 or .A:480 or .A:481 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:535 or .A:571 or .A:581; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| Ligand Name: Kdm5-IN-1 | Ligand Info | |||||
| Structure Description | LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 5-(1-(tert-butyl)-1H-pyrazol-4-yl)-6-isopropyl-7-oxo-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile (Compound N75/CPI-48) | PDB:6BH4 | ||||
| Method | X-ray diffraction | Resolution | 2.05 Å | Mutation | No | [6] |
| PDB Sequence |
AEFVPPPECP
20 VFEPSWEEFT30 DPLSFIGRIR40 PLAEKTGICK50 IRPPKDWQPP60 FACEVKSFRF 70 TPRVQRLNEL80 EAMTFEQVRE360 YTLQSFGEMA370 DNFKSDYFNM380 PVHMVPTELV 390 EKEFWRLVSS400 IEEDVIVEYG410 ADISSKDFGS420 GFPVKDGRRK430 ILPEEEEYAL 440 SGWNLNNMPV450 LEQSKVPWLY472 VGMCFSSFCW482 HIEDHWSYSI492 NYLHWGEPKT 502 WYGVPSHAAE512 QLEEVMRELA522 PELFESQPDL532 LHQLVTIMNP542 NVLMEHGVPV 552 YRTNQCAGEF562 VVTFPRAYHS572 GFNQGYNFAE582 AVNFCT
|
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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 .DQS or .DQS2 or .DQS3 or :3DQS;style chemicals stick;color identity;select .A:73 or .A:409 or .A:410 or .A:411 or .A:412 or .A:472 or .A:473 or .A:474 or .A:478 or .A:479 or .A:480 or .A:483 or .A:485 or .A:493 or .A:501 or .A:503 or .A:536 or .A:571 or .A:575; 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 | Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds. Cell Chem Biol. 2016 Jul 21;23(7):769-781. | ||||
| REF 2 | Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A. J Med Chem. 2018 Dec 13;61(23):10588-10601. | ||||
| REF 3 | From a novel HTS hit to potent, selective, and orally bioavailable KDM5 inhibitors. Bioorg Med Chem Lett. 2017 Jul 1;27(13):2974-2981. | ||||
| REF 4 | An inhibitor of KDM5 demethylases reduces survival of drug-tolerant cancer cells. Nat Chem Biol. 2016 Jul;12(7):531-8. | ||||
| REF 5 | Design and evaluation of 1,7-naphthyridones as novel KDM5 inhibitors. Bioorg Med Chem Lett. 2016 Sep 15;26(18):4492-4496. | ||||
| REF 6 | Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A. J Med Chem. 2018 Apr 12;61(7):3193-3208. | ||||
| REF 7 | To be determined | ||||
| REF 8 | To be determined | ||||
| REF 9 | To be determined | ||||
| REF 10 | Structure-based Engineering of Reversible Covalent Inhibitors Against Histone Lysine Demethylase 5A | ||||
| REF 11 | To be determined | ||||
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