Target Binding Site Detail

Content Navigation (  All   None )                                      
Target General Information
Ligand General Information
Drug Binding Sites of Target
References
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
KDM5A_HUMAN
Ligand General Information  Top
Ligand Name Alpha-ketoglutaric acid Ligand Info
Canonical SMILES C(CC(=O)O)C(=O)C(=O)O
InChI 1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)
InChIKey KPGXRSRHYNQIFN-UHFFFAOYSA-N
PubChem Compound ID 51
Drug Binding Sites of Target  Top
PDB ID: 5IVB      A High Resolution Structure of a Linked KDM5A Jmj Domain with Alpha-Ketoglutarate
Method X-ray diffraction Resolution 1.39 Å Mutation No [1]
PDB Sequence
EFVPPPECPV
21
FEPSWEEFTD
31
PLSFIGRIRP
41
LAEKTGICKI
51
RPPKDWQPPF
61

ACEVKSFRFT
71
PRVQRLNELE
81
AMTEQAVREY
361
TLQSFGEMAD
371
NFKSDYFNMP
381

VHMVPTELVE
391
KEFWRLVSSI
401
EEDVIVEYGA
411
DISSKDFGSG
421
FPVKDGRRKI
431

LPEEEEYALS
441
GWNLNNMPVL
451
EKVPWLYVGM
475
CFSSFCWHIE
485
DHWSYSINYL
495

HWGEPKTWYG
505
VPSHAAEQLE
515
EVMRELAPEL
525
FESQPDLLHQ
535
LVTIMNPNVL
545

MEHGVPVYRT
555
NQCAGEFVVT
565
FPRAYHSGFN
575
QGYNFAEAVN
585
FCT
Residue
Distance (Å)
TYR409
2.458
TYR472
3.469
PHE480
3.281
HIS483
3.002
GLU485
3.235
SER491
3.052
ILE492
4.698
Residue
Distance (Å)
ASN493
3.001
LYS501
2.768
TRP503
3.484
THR565
4.807
HIS571
3.228
ALA583
3.354
PDB ID: 5IW0      Linked KDM5A Jmj Domain Bound to the Inhibitor N19 [2-(5-((4-chloro-2-methylbenzyl)oxy)-1H-pyrazol-1-yl)isonicotinic acid]
Method X-ray diffraction Resolution 1.63 Å Mutation No [1]
PDB Sequence
EFVPPPECPV
21
FEPSWEEFTD
31
PLSFIGRIRP
41
LAEKTGICKI
51
RPPKDWQPPF
61

ACEVKSFRFT
71
PRVQRLNELE
81
AMREAFGFEQ
356
AVREYTLQSF
366
GEMADNFKSD
376

YFNMPVHMVP
386
TELVEKEFWR
396
LVSSIEEDVI
406
VEYGADISSK
416
DFGSGFPVKD
426

GRRKILPEEE
436
EYALSGWNLN
446
NMPVLEQSVL
456
AHINKVPWLY
472
VGMCFSSFCW
482

HIEDHWSYSI
492
NYLHWGEPKT
502
WYGVPSHAAE
512
QLEEVMRELA
522
PELFESQPDL
532

LHQLVTIMNP
542
NVLMEHGVPV
552
YRTNQCAGEF
562
VVTFPRAYHS
572
GFNQGYNFAE
582

AVNFCT
Residue
Distance (Å)
ARG73
4.919
GLN75
4.215
SER479
4.614
PHE480
3.461
CYS481
3.295
Residue
Distance (Å)
TRP482
4.442
HIS483
3.331
GLN535
2.737
LEU536
3.491
PDB ID: 5E6H      A Linked Jumonji Domain of the KDM5A Lysine Demethylase
Method X-ray diffraction Resolution 2.24 Å Mutation No [2]
PDB Sequence
EFVPPPECPV
21
FEPSWEEFTD
31
PLSFIGRIRP
41
LAEKTGICKI
51
RPPKDWQPPF
61

ACEVKSFRFT
71
PRVQRLNELE
81
AMTAVREYTL
363
QSFGEMADNF
373
KSDYFNMPVH
383

MVPTELVEKE
393
FWRLVSSIEE
403
DVIVEYGADI
413
SSKDFGSGFP
423
VKDGRRKILP
433

EEEEYALSGW
443
NLNNMPVLEQ
453
SVKVPWLYVG
474
MCFSSFCWHI
484
EDHWSYSINY
494

LHWGEPKTWY
504
GVPSHAAEQL
514
EEVMRELAPE
524
LFESQPDLLH
534
QLVTIMNPNV
544

LMEHGVPVYR
554
TNQCAGEFVV
564
TFPRAYHSGF
574
NQGYNFAEAV
584
NFCT
Residue
Distance (Å)
TYR409
2.503
TYR472
3.497
PHE480
3.132
HIS483
3.107
GLU485
3.299
SER491
2.609
ILE492
4.503
Residue
Distance (Å)
ASN493
3.189
LYS501
2.905
TRP503
3.409
THR565
4.712
HIS571
3.292
ALA581
4.985
ALA583
3.280
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 Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases. J Biol Chem. 2016 Feb 5;291(6):2631-46.

If You Find Any Error in Data or Bug in Web Service, Please Kindly Report It to Dr. Zhou and Dr. Zhang.