Target Binding Site Detail

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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 2-{(S)-(2-chlorophenyl)[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid Ligand Info
Canonical SMILES C1CCN(CC1)CCOC(C2=CC=CC=C2Cl)C3=CC4=NC=CC(=C4N3)C(=O)O
InChI 1S/C22H24ClN3O3/c23-17-7-3-2-6-15(17)21(29-13-12-26-10-4-1-5-11-26)19-14-18-20(25-19)16(22(27)28)8-9-24-18/h2-3,6-9,14,21,25H,1,4-5,10-13H2,(H,27,28)/t21-/m0/s1
InChIKey AWPYWZMMJZGPOX-NRFANRHFSA-N
PubChem Compound ID 132472258
Drug Binding Sites of Target  Top
PDB ID: 6BGV      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)
Method X-ray diffraction Resolution 1.59 Å Mutation No [1]
PDB Sequence
AEFVPPPECP
20
VFEPSWEEFT
30
DPLSFIGRIR
40
PLAEKTGICK
50
IRPPKDWQPP
60

FACEVKSFRF
70
TPRVQRLNEL
80
EAMTPREAFG
353
FEQAVREYTL
363
QSFGEMADNF
373

KSDYFNMPVH
383
MVPTELVEKE
393
FWRLVSSIEE
403
DVIVEYGADI
413
SSKDFGSGFP
423

VKDGRRKILP
433
EEEEYALSGW
443
NLNNMPVLEQ
453
SVLAHINKVP
469
WLYVGMCFSS
479

FCWHIEDHWS
489
YSINYLHWGE
499
PKTWYGVPSH
509
AAEQLEEVMR
519
ELAPELFESQ
529

PDLLHQLVTI
539
MNPNVLMEHG
549
VPVYRTNQCA
559
GEFVVTFPRA
569
YHSGFNQGYN
579

FAEAVNFCT
Residue
Distance (Å)
ARG73
4.133
GLN75
4.198
TYR409
2.451
ALA411
3.351
ASP412
2.680
TRP470
3.499
TYR472
3.378
SER479
3.474
PHE480
3.280
CYS481
3.403
Residue
Distance (Å)
HIS483
3.192
GLU485
4.373
ASN493
3.713
LYS501
2.745
TRP503
3.644
GLN535
4.174
LEU536
4.361
HIS571
3.576
ALA581
4.842
PDB ID: 6BH1      LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (S)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1l2-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N52)
Method X-ray diffraction Resolution 1.93 Å Mutation No [1]
PDB Sequence
AEFVPPPECP
20
VFEPSWEEFT
30
DPLSFIGRIR
40
PLAEKTGICK
50
IRPPKDWQPP
60

FACEVKSFRF
70
TPRVQRLNEL
80
EAMTQAVREY
361
TLQSFGEMAD
371
NFKSDYFNMP
381

VHMVPTELVE
391
KEFWRLVSSI
401
EEDVIVEYGA
411
DISSKDFGSG
421
FPVKDGRRKI
431

LPEEEEYALS
441
GWNLNNMPVL
451
EQSVLKVPWL
471
YVGMCFSSFC
481
WHIEDHWSYS
491

INYLHWGEPK
501
TWYGVPSHAA
511
EQLEEVMREL
521
APELFESQPD
531
LLHQLVTIMN
541

PNVLMEHGVP
551
VYRTNQCAGE
561
FVVTFPRAYH
571
SGFNQGYNFA
581
EAVNFCT
Residue
Distance (Å)
ARG73
3.805
GLN75
4.158
TYR409
2.449
ALA411
3.397
ASP412
2.723
TRP470
3.465
TYR472
3.371
SER479
3.623
PHE480
3.229
CYS481
3.515
Residue
Distance (Å)
HIS483
3.225
GLU485
4.417
ASN493
3.678
LYS501
2.754
TRP503
3.519
GLN535
4.306
LEU536
4.851
HIS571
3.453
ALA581
4.834
References  Top
REF 1 Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A. J Med Chem. 2018 Apr 12;61(7):3193-3208.

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