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 T18904 Target Info
Target Name Lysine-specific demethylase 4A (KDM4A)
Synonyms KIAA0677; Jumonji domain-containing protein 2A; JmjC domain-containing histone demethylation protein 3A; JMJD2A; JMJD2; JHDM3A
Target Type Patented-recorded Target
Gene Name KDM4A
Biochemical Class Paired donor oxygen oxidoreductase
UniProt ID
KDM4A_HUMAN
Ligand General Information  Top
Ligand Name (2R)-2-hydroxypentanedioic acid Ligand Info
Canonical SMILES C(CC(=O)O)C(C(=O)O)O
InChI 1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/t3-/m1/s1
InChIKey HWXBTNAVRSUOJR-GSVOUGTGSA-N
PubChem Compound ID 439391
Drug Binding Sites of Target  Top
PDB ID: 2YBP      JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41)
Method X-ray diffraction Resolution 2.02 Å Mutation No [1]
PDB Sequence
TLNPSARIMT
16
FYPTMEEFRN
26
FSRYIAYIES
36
QGAHRAGLAK
46
VVPPKEWKPR
56

ASYDDIDDLV
66
IPAPIQQLVT
76
GQSGLFTQYN
86
IQKKAMTVRE
96
FRKIANSDKY
106

CTPRYSEFEE
116
LERKYWKNLT
126
FNPPIYGADV
136
NGTLYEKHVD
146
EWNIGRLRTI
156

LDLVEKESGI
166
TIEGVNTPYL
176
YFGMWKTSFA
186
WHTEDMDLYS
196
INYLHFGEPK
206

SWYSVPPEHG
216
KRLERLAKGF
226
FPGSAQSCEA
236
FLRHKMTLIS
246
PLMLKKYGIP
256

FDKVTQEAGE
266
FMITFPYGYH
276
AGFNHGFNCA
286
ESTNFATRRW
296
IEYGKQAVLC
306

SCRKDMVKIS
316
MDVFVRKFQP
326
ERYKLWKAGK
336
DNTVIDHTLP
346
TPEAAEFLK
Residue
Distance (Å)
TYR132
2.659
TYR177
3.713
PHE185
3.379
HIS188
3.359
GLU190
3.209
SER196
2.866
ILE197
4.380
Residue
Distance (Å)
ASN198
2.935
LYS206
2.768
TRP208
3.542
THR270
3.945
HIS276
3.398
ALA286
4.913
SER288
2.754
PDB ID: 2YBK      JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE
Method X-ray diffraction Resolution 2.40 Å Mutation No [1]
PDB Sequence
TLNPSARIMT
16
FYPTMEEFRN
26
FSRYIAYIES
36
QGAHRAGLAK
46
VVPPKEWKPR
56

ASYDDIDDLV
66
IPAPIQQLVT
76
GQSGLFTQYN
86
IQKKAMTVRE
96
FRKIANSDKY
106

CTPRYSEFEE
116
LERKYWKNLT
126
FNPPIYGADV
136
NGTLYEKHVD
146
EWNIGRLRTI
156

LDLVEKESGI
166
TIEGVNTPYL
176
YFGMWKTSFA
186
WHTEDMDLYS
196
INYLHFGEPK
206

SWYSVPPEHG
216
KRLERLAKGF
226
FPGSAQSCEA
236
FLRHKMTLIS
246
PLMLKKYGIP
256

FDKVTQEAGE
266
FMITFPYGYH
276
AGFNHGFNCA
286
ESTNFATRRW
296
IEYGKQAVLC
306

SCRKDMVKIS
316
MDVFVRKFQP
326
ERYKLWKAGK
336
DNTVIDHTLP
346
TPEAAEFLK
Residue
Distance (Å)
TYR132
2.079
TYR177
3.652
PHE185
3.218
HIS188
2.505
GLU190
3.231
SER196
3.363
ASN198
3.416
Residue
Distance (Å)
LYS206
3.282
TRP208
3.814
LYS241
4.496
THR270
4.307
HIS276
2.863
ASN280
4.896
SER288
4.491
References  Top
REF 1 The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases. EMBO Rep. 2011 May;12(5):463-9.

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