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 N(6)-Methyllysine Ligand Info
Canonical SMILES CNCCCCC(C(=O)O)N
InChI 1S/C7H16N2O2/c1-9-5-3-2-4-6(8)7(10)11/h6,9H,2-5,8H2,1H3,(H,10,11)/t6-/m0/s1
InChIKey PQNASZJZHFPQLE-LURJTMIESA-N
PubChem Compound ID 164795
Drug Binding Sites of Target  Top
PDB ID: 2OT7      Crystal structure of JMJD2A complexed with histone H3 peptide monomethylated at Lys9
Method X-ray diffraction Resolution 2.13 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)
ASP135
4.272
ILE168
4.564
GLU169
2.870
GLY170
3.417
VAL171
3.821
TYR175
2.660
TYR177
3.428
GLU190
3.150
Residue
Distance (Å)
ASP191
4.037
SER196
3.941
LYS241
4.374
SER288
3.744
THR289
3.677
ASN290
3.155
VAL313
4.097
PDB ID: 2PXJ      The complex structure of JMJD2A and monomethylated H3K36 peptide
Method X-ray diffraction Resolution 2.00 Å Mutation No [2]
PDB Sequence
ASESETLNPS
11
ARIMTFYPTM
21
EEFRNFSRYI
31
AYIESQGAHR
41
AGLAKVVPPK
51

EWKPRASYDD
61
IDDLVIPAPI
71
QQLVTGQSGL
81
FTQYNIQKKA
91
MTVREFRKIA
101

NSDKYCTPRY
111
SEFEELERKY
121
WKNLTFNPPI
131
YGADVNGTLY
141
EKHVDEWNIG
151

RLRTILDLVE
161
KESGITIEGV
171
NTPYLYFGMW
181
KTSFAWHTED
191
MDLYSINYLH
201

FGEPKSWYSV
211
PPEHGKRLER
221
LAKGFFPGSA
231
QSCEAFLRHK
241
MTLISPLMLK
251

KYGIPFDKVT
261
QEAGEFMITF
271
PYGYHAGFNH
281
GFNCAESTNF
291
ATRRWIEYGK
301

QAVLCSCRKD
311
MVKISMDVFV
321
RKFQPERYKL
331
WKAGKDNTVI
341
DHTLPTP
Residue
Distance (Å)
ASP135
4.608
ILE168
4.775
GLU169
2.812
GLY170
3.019
VAL171
3.938
TYR175
3.268
TYR177
3.402
GLU190
3.909
Residue
Distance (Å)
ASP191
3.968
SER196
4.757
LYS241
4.652
SER288
3.515
THR289
3.859
ASN290
3.653
VAL313
4.262
References  Top
REF 1 Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity. Nature. 2007 Jul 5;448(7149):87-91.
REF 2 Structural basis of the recognition of a methylated histone tail by JMJD2A. Proc Natl Acad Sci U S A. 2007 Jun 26;104(26):10818-23.

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