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 T35792 Target Info
Target Name Histone-lysine N-methyltransferase SMYD3 (SMYD3)
Synonyms SET and MYND domain-containing protein 3; Zinc finger MYND domain-containing protein 1
Target Type Preclinical Target
Gene Name SMYD3
UniProt ID
SMYD3_HUMAN
Ligand General Information  Top
Ligand Name Sinefungin Ligand Info
Canonical SMILES C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
InChI 1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
InChIKey LMXOHSDXUQEUSF-YECHIGJVSA-N
PubChem Compound ID 65482
Drug Binding Sites of Target  Top
PDB ID: 3PDN      Crystal structure of SmyD3 in complex with methyltransferase inhibitor sinefungin
Method X-ray diffraction Resolution 1.70 Å Mutation No [1]
PDB Sequence
EPLKVEKFAT
11
ANRGNGLRAV
21
TPLRPGELLF
31
RSDPLAYTVC
41
KGSRGVVCDR
51

CLLGKEKLMR
61
CSQCRVAKYC
71
SAKCQKKAWP
81
DHKRECKCLK
91
SCKPRYPPDS
101

VRLLGRVVFK
111
LMDGAPSESE
121
KLYSFYDLES
131
NINKLTEDRK
141
EGLRQLVMTF
151

QHFMREEIQD
161
ASQLPPAFDL
171
FEAFAKVICN
181
SFTICNAEMQ
191
EVGVGLYPSI
201

SLLNHSCDPN
211
CSIVFNGPHL
221
LLRAVRDIEV
231
GEELTICYLD
241
MLMTSEERRK
251

QLRDQYCFEC
261
DCFRCQTQDK
271
DADMLTGDEQ
281
VWKEVQESLK
291
KIEELKAHWK
301

WEQVLAMCQA
311
IISSNSERLP
321
DINIYQLKVL
331
DCAMDACINL
341
GLLEEALFYG
351

TRTMEPYRIF
361
FPGSHPVRGV
371
QVMKVGKLQL
381
HQGMFPQAMK
391
NLRLAFDIMR
401

VTHGREHSLI
411
EDLILLLEEC
421
DANIRAS
Residue
Distance (Å)
ASN13
4.372
ARG14
2.725
GLY15
3.714
ASN16
2.795
TYR124
2.647
ASP128
4.838
LEU129
4.785
GLU130
3.567
ASN132
2.919
CYS180
3.697
ASN181
3.029
Residue
Distance (Å)
SER202
2.947
LEU203
3.662
LEU204
3.644
ASN205
2.831
HIS206
2.905
TYR239
3.263
TYR257
2.635
CYS258
4.698
PHE259
3.379
GLU260
4.761
PDB ID: 3RU0      Cocrystal structure of human SMYD3 with inhibitor Sinefungin bound
Method X-ray diffraction Resolution 1.85 Å Mutation No [2]
PDB Sequence
LKVEKFATAN
13
RGNGLRAVTP
23
LRPGELLFRS
33
DPLAYTVCKG
43
SRGVVCDRCL
53

LGKEKLMRCS
63
QCRVAKYCSA
73
KCQKKAWPDH
83
KRECKCLKSC
93
KPRYPPDSVR
103

LLGRVVFKLM
113
DGAPSESEKL
123
YSFYDLESNI
133
NKLTEDKKEG
143
LRQLVMTFQH
153

FMREEIQDAS
163
QLPPAFDLFE
173
AFAKVICNSF
183
TICNAEMQEV
193
GVGLYPSISL
203

LNHSCDPNCS
213
IVFNGPHLLL
223
RAVRDIEVGE
233
ELTICYLDML
243
MTSEERRKQL
253

RDQYCFECDC
263
FRCQTQDKDA
273
DMLTGDEQVW
283
KEVQESLKKI
293
EELKAHWKWE
303

QVLAMCQAII
313
SSNSERLPDI
323
NIYQLKVLDC
333
AMDACINLGL
343
LEEALFYGTR
353

TMEPYRIFFP
363
GSHPVRGVQV
373
MKVGKLQLHQ
383
GMFPQAMKNL
393
RLAFDIMRVT
403

HGREHSLIED
413
LILLLEECDA
423
NIRAS
Residue
Distance (Å)
ARG14
2.720
GLY15
3.727
ASN16
2.808
TYR124
2.669
ASP128
4.573
LEU129
4.993
GLU130
3.728
ASN132
2.991
CYS180
3.376
ASN181
2.880
SER202
2.898
Residue
Distance (Å)
LEU203
3.514
LEU204
3.702
ASN205
2.749
HIS206
2.941
TYR239
3.394
TYR257
2.678
CYS258
4.732
PHE259
3.259
GLU260
4.731
CYS261
4.890
References  Top
REF 1 Structural insights into the autoinhibition and posttranslational activation of histone methyltransferase SmyD3. J Mol Biol. 2011 Feb 11;406(1):149-59.
REF 2 Structural and functional profiling of the human histone methyltransferase SMYD3. PLoS One. 2011;6(7):e22290.

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