Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T15797 | Target Info | |||
| Target Name | SET and MYND domain-containing protein 2 (SMYD2) | ||||
| Synonyms | Nlysine methyltransferase SMYD2; N-lysine methyltransferase SMYD2; Lysine Nmethyltransferase 3C; Lysine N-methyltransferase 3C; KMT3C; Histone methyltransferase SMYD2; HSKMB; HSKM-B | ||||
| Target Type | Preclinical Target | ||||
| Gene Name | SMYD2 | ||||
| Biochemical Class | Methyltransferase | ||||
| UniProt ID | |||||
| Ligand General Information | Top | ||||
|---|---|---|---|---|---|
| Ligand Name | (R,R)-2,3-butanediol | Ligand Info | |||
| Canonical SMILES | CC(C(C)O)O | ||||
| InChI | 1S/C4H10O2/c1-3(5)4(2)6/h3-6H,1-2H3/t3-,4-/m1/s1 | ||||
| InChIKey | OWBTYPJTUOEWEK-QWWZWVQMSA-N | ||||
| PubChem Compound ID | 225936 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 3S7D Structural Basis of Substrate Methylation and Inhibition of SMYD2 | ||||||
| Method | X-ray diffraction | Resolution | 2.30 Å | Mutation | No | [1] |
| PDB Sequence |
GLGGLERFCS
14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY54 CFTRKEGLSK 64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE104 TVRLTARILA 114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA154 ALHHFYSKHL 164 EFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL204 MNHSCCPNVI 214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL254 RDSYFFTCEC 264 QECTTKDKDK274 AKVEIRKLSD284 PPKAEAIRDM294 VRYARNVIEE304 FRRAKHYKSP 314 SELLEICELS324 QEKMSSVFED334 SNVYMLHMMY344 QAMGVCLYMQ354 DWEGALQYGQ 364 KIIKPYSKHY374 PLYSLNVASM384 WLKLGRLYMG394 LEHKAAGEKA404 LKKAIAIMEV 414 AHGKDHPYIS424 EIKQEIESH
|
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| PDB ID: 3S7B Structural Basis of Substrate Methylation and Inhibition of SMYD2 | ||||||
| Method | X-ray diffraction | Resolution | 2.42 Å | Mutation | No | [1] |
| PDB Sequence |
GLGGLERFCS
14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY54 CFTRKEGLSK 64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE104 TVRLTARILA 114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA154 ALHHFYSKHL 164 EFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL204 MNHSCCPNVI 214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL254 RDSYFFTCEC 264 QECTTKDKDK274 AKVEIRKLSD284 PPKAEAIRDM294 VRYARNVIEE304 FRRAKHYKSP 314 SELLEICELS324 QEKMSSVFED334 SNVYMLHMMY344 QAMGVCLYMQ354 DWEGALQYGQ 364 KIIKPYSKHY374 PLYSLNVASM384 WLKLGRLYMG394 LEHKAAGEKA404 LKKAIAIMEV 414 AHGKDHPYIS424 EIKQEIESH
|
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GLY18
3.606
ARG19
2.952
TYR41
3.249
TYR54
3.131
CYS55
3.535
CYS65
4.988
ARG67
3.348
GLN79
4.028
LYS80
4.294
TRP83
3.702
GLU135
3.664
THR220
2.688
|
|||||
| PDB ID: 3S7F Structural Basis of Substrate Methylation and Inhibition of SMYD2 | ||||||
| Method | X-ray diffraction | Resolution | 2.85 Å | Mutation | No | [1] |
| PDB Sequence |
GLGGLERFCS
14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY54 CFTRKEGLSK 64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE104 TVRLTARILA 114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA154 ALHHFYSKHL 164 EFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL204 MNHSCCPNVI 214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL254 RDSYFFTCEC 264 QECTTKDKDK274 AKVEIRKLSD284 PPKAEAIRDM294 VRYARNVIEE304 FRRAKHYKSP 314 SELLEICELS324 QEKMSSVFED334 SNVYMLHMMY344 QAMGVCLYMQ354 DWEGALQYGQ 364 KIIKPYSKHY374 PLYSLNVASM384 WLKLGRLYMG394 LEHKAAGEKA404 LKKAIAIMEV 414 AHGKDHPYIS424 EIKQEIESH
|
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| PDB ID: 5KJK SMYD2 in complex with AZ370 | ||||||
| Method | X-ray diffraction | Resolution | 1.93 Å | Mutation | Yes | [2] |
| PDB Sequence |
GLGGLERFCS
14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY54 CFTRKEGLSK 64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE104 TVRLTARILA 114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA154 ALHHFYSKHL 164 EFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL204 MNHSCCPNVI 214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL254 RDSYFFTCEC 264 QECTTKDKDK274 AKVEIRKLSD284 PPKAEAIRDM294 VRYARNVIEE304 FRRAKHYKSP 314 SELLEICELS324 QEKMSSVFED334 SNVYMLHMMY344 QAMGVCLYMQ354 DWEGALQYGQ 364 KIIKPYSKHY374 PLYSLNVASM384 WLKLGRLYMG394 LEHKAAGEKA404 LKKAIAIMEV 414 AHGKDHPYIS424 EIKQEIESH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BU3 or .BU32 or .BU33 or :3BU3;style chemicals stick;color identity;select .A:5 or .A:65 or .A:67 or .A:79 or .A:80 or .A:83 or .A:122 or .A:126 or .A:127 or .A:247 or .A:248 or .A:251 or .A:252 or .A:255 or .A:261 or .A:270 or .A:356 or .A:390 or .A:391 or .A:394 or .A:395; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLY5
3.171
CYS65
4.926
ARG67
3.430
GLN79
3.598
LYS80
4.340
TRP83
3.603
ARG122
3.438
GLU126
4.675
LYS127
3.620
THR247
3.303
GLU248
3.425
|
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| PDB ID: 5KJN SMYD2 in complex with AZ506 | ||||||
| Method | X-ray diffraction | Resolution | 2.72 Å | Mutation | Yes | [2] |
| PDB Sequence |
GLGGLERFCS
14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY54 CFTRKEGLSK 64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE104 TVRLTARILA 114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA154 ALHHFYSKHL 164 EFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL204 MNHSCCPNVI 214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL254 RDSYFFTCEC 264 QECTTKDKDK274 AKVEIRKLSD284 PPKAEAIRDM294 VRYARNVIEE304 FRRAKHYKSP 314 SELLEICELS324 QEKMSSVFED334 SNVYMLHMMY344 QAMGVCLYMQ354 DWEGALQYGQ 364 KIIKPYSKHY374 PLYSLNVASM384 WLKLGRLYMG394 LEHKAAGEKA404 LKKAIAIMEV 414 AHGKDHPYIS424 EIKQEIESH
|
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|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BU3 or .BU32 or .BU33 or :3BU3;style chemicals stick;color identity;select .A:38 or .A:39 or .A:40 or .A:41 or .A:58 or .A:65 or .A:67 or .A:79 or .A:80 or .A:83 or .A:85 or .A:104 or .A:105 or .A:115 or .A:122 or .A:123 or .A:124 or .A:125 or .A:126 or .A:127 or .A:185 or .A:188 or .A:189 or .A:190 or .A:192 or .A:193 or .A:196 or .A:356 or .A:390 or .A:391 or .A:394 or .A:395; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ALA38
2.994
TYR39
3.275
ALA40
4.456
TYR41
3.728
ARG58
3.992
CYS65
4.884
ARG67
3.255
GLN79
4.192
LYS80
4.420
TRP83
3.722
MET85
4.264
GLU104
3.574
THR105
3.384
LYS115
3.171
ARG122
3.387
THR123
3.697
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural basis of substrate methylation and inhibition of SMYD2. Structure. 2011 Sep 7;19(9):1262-73. | ||||
| REF 2 | Design, Synthesis, and Biological Activity of Substrate Competitive SMYD2 Inhibitors. J Med Chem. 2016 Dec 22;59(24):11079-11097. | ||||
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