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 | Ademetionine | Ligand Info | |||
| Canonical SMILES | C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)N2C=NC3=C(N=CN=C32)N)O)O | ||||
| InChI | 1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27?/m0/s1 | ||||
| InChIKey | MEFKEPWMEQBLKI-AIRLBKTGSA-N | ||||
| PubChem Compound ID | 34755 | ||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| PDB ID: 5ARF SMYD2 in complex with small molecule inhibitor compound-2 | ||||||
| Method | X-ray diffraction | Resolution | 1.92 Å | Mutation | No | [1] |
| PDB Sequence |
LGGLERFCSP
15 GKGRGLRALQ25 PFQVGDLLFS35 CPAYAYVLTV45 NERGNHCEYC55 FTRKEGLSKC 65 GRCKQAFYCN75 VECQKEDWPM85 HKLECSPMVV95 FGENWNPSET105 VRLTARILAK 115 QKIHPERTPS125 EKLLAVKEFE135 SHLDKLDNEK145 KDLIQSDIAA155 LHHFYSKHLG 165 FPDNDSLVVL175 FAQVNCNGFT185 IEDEELSHLG195 SAIFPDVALM205 NHSCCPNVIV 215 TYKGTLAEVR225 AVQEIKPGEE235 VFTSYIDLLY245 PTEDRNDRLR255 DSYFFTCECQ 265 ECTTKDKDKA275 KVEIRKLSDP285 PKAEAIRDMV295 RYARNVIEEF305 RRAKHYKSPS 315 ELLEICELSQ325 EKMSSVFEDS335 NVYMLHMMYQ345 AMGVCLYMQD355 WEGALQYGQK 365 IIKPYSKHYP375 LYSLNVASMW385 LKLGRLYMGL395 EHKAAGEKAL405 KKAIAIMEVA 415 HGKDHPYISE425 IKQEI
|
|||||
|
|
GLY16
3.297
LYS17
2.882
GLY18
3.932
ARG19
2.058
GLY20
4.258
LEU129
4.875
GLU135
3.341
HIS137
3.020
CYS181
3.590
ASN182
2.978
ALA203
2.634
|
|||||
| PDB ID: 5ARG SMYD2 in complex with SGC probe BAY-598 | ||||||
| Method | X-ray diffraction | Resolution | 1.99 Å | Mutation | No | [1] |
| PDB Sequence |
LGGLERFCSP
15 GKGRGLRALQ25 PFQVGDLLFS35 CPAYAYVLTV45 NERGNHCEYC55 FTRKEGLSKC 65 GRCKQAFYCN75 VECQKEDWPM85 HKLECSPMVV95 FGENWNPSET105 VRLTARILAK 115 QKIHPERTPS125 EKLLAVKEFE135 SHLDKLDNEK145 KDLIQSDIAA155 LHHFYSKHLG 165 FPDNDSLVVL175 FAQVNCNGFT185 IEDEELSHLG195 SAIFPDVALM205 NHSCCPNVIV 215 TYKGTLAEVR225 AVQEIKPGEE235 VFTSYIDLLY245 PTEDRNDRLR255 DSYFFTCECQ 265 ECTTKDKDKA275 KVEIRKLSDP285 PKAEAIRDMV295 RYARNVIEEF305 RRAKHYKSPS 315 ELLEICELSQ325 EKMSSVFEDS335 NVYMLHMMYQ345 AMGVCLYMQD355 WEGALQYGQK 365 IIKPYSKHYP375 LYSLNVASMW385 LKLGRLYMGL395 EHKAAGEKAL405 KKAIAIMEVA 415 HGKDHPYISE425 IKQEIE
|
|||||
|
|
GLY16
3.166
LYS17
2.984
GLY18
3.735
ARG19
2.342
GLY20
4.626
LEU129
4.501
GLU135
3.795
HIS137
2.982
CYS181
3.573
ASN182
3.255
ALA203
2.925
|
|||||
| PDB ID: 3TG4 Structure of SMYD2 in complex with SAM | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [2] |
| PDB Sequence |
LGGLERFCSP
15 GKGRGLRALQ25 PFQVGDLLFS35 CPAYAYVLTV45 NERGNHCEYC55 FTRKEGLSKC 65 GRCKQAFYCN75 VECQKEDWPM85 HKLECSPMVV95 FGENWNPSET105 VRLTARILAK 115 QKIHPERTPS125 EKLLAVKEFE135 SHLDKLDNEK145 KDLIQSDIAA155 LHHFYSKHLG 165 FPDNDSLVVL175 FAQVNCNGFT185 IEDEELSHLG195 SAIFPDVALM205 NHSCCPNVIV 215 TYKGTLAEVR225 AVQEIKPGEE235 VFTSYIDLLY245 PTEDRNDRLR255 DSYFFTCECQ 265 ECTTKDKDKA275 KVEIRKLSDP285 PKAEAIRDMV295 RYARNVIEEF305 RRAKHYKSPS 315 ELLEICELSQ325 EKMSSVFEDS335 NVYMLHMMYQ345 AMGVCLYMQD355 WEGALQYGQK 365 IIKPYSKHYP375 LYSLNVASMW385 LKLGRLYMGL395 EHKAAGEKAL405 KKAIAIMEVA 415 HGKDHPYISE425 IKQEIES
|
|||||
|
|
GLY16
3.302
LYS17
2.800
GLY18
3.814
ARG19
2.704
LEU129
4.499
GLU135
4.238
HIS137
2.788
CYS181
3.557
ASN182
3.314
ALA203
3.056
LEU204
3.515
|
|||||
| PDB ID: 3S7B Structural Basis of Substrate Methylation and Inhibition of SMYD2 | ||||||
| Method | X-ray diffraction | Resolution | 2.42 Å | Mutation | No | [3] |
| 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
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:129 or .A:135 or .A:137 or .A:181 or .A:182 or .A:203 or .A:204 or .A:205 or .A:206 or .A:207 or .A:208 or .A:237 or .A:240 or .A:258 or .A:259 or .A:260 or .A:261 or .A:262; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLY16
3.531
LYS17
2.802
GLY18
3.917
ARG19
2.695
GLY20
4.909
LEU129
4.615
GLU135
2.852
HIS137
2.949
CYS181
3.369
ASN182
3.024
ALA203
3.085
LEU204
3.453
|
|||||
| PDB ID: 3S7F Structural Basis of Substrate Methylation and Inhibition of SMYD2 | ||||||
| Method | X-ray diffraction | Resolution | 2.85 Å | Mutation | No | [3] |
| 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
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:129 or .A:135 or .A:137 or .A:181 or .A:182 or .A:203 or .A:204 or .A:205 or .A:206 or .A:207 or .A:208 or .A:237 or .A:240 or .A:258 or .A:259 or .A:260 or .A:261 or .A:262; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLY16
3.599
LYS17
2.802
GLY18
3.860
ARG19
2.740
GLY20
4.955
LEU129
4.635
GLU135
2.806
HIS137
2.917
CYS181
3.381
ASN182
2.924
ALA203
3.100
LEU204
3.453
|
|||||
| PDB ID: 3S7J Structural Basis of Substrate Methylation and Inhibition of SMYD2 | ||||||
| Method | X-ray diffraction | Resolution | 3.04 Å | Mutation | No | [3] |
| PDB Sequence |
LGGLERFCSP
15 GKGRGLRALQ25 PFQVGDLLFS35 CPAYAYVLTV45 NERGNHCEYC55 FTRKEGLSKC 65 GRCKQAFYCN75 VECQKEDWPM85 HKLECSPMVV95 FGENWNPSET105 VRLTARILAK 115 QKIHPERTPS125 EKLLAVKEFE135 SHLDKLDNEK145 KDLIQSDIAA155 LHHFYSKHLE 165 FPDNDSLVVL175 FAQVNCNGFT185 IEDEELSHLG195 SAIFPDVALM205 NHSCCPNVIV 215 TYKGTLAEVR225 AVQEIKPGEE235 VFTSYIDLLY245 PTEDRNDRLR255 DSYFFTCECQ 265 ECTTKDKDKA275 KVEIRKLSDP285 PKAEAIRDMV295 RYARNVIEEF305 RRAKHYKSPS 315 ELLEICELSQ325 EKMSSVFEDS335 NVYMLHMMYQ345 AMGVCLYMQD355 WEGALQYGQK 365 IIKPYSKHYP375 LYSLNVASMW385 LKLGRLYMGL395 EHKAAGEKAL405 KKAIAIMEVA 415 HGKDHPYISE425 IKQEIESH
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:129 or .A:135 or .A:137 or .A:181 or .A:182 or .A:203 or .A:204 or .A:205 or .A:206 or .A:207 or .A:208 or .A:240 or .A:258 or .A:259 or .A:260 or .A:261 or .A:262; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLY16
3.455
LYS17
2.749
GLY18
4.003
ARG19
2.759
GLY20
4.914
LEU129
4.924
GLU135
2.902
HIS137
2.949
CYS181
3.457
ASN182
3.368
ALA203
3.020
|
|||||
| PDB ID: 5KJK SMYD2 in complex with AZ370 | ||||||
| Method | X-ray diffraction | Resolution | 1.93 Å | Mutation | Yes | [4] |
| 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
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:129 or .A:135 or .A:137 or .A:181 or .A:182 or .A:203 or .A:204 or .A:205 or .A:206 or .A:207 or .A:208 or .A:237 or .A:240 or .A:258 or .A:259 or .A:260 or .A:261 or .A:262; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLY16
3.629
LYS17
2.831
GLY18
3.856
ARG19
2.730
GLY20
4.945
LEU129
4.577
GLU135
2.899
HIS137
2.972
CYS181
3.414
ASN182
3.081
ALA203
3.108
LEU204
3.432
|
|||||
| PDB ID: 5KJM SMYD2 in complex with AZ931 | ||||||
| Method | X-ray diffraction | Resolution | 2.19 Å | Mutation | Yes | [4] |
| 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
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:129 or .A:135 or .A:137 or .A:181 or .A:182 or .A:203 or .A:204 or .A:205 or .A:206 or .A:207 or .A:237 or .A:240 or .A:258 or .A:259 or .A:260 or .A:261 or .A:262; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLY16
3.551
LYS17
2.816
GLY18
3.900
ARG19
2.737
GLY20
4.972
LEU129
4.479
GLU135
2.984
HIS137
2.726
CYS181
3.418
ASN182
3.005
ALA203
3.051
|
|||||
| PDB ID: 5KJL SMYD2 in complex with AZ378 | ||||||
| Method | X-ray diffraction | Resolution | 2.70 Å | Mutation | Yes | [4] |
| PDB Sequence |
LGGLERFCSP
15 GKGRGLRALQ25 PFQVGDLLFS35 CPAYAYVLTV45 NERGNHCEYC55 FTRKEGLSKC 65 GRCKQAFYCN75 VECQKEDWPM85 HKLECSPMVV95 FGENWNPSET105 VRLTARILAK 115 QKIHPERTPS125 EKLLAVKEFE135 SHLDKLDNEK145 KDLIQSDIAA155 LHHFYSKHLE 165 FPDNDSLVVL175 FAQVNCNGFT185 IEDEELSHLG195 SAIFPDVALM205 NHSCCPNVIV 215 TYKGTLAEVR225 AVQEIKPGEE235 VFTSYIDLLY245 PTEDRNDRLR255 DSYFFTCECQ 265 ECTTKDKDKA275 KVEIRKLSDP285 PKAEAIRDMV295 RYARNVIEEF305 RRAKHYKSPS 315 ELLEICELSQ325 EKMSSVFEDS335 NVYMLHMMYQ345 AMGVCLYMQD355 WEGALQYGQK 365 IIKPYSKHYP375 LYSLNVASMW385 LKLGRLYMGL395 EHKAAGEKAL405 KKAIAIMEVA 415 HGKDHPYISE425 IKQEIESH
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:16 or .A:17 or .A:18 or .A:19 or .A:129 or .A:133 or .A:135 or .A:137 or .A:181 or .A:182 or .A:203 or .A:204 or .A:205 or .A:206 or .A:207 or .A:237 or .A:240 or .A:258 or .A:259 or .A:260 or .A:261 or .A:262; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLY16
3.553
LYS17
2.899
GLY18
3.897
ARG19
2.757
LEU129
4.415
GLU133
4.783
GLU135
2.807
HIS137
2.939
CYS181
3.489
ASN182
3.223
ALA203
3.063
|
|||||
| PDB ID: 5KJN SMYD2 in complex with AZ506 | ||||||
| Method | X-ray diffraction | Resolution | 2.72 Å | Mutation | Yes | [4] |
| 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
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:135 or .A:137 or .A:181 or .A:182 or .A:203 or .A:204 or .A:205 or .A:206 or .A:207 or .A:237 or .A:240 or .A:258 or .A:259 or .A:260 or .A:261 or .A:262; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLY16
3.485
LYS17
2.835
GLY18
3.950
ARG19
2.725
GLY20
4.984
GLU135
3.254
HIS137
2.957
CYS181
3.650
ASN182
3.060
ALA203
2.924
LEU204
3.494
|
|||||
| PDB ID: 5V3H Crystal structure of SMYD2 with SAM and EPZ033294 | ||||||
| Method | X-ray diffraction | Resolution | 2.69 Å | Mutation | No | [5] |
| PDB Sequence |
KDDDDKMRAE
4 GLGGLERFCS14 PGKGRGLRAL24 QPFQVGDLLF34 SCPAYAYVLT44 VNERGNHCEY 54 CFTRKEGLSK64 CGRCKQAFYC74 NVECQKEDWP84 MHKLECSPMV94 VFGENWNPSE 104 TVRLTARILA114 KQKIHPERTP124 SEKLLAVKEF134 ESHLDKLDNE144 KKDLIQSDIA 154 ALHHFYSKHL164 GFPDNDSLVV174 LFAQVNCNGF184 TIEDEELSHL194 GSAIFPDVAL 204 MNHSCCPNVI214 VTYKGTLAEV224 RAVQEIKPGE234 EVFTSYIDLL244 YPTEDRNDRL 254 RDSYFFTCEC264 QECTTKDKDK274 AKVEIRKLSD284 PPKAEAIRDM294 VRYARNVIEE 304 FRRAKHYKSP314 SELLEICELS324 QEKMSSVFED334 SNVYMLHMMY344 QAMGVCLYMQ 354 DWEGALQYGQ364 KIIKPYSKHY374 PLYSLNVASM384 WLKLGRLYMG394 LEHKAAGEKA 404 LKKAIAIMEV414 AHGKDHPYIS424 EIKQEIES
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:135 or .A:137 or .A:181 or .A:182 or .A:203 or .A:204 or .A:205 or .A:206 or .A:207 or .A:240 or .A:258 or .A:259 or .A:260 or .A:261 or .A:262; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
||||||
| PDB ID: 4YND The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2 | ||||||
| Method | X-ray diffraction | Resolution | 2.79 Å | Mutation | No | [6] |
| PDB Sequence |
AEGLGGLERF
12 CSPGKGRGLR22 ALQPFQVGDL32 LFSCPAYAYV42 LTVNERGNHC52 EYCFTRKEGL 62 SKCGRCKQAF72 YCNVECQKED82 WPMHKLECSP92 MVVFGENWNP102 SETVRLTARI 112 LAKQKIHPER122 TPSEKLLAVK132 EFESHLDKLD142 NEKKDLIQSD152 IAALHHFYSK 162 HLGFPDNDSL172 VVLFAQVNCN182 GFTIEDEELS192 HLGSAIFPDV202 ALMNHSCCPN 212 VIVTYKGTLA222 EVRAVQEIKP232 GEEVFTSYID242 LLYPTEDRND252 RLRDSYFFTC 262 ECQECTTKDK272 DKAKVEIRKL282 SDPPKAEAIR292 DMVRYARNVI302 EEFRRAKHYK 312 SPSELLEICE322 LSQEKMSSVF332 EDSNVYMLHM342 MYQAMGVCLY352 MQDWEGALQY 362 GQKIIKPYSK372 HYPLYSLNVA382 SMWLKLGRLY392 MGLEHKAAGE402 KALKKAIAIM 412 EVAHGKDHPY422 ISEIKQEI
|
|||||
|
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:16 or .A:17 or .A:18 or .A:19 or .A:20 or .A:129 or .A:135 or .A:137 or .A:181 or .A:182 or .A:203 or .A:204 or .A:205 or .A:206 or .A:207 or .A:208 or .A:237 or .A:240 or .A:258 or .A:259 or .A:260 or .A:261 or .A:262; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLY16
3.584
LYS17
2.813
GLY18
4.264
ARG19
2.802
GLY20
4.997
LEU129
4.222
GLU135
4.463
HIS137
2.787
CYS181
3.427
ASN182
3.481
ALA203
3.238
LEU204
3.694
|
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Discovery and Characterization of a Highly Potent and Selective Aminopyrazoline-Based in Vivo Probe (BAY-598) for the Protein Lysine Methyltransferase SMYD2. J Med Chem. 2016 May 26;59(10):4578-600. | ||||
| REF 2 | Structure of human SMYD2 protein reveals the basis of p53 tumor suppressor methylation. J Biol Chem. 2011 Nov 4;286(44):38725-38737. | ||||
| REF 3 | Structural basis of substrate methylation and inhibition of SMYD2. Structure. 2011 Sep 7;19(9):1262-73. | ||||
| REF 4 | Design, Synthesis, and Biological Activity of Substrate Competitive SMYD2 Inhibitors. J Med Chem. 2016 Dec 22;59(24):11079-11097. | ||||
| REF 5 | Small molecule inhibitors and CRISPR/Cas9 mutagenesis demonstrate that SMYD2 and SMYD3 activity are dispensable for autonomous cancer cell proliferation. PLoS One. 2018 Jun 1;13(6):e0197372. | ||||
| REF 6 | Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2. ACS Med Chem Lett. 2015 Apr 29;6(6):695-700. | ||||
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