Target Binding Site Detail
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T53251 | Target Info | |||
| Target Name | Histone-lysine N-methyltransferase EHMT2 (EHMT2) | ||||
| Synonyms | Protein G9a; NG36; Lysine N-methyltransferase 1C; KMT1C; Histone H3-K9 methyltransferase 3; HLA-B-associated transcript 8; H3-K9-HMTase 3; G9A; Euchromatic histone-lysine N-methyltransferase 2; C6orf30; BAT8 | ||||
| Target Type | Preclinical Target | ||||
| Gene Name | EHMT2 | ||||
| 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: 5TTF Crystal structure of catalytic domain of G9a with MS012 | ||||||
| Method | X-ray diffraction | Resolution | 1.72 Å | Mutation | No | [1] |
| PDB Sequence |
TEKIICRDVA
927 RGYENVPIPC937 VNGVDGEPCP947 EDYKYISENC957 ETSTMNIDRN967 ITHLQHCTCV 977 DDCSSSNCLC987 GQLSIRCWYD997 KDGRLLQEFN1007 KIEPPLIFEC1017 NQACSCWRNC 1027 KNRVVQSGIK1037 VRLQLYRTAK1047 MGWGVRALQT1057 IPQGTFICEY1067 VGELISDAEA 1077 DVREDDSYLF1087 DLDEVYCIDA1101 RYYGNISRFI1111 NHLCDPNIIP1121 VRVFMLHQDL 1131 RFPRIAFFSS1141 RDIRTGEELG1151 FDYGDRFWDI1161 KSKYFTCQCG1171 SEKCKHSAEA 1181 IALEQ
|
|||||
|
|
ARG1044
4.612
MET1048
2.683
GLY1049
3.709
TRP1050
2.834
SER1084
3.276
TYR1085
2.792
ARG1109
3.157
PHE1110
3.538
ILE1111
3.806
ASN1112
2.672
HIS1113
2.949
|
|||||
| PDB ID: 5V9I Crystal structure of catalytic domain of G9a with MS0105 | ||||||
| Method | X-ray diffraction | Resolution | 1.74 Å | Mutation | No | [2] |
| PDB Sequence |
IRTEKIICRD
925 VARGYENVPI935 PCVNGVDGEP945 CPEDYKYISE955 NCETSTMNID965 RNITHLQHCT 975 CVDDCSSSNC985 LCGQLSIRCW995 YDKDGRLLQE1005 FNKIEPPLIF1015 ECNQACSCWR 1025 NCKNRVVQSG1035 IKVRLQLYRT1045 AKMGWGVRAL1055 QTIPQGTFIC1065 EYVGELISDA 1075 EADVREDDSY1085 LFDLDEVYCI1099 DARYYGNISR1109 FINHLCDPNI1119 IPVRVFMLHQ 1129 DLRFPRIAFF1139 SSRDIRTGEE1149 LGFDYGDRFW1159 DIKSKYFTCQ1169 CGSEKCKHSA 1179 EAIALE
|
|||||
|
|
ARG1044
4.599
MET1048
2.666
GLY1049
3.777
TRP1050
2.838
SER1084
3.446
TYR1085
2.736
ARG1109
3.138
PHE1110
3.325
ILE1111
3.730
ASN1112
2.790
HIS1113
2.882
|
|||||
| PDB ID: 7DCF Crystal structure of EHMT2 SET domain in complex with compound 10 | ||||||
| Method | X-ray diffraction | Resolution | 1.80 Å | Mutation | No | [3] |
| PDB Sequence |
TEKIICRDVA
927 RGYENVPIPC937 VNGVDGEPCP947 EDYKYISENC957 ETSTMNIDRN967 ITHLQHCTCV 977 DDCSSSNCLC987 CWYDKDGRLL1003 QEFNKIEPPL1013 IFECNQACSC1023 WRNCKNRVVQ 1033 SGIKVRLQLY1043 RTAKMGWGVR1053 ALQTIPQGTF1063 ICEYVGELIS1073 DAEADVREDD 1083 SYLFDLDNKE1095 VYCIDARYYG1105 NISRFINHLC1115 DPNIIPVRVF1125 MLHQDLRFPR 1135 IAFFSSRDIR1145 TGEELGFDYG1155 DRFWDIKSKY1165 FTCQCGSEKC1175 KHSAEAIALE 1185
|
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|
|
ARG1044
4.494
MET1048
2.771
GLY1049
3.798
TRP1050
2.712
GLY1051
4.993
TYR1067
4.704
SER1084
3.108
TYR1085
2.722
ARG1109
3.268
PHE1110
3.672
ILE1111
3.615
ASN1112
2.782
|
|||||
| PDB ID: 7BTV Crystal structure of EHMT2 SET domain in complex with compound 5. | ||||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [4] |
| PDB Sequence |
TEKIICRDVA
927 RGYENVPIPC937 VNGVDGEPCP947 EDYKYISENC957 ETSTMNIDRN967 ITHLQHCTCV 977 DDCSSSNCLC987 GQLSIRCWYD997 KDGRLLQEFN1007 KIEPPLIFEC1017 NQACSCWRNC 1027 KNRVVQSGIK1037 VRLQLYRTAK1047 MGWGVRALQT1057 IPQGTFICEY1067 VGELISDAEA 1077 DVREDDSYLF1087 DLDNDGEVYC1098 IDARYYGNIS1108 RFINHLCDPN1118 IIPVRVFMLH 1128 QDLRFPRIAF1138 FSSRDIRTGE1148 ELGFDYGDRF1158 WDIKSKYFTC1168 QCGSEKCKHS 1178 AEAIALEQSR1188 L
|
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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 .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:1044 or .A:1048 or .A:1049 or .A:1050 or .A:1067 or .A:1084 or .A:1085 or .A:1109 or .A:1110 or .A:1111 or .A:1112 or .A:1113 or .A:1114 or .A:1154 or .A:1158 or .A:1159 or .A:1162 or .A:1166 or .A:1167 or .A:1168 or .A:1169 or .A:1170; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG1044
4.657
MET1048
2.850
GLY1049
3.823
TRP1050
2.840
TYR1067
4.957
SER1084
3.450
TYR1085
3.053
ARG1109
3.065
PHE1110
3.588
ILE1111
3.723
ASN1112
2.820
|
|||||
| PDB ID: 7T7L Structure of human G9a SET-domain (EHMT2) in complex with covalent inhibitor (Compound 1) | ||||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [5] |
| PDB Sequence |
IICRDVARGY
930 ENVPIPCVNG940 VDGEPCPEDY950 KYISENCETS960 TMNIDRNITH970 LQHCTCVDDC 980 SSSNCLCGQL990 SIRCWYDKDG1000 RLLQEFNKIE1010 PPLIFECNQA1020 CSCWRNCKNR 1030 VVQSGIKVRL1040 QLYRTAKMGW1050 GVRALQTIPQ1060 GTFICEYVGE1070 LISDAEADVR 1080 EDDSYLFDLD1090 NGEVYCIDAR1102 YYGNISRFIN1112 HLCDPNIIPV1122 RVFMLHQDLR 1132 FPRIAFFSSR1142 DIRTGEELGF1152 DYGDRFWDIK1162 SKYFTCQCGS1172 EKCKHSAEAI 1182 ALEQSR
|
|||||
|
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:1044 or .A:1047 or .A:1048 or .A:1049 or .A:1050 or .A:1067 or .A:1084 or .A:1085 or .A:1109 or .A:1110 or .A:1111 or .A:1112 or .A:1113 or .A:1114 or .A:1154 or .A:1158 or .A:1159 or .A:1162 or .A:1166 or .A:1167 or .A:1168 or .A:1169 or .A:1170; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG1044
4.976
LYS1047
4.731
MET1048
2.896
GLY1049
3.858
TRP1050
2.845
TYR1067
4.846
SER1084
3.286
TYR1085
2.892
ARG1109
3.309
PHE1110
3.599
ILE1111
3.642
ASN1112
2.678
|
|||||
| PDB ID: 7BUC Crystal structure of EHMT2 SET domain in complex with compound 13 | ||||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [4] |
| PDB Sequence |
TEKIICRDVA
927 RGYENVPIPC937 VNGVDGEPCP947 EDYKYISENC957 ETSTMNIDRN967 ITHLQHCTCV 977 DDCSSSNCLC987 GQLSIRCWYD997 KDGRLLQEFN1007 KIEPPLIFEC1017 NQACSCWRNC 1027 KNRVVQSGIK1037 VRLQLYRTAK1047 MGWGVRALQT1057 IPQGTFICEY1067 VGELISDAEA 1077 DVREDDSYLF1087 DLDNKDGEVY1097 CIDARYYGNI1107 SRFINHLCDP1117 NIIPVRVFML 1127 HQDLRFPRIA1137 FFSSRDIRTG1147 EELGFDYGDR1157 FWDIKSKYFT1167 CQCGSEKCKH 1177 SAEAIALEQS1187 RLA
|
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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 .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:1044 or .A:1047 or .A:1048 or .A:1049 or .A:1050 or .A:1051 or .A:1084 or .A:1085 or .A:1109 or .A:1110 or .A:1111 or .A:1112 or .A:1113 or .A:1114 or .A:1154 or .A:1158 or .A:1159 or .A:1162 or .A:1166 or .A:1167 or .A:1168 or .A:1169 or .A:1170; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG1044
4.944
LYS1047
4.946
MET1048
2.785
GLY1049
3.933
TRP1050
2.665
GLY1051
4.920
SER1084
3.325
TYR1085
2.803
ARG1109
3.160
PHE1110
3.581
ILE1111
3.390
ASN1112
2.631
|
|||||
| PDB ID: 5T0K Structure of G9a SET-domain with H3K9M mutant peptide and SAM | ||||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [6] |
| PDB Sequence |
KIICRDVARG
929 YENVPIPCVN939 GVDGEPCPED949 YKYISENCET959 STMNIDRNIT969 HLQHCTCVDD 979 CSSSNCLCGQ989 LSIRCWYDKD999 GRLLQEFNKI1009 EPPLIFECNQ1019 ACSCWRNCKN 1029 RVVQSGIKVR1039 LQLYRTAKMG1049 WGVRALQTIP1059 QGTFICEYVG1069 ELISDAEADV 1079 REDDSYLFDL1089 DEVYCIDARY1103 YGNISRFINH1113 LCDPNIIPVR1123 VFMLHQDLRF 1133 PRIAFFSSRD1143 IRTGEELGFD1153 YGDRFWDIKS1163 KYFTCQCGSE1173 KCKHSAEAIA 1183 LEQS
|
|||||
|
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:1047 or .A:1048 or .A:1049 or .A:1050 or .A:1067 or .A:1084 or .A:1085 or .A:1109 or .A:1110 or .A:1111 or .A:1112 or .A:1113 or .A:1114 or .A:1154 or .A:1158 or .A:1159 or .A:1162 or .A:1166 or .A:1167 or .A:1168 or .A:1169 or .A:1170; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LYS1047
4.969
MET1048
2.738
GLY1049
3.845
TRP1050
2.822
TYR1067
4.833
SER1084
3.264
TYR1085
2.645
ARG1109
3.245
PHE1110
3.562
ILE1111
3.645
ASN1112
2.803
|
|||||
| PDB ID: 5T0M A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading | ||||||
| Method | X-ray diffraction | Resolution | 1.90 Å | Mutation | No | [6] |
| PDB Sequence |
IICRDVARGY
930 ENVPIPCVNG940 VDGEPCPEDY950 KYISENCETS960 TMNIDRNITH970 LQHCTCVDDC 980 SSSNCLCGQL990 SIRCWYDKDG1000 RLLQEFNKIE1010 PPLIFECNQA1020 CSCWRNCKNR 1030 VVQSGIKVRL1040 QLYRTAKMGW1050 GVRALQTIPQ1060 GTFICEYVGE1070 LISDAEADVR 1080 EDDSYLFDLD1090 EVYCIDARYY1104 GNISRFINHL1114 CDPNIIPVRV1124 FMLHQDLRFP 1134 RIAFFSSRDI1144 RTGEELGFDY1154 GDRFWDIKSK1164 YFTCQCGSEK1174 CKHSAEAIAL 1184
|
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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 .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:1044 or .A:1047 or .A:1048 or .A:1049 or .A:1050 or .A:1067 or .A:1084 or .A:1085 or .A:1109 or .A:1110 or .A:1111 or .A:1112 or .A:1113 or .A:1114 or .A:1154 or .A:1158 or .A:1159 or .A:1162 or .A:1166 or .A:1167 or .A:1168 or .A:1169 or .A:1170; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG1044
4.932
LYS1047
4.950
MET1048
2.679
GLY1049
3.903
TRP1050
2.775
TYR1067
4.695
SER1084
3.136
TYR1085
2.736
ARG1109
3.156
PHE1110
3.649
ILE1111
3.581
ASN1112
2.688
|
|||||
| PDB ID: 5VSC Structure of human G9a SET-domain (EHMT2) in complex with inhibitor 13 | ||||||
| Method | X-ray diffraction | Resolution | 1.40 Å | Mutation | No | [7] |
| PDB Sequence |
TEKIICRDVA
927 RGYENVPIPC937 VNGVDGEPCP947 EDYKYISENC957 ETSTMNIDRN967 ITHLQHCTCV 977 DDCSSSNCLC987 GQLSIRCWYD997 KDGRLLQEFN1007 KIEPPLIFEC1017 NQACSCWRNC 1027 KNRVVQSGIK1037 VRLQLYRTAK1047 MGWGVRALQT1057 IPQGTFICEY1067 VGELISDAEA 1077 DVREDDSYLF1087 DLDEVYCIDA1101 RYYGNISRFI1111 NHLCDPNIIP1121 VRVFMLHQDL 1131 RFPRIAFFSS1141 RDIRTGEELG1151 FDYGDRFWDI1161 KSKYFTCQCG1171 SEKCKHSAEA 1181 IALEQSRLA
|
|||||
|
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:1044 or .A:1048 or .A:1049 or .A:1050 or .A:1084 or .A:1085 or .A:1109 or .A:1110 or .A:1111 or .A:1112 or .A:1113 or .A:1114 or .A:1154 or .A:1158 or .A:1159 or .A:1162 or .A:1166 or .A:1167 or .A:1168 or .A:1169 or .A:1170; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG1044
4.530
MET1048
2.659
GLY1049
3.727
TRP1050
2.826
SER1084
3.356
TYR1085
2.791
ARG1109
3.063
PHE1110
3.639
ILE1111
3.780
ASN1112
2.878
HIS1113
2.915
|
|||||
| PDB ID: 5VSE Structure of human G9a SET-domain (EHMT2) in complex with inhibitor 17: N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine | ||||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [7] |
| PDB Sequence |
EKIICRDVAR
928 GYENVPIPCV938 NGVDGEPCPE948 DYKYISENCE958 TSTMNIDRNI968 THLQHCTCVD 978 DCSSSNCLCG988 QLSIRCWYDK998 DGRLLQEFNK1008 IEPPLIFECN1018 QACSCWRNCK 1028 NRVVQSGIKV1038 RLQLYRTAKM1048 GWGVRALQTI1058 PQGTFICEYV1068 GELISDAEAD 1078 VREDDSYLFD1088 LDNEVYCIDA1101 RYYGNISRFI1111 NHLCDPNIIP1121 VRVFMLHQDL 1131 RFPRIAFFSS1141 RDIRTGEELG1151 FDYGDRFWDI1161 KSKYFTCQCG1171 SEKCKHSAEA 1181 IALEQSRLA
|
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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 .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:1044 or .A:1047 or .A:1048 or .A:1049 or .A:1050 or .A:1084 or .A:1085 or .A:1109 or .A:1110 or .A:1111 or .A:1112 or .A:1113 or .A:1114 or .A:1154 or .A:1158 or .A:1159 or .A:1162 or .A:1166 or .A:1167 or .A:1168 or .A:1169 or .A:1170; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG1044
4.623
LYS1047
4.999
MET1048
2.689
GLY1049
3.761
TRP1050
2.794
SER1084
3.385
TYR1085
2.851
ARG1109
3.081
PHE1110
3.616
ILE1111
3.772
ASN1112
2.908
|
|||||
| PDB ID: 5JIY Structure of G9a SET-domain with Histone H3K9norLeucine mutant peptide and bound S-adenosylmethionine | ||||||
| Method | X-ray diffraction | Resolution | 1.48 Å | Mutation | No | [8] |
| PDB Sequence |
IRTEKIICRD
925 VARGYENVPI935 PCVNGVDGEP945 CPEDYKYISE955 NCETSTMNID965 RNITHLQHCT 975 CVDDCSSSNC985 LCGQLSIRCW995 YDKDGRLLQE1005 FNKIEPPLIF1015 ECNQACSCWR 1025 NCKNRVVQSG1035 IKVRLQLYRT1045 AKMGWGVRAL1055 QTIPQGTFIC1065 EYVGELISDA 1075 EADVREDDSY1085 LFDLDNKDGE1095 VYCIDARYYG1105 NISRFINHLC1115 DPNIIPVRVF 1125 MLHQDLRFPR1135 IAFFSSRDIR1145 TGEELGFDYG1155 DRFWDIKSKY1165 FTCQCGSEKC 1175 KHSAEAIALE1185 QSR
|
|||||
|
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:1044 or .A:1047 or .A:1048 or .A:1049 or .A:1050 or .A:1067 or .A:1084 or .A:1085 or .A:1109 or .A:1110 or .A:1111 or .A:1112 or .A:1113 or .A:1114 or .A:1154 or .A:1158 or .A:1159 or .A:1162 or .A:1166 or .A:1167 or .A:1168 or .A:1169 or .A:1170; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG1044
4.722
LYS1047
4.985
MET1048
2.682
GLY1049
3.795
TRP1050
2.840
TYR1067
4.857
SER1084
3.187
TYR1085
2.785
ARG1109
3.105
PHE1110
3.563
ILE1111
3.688
ASN1112
2.885
|
|||||
| PDB ID: 5JHN Structure of G9a SET-domain with Histone H3K9Ala mutant peptide and bound S-adenosylmethionine | ||||||
| Method | X-ray diffraction | Resolution | 1.67 Å | Mutation | No | [8] |
| PDB Sequence |
IRTEKIICRD
925 VARGYENVPI935 PCVNGVDGEP945 CPEDYKYISE955 NCETSTMNID965 RNITHLQHCT 975 CVDDCSSSNC985 LCGQLSIRCW995 YDKDGRLLQE1005 FNKIEPPLIF1015 ECNQACSCWR 1025 NCKNRVVQSG1035 IKVRLQLYRT1045 AKMGWGVRAL1055 QTIPQGTFIC1065 EYVGELISDA 1075 EADVREDDSY1085 LFDLDNKDGE1095 VYCIDARYYG1105 NISRFINHLC1115 DPNIIPVRVF 1125 MLHQDLRFPR1135 IAFFSSRDIR1145 TGEELGFDYG1155 DRFWDIKSKY1165 FTCQCGSEKC 1175 KHSAEAIALE1185 QSR
|
|||||
|
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:1044 or .A:1048 or .A:1049 or .A:1050 or .A:1084 or .A:1085 or .A:1109 or .A:1110 or .A:1111 or .A:1112 or .A:1113 or .A:1114 or .A:1154 or .A:1158 or .A:1159 or .A:1162 or .A:1166 or .A:1167 or .A:1168 or .A:1169 or .A:1170; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG1044
4.743
MET1048
2.833
GLY1049
3.800
TRP1050
2.806
SER1084
3.118
TYR1085
2.761
ARG1109
3.034
PHE1110
3.635
ILE1111
3.791
ASN1112
2.886
HIS1113
2.871
|
|||||
| PDB ID: 5JJ0 Structure of G9a SET-domain with Histone H3K9M peptide and excess SAH | ||||||
| Method | X-ray diffraction | Resolution | 1.72 Å | Mutation | No | [8] |
| PDB Sequence |
IRTEKIICRD
925 VARGYENVPI935 PCVNGVDGEP945 CPEDYKYISE955 NCETSTMNID965 RNITHLQHCT 975 CVDDCSSSNC985 LCGQLSIRCW995 YDKDGRLLQE1005 FNKIEPPLIF1015 ECNQACSCWR 1025 NCKNRVVQSG1035 IKVRLQLYRT1045 AKMGWGVRAL1055 QTIPQGTFIC1065 EYVGELISDA 1075 EADVREDDSY1085 LFDLDNKDGE1095 VYCIDARYYG1105 NISRFINHLC1115 DPNIIPVRVF 1125 MLHQDLRFPR1135 IAFFSSRDIR1145 TGEELGFDYG1155 DRFWDIKSKY1165 FTCQCGSEKC 1175 KHSAEAIALE1185 QSR
|
|||||
|
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:1044 or .A:1047 or .A:1048 or .A:1049 or .A:1050 or .A:1067 or .A:1084 or .A:1085 or .A:1109 or .A:1110 or .A:1111 or .A:1112 or .A:1113 or .A:1114 or .A:1154 or .A:1158 or .A:1159 or .A:1162 or .A:1166 or .A:1167 or .A:1168 or .A:1169 or .A:1170; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG1044
4.727
LYS1047
4.949
MET1048
2.794
GLY1049
3.770
TRP1050
2.854
TYR1067
4.921
SER1084
3.147
TYR1085
3.080
ARG1109
3.069
PHE1110
3.600
ILE1111
3.847
ASN1112
2.938
|
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| PDB ID: 5JIN Structure of G9a SET-domain with Histone H3K9M mutant peptide and bound S-adenosylmethionine | ||||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [8] |
| PDB Sequence |
IRTEKIICRD
925 VARGYENVPI935 PCVNGVDGEP945 CPEDYKYISE955 NCETSTMNID965 RNITHLQHCT 975 CVDDCSSSNC985 LCGQLSIRCW995 YDKDGRLLQE1005 FNKIEPPLIF1015 ECNQACSCWR 1025 NCKNRVVQSG1035 IKVRLQLYRT1045 AKMGWGVRAL1055 QTIPQGTFIC1065 EYVGELISDA 1075 EADVREDDSY1085 LFDLDNKDGE1095 VYCIDARYYG1105 NISRFINHLC1115 DPNIIPVRVF 1125 MLHQDLRFPR1135 IAFFSSRDIR1145 TGEELGFDYG1155 DRFWDIKSKY1165 FTCQCGSEKC 1175 KHSAEAIALE1185 QSR
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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 .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:1044 or .A:1048 or .A:1049 or .A:1050 or .A:1067 or .A:1084 or .A:1085 or .A:1109 or .A:1110 or .A:1111 or .A:1112 or .A:1113 or .A:1114 or .A:1154 or .A:1158 or .A:1159 or .A:1162 or .A:1166 or .A:1167 or .A:1168 or .A:1169 or .A:1170; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG1044
4.646
MET1048
2.709
GLY1049
3.856
TRP1050
2.781
TYR1067
4.781
SER1084
3.204
TYR1085
2.996
ARG1109
3.220
PHE1110
3.637
ILE1111
3.796
ASN1112
2.846
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| PDB ID: 5TUY Structure of human G9a SET-domain (EHMT2) in complex with inhibitor MS0124 | ||||||
| Method | X-ray diffraction | Resolution | 2.60 Å | Mutation | No | [1] |
| PDB Sequence |
IICRDVARGY
930 ENVPIPCVNG940 VDGEPCPEDY950 KYISENCETS960 TMNIDRNITH970 LQHCTCVDDC 980 SSSNCLCGQL990 SIRCWYDKDG1000 RLLQEFNKIE1010 PPLIFECNQA1020 CSCWRNCKNR 1030 VVQSGIKVRL1040 QLYRTAKMGW1050 GVRALQTIPQ1060 GTFICEYVGE1070 LISDAEADVR 1080 EDDSYLFDLD1090 NKDGEVYCID1100 ARYYGNISRF1110 INHLCDPNII1120 PVRVFMLHQD 1130 LRFPRIAFFS1140 SRDIRTGEEL1150 GFDYGDRFWD1160 IKSKYFTCQC1170 GSEKCKHSAE 1180 AIALEQS
|
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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 .SAM or .SAM2 or .SAM3 or :3SAM;style chemicals stick;color identity;select .A:1044 or .A:1048 or .A:1049 or .A:1050 or .A:1084 or .A:1085 or .A:1109 or .A:1110 or .A:1111 or .A:1112 or .A:1113 or .A:1114 or .A:1154 or .A:1158 or .A:1159 or .A:1162 or .A:1166 or .A:1167 or .A:1168 or .A:1169 or .A:1170; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ARG1044
4.882
MET1048
2.755
GLY1049
3.715
TRP1050
2.683
SER1084
3.184
TYR1085
2.709
ARG1109
3.083
PHE1110
3.767
ILE1111
3.906
ASN1112
2.942
HIS1113
2.760
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Discovery of Potent and Selective Inhibitors for G9a-Like Protein (GLP) Lysine Methyltransferase. J Med Chem. 2017 Mar 9;60(5):1876-1891. | ||||
| REF 2 | Crystal structure of catalytic domain of G9a with MS0105 | ||||
| REF 3 | Discovery of DS79932728: A Potent, Orally Available G9a/GLP Inhibitor for Treating beta-Thalassemia and Sickle Cell Disease. ACS Med Chem Lett. 2020 Dec 28;12(1):121-128. | ||||
| REF 4 | Discovery of novel histone lysine methyltransferase G9a/GLP (EHMT2/1) inhibitors: Design, synthesis, and structure-activity relationships of 2,4-diamino-6-methylpyrimidines. Bioorg Med Chem Lett. 2020 Oct 15;30(20):127475. | ||||
| REF 5 | Discovery of the First-in-Class G9a/GLP Covalent Inhibitors. J Med Chem. 2022 Aug 11;65(15):10506-10522. | ||||
| REF 6 | A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading. Elife. 2016 Sep 20;5:e17903. | ||||
| REF 7 | Structure-activity relationship studies of G9a-like protein (GLP) inhibitors. Bioorg Med Chem. 2017 Aug 15;25(16):4414-4423. | ||||
| REF 8 | S-adenosyl methionine is necessary for inhibition of the methyltransferase G9a by the lysine 9 to methionine mutation on histone H3. Proc Natl Acad Sci U S A. 2016 May 31;113(22):6182-7. | ||||
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