Receptor
PDB id Resolution Class Description Source Keywords
2H23 2.45 Å EC: 2.1.1.127 STRUCTURE OF RUBISCO LSMT BOUND TO TRIMETHYLLYSINE AND ADOHC PISUM SATIVUM SET DOMAIN PROTEIN LYSINE METHYLTRANSFERASE TRANSFERASE
Ref.: CATALYTIC ROLES FOR CARBON-OXYGEN HYDROGEN BONDING DOMAIN LYSINE METHYLTRANSFERASES. J.BIOL.CHEM. V. 281 19280 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
M3L A:501;
B:502;
C:500;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
189.275 C9 H21 N2 O2 C[N+]...
SAH A:800;
B:801;
C:802;
 Valid;
Valid;
Valid;
 none;
none;
none;
 Kd = 21.2 uM
384.411 C14 H20 N6 O5 S c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2H21 2.45 Å EC: 2.1.1.127 STRUCTURE OF RUBISCO LSMT BOUND TO ADOMET PISUM SATIVUM SET DOMAIN PROTEIN LYSINE METHYLTRANSFERASE TRANSFERASE
Ref.: CATALYTIC ROLES FOR CARBON-OXYGEN HYDROGEN BONDING DOMAIN LYSINE METHYLTRANSFERASES. J.BIOL.CHEM. V. 281 19280 2006
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2H21 Kd = 0.29 uM SAM C15 H22 N6 O5 S C[S@@+](CC....
2 2H23 Kd = 21.2 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 2H2J Kd = 4.2 uM SFG C15 H23 N7 O5 c1nc(c2c(n....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2H21 Kd = 0.29 uM SAM C15 H22 N6 O5 S C[S@@+](CC....
2 2H23 Kd = 21.2 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 2H2J Kd = 4.2 uM SFG C15 H23 N7 O5 c1nc(c2c(n....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2H21 Kd = 0.29 uM SAM C15 H22 N6 O5 S C[S@@+](CC....
2 2H23 Kd = 21.2 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 2H2J Kd = 4.2 uM SFG C15 H23 N7 O5 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: M3L; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 M3L 1 1
2 MLZ 0.552632 0.744186
3 LYS 0.527778 0.604651
4 MLY 0.512821 0.880952
5 MSE 0.421053 0.613636
Ligand no: 2; Ligand: SAH; Similar ligands found: 256
No: Ligand ECFP6 Tc MDL keys Tc
1 SAH 1 1
2 5X8 0.759494 0.969697
3 A7D 0.734177 0.926471
4 TT8 0.709302 0.970588
5 DSH 0.692308 0.914286
6 SXZ 0.692308 0.916667
7 DTA 0.666667 0.857143
8 3DH 0.662338 0.869565
9 S8M 0.655556 0.901408
10 U4Y 0.64 0.956522
11 SFG 0.635294 0.954545
12 SA8 0.62069 0.915493
13 EEM 0.617977 0.890411
14 MTA 0.615385 0.869565
15 SAI 0.613636 0.955882
16 S7M 0.586957 0.916667
17 36A 0.586538 0.90411
18 K15 0.583333 0.878378
19 ADN 0.573333 0.84058
20 RAB 0.573333 0.84058
21 XYA 0.573333 0.84058
22 62X 0.572917 0.855263
23 5CD 0.571429 0.852941
24 0UM 0.5625 0.876712
25 5N5 0.558442 0.84058
26 A4D 0.551282 0.867647
27 KYE 0.54902 0.866667
28 SAM 0.537634 0.916667
29 SSA 0.536842 0.712644
30 SMM 0.536842 0.88
31 KB1 0.534653 0.902778
32 A5D 0.532609 0.857143
33 SIB 0.53125 0.928571
34 EP4 0.530864 0.819444
35 DSZ 0.530612 0.732558
36 GSU 0.53 0.752941
37 LMS 0.529412 0.694118
38 AMP 0.529412 0.763158
39 A 0.529412 0.763158
40 5CA 0.525773 0.712644
41 ME8 0.524752 0.8125
42 M2T 0.52439 0.821918
43 6RE 0.523256 0.824324
44 GJV 0.522727 0.813333
45 OZP 0.518519 0.915493
46 AAT 0.515789 0.863014
47 LSS 0.515152 0.696629
48 KAA 0.514852 0.727273
49 KXW 0.514019 0.915493
50 NWW 0.5125 0.80597
51 J7C 0.511364 0.835616
52 KG4 0.51087 0.769231
53 A5A 0.510417 0.697674
54 AMP MG 0.505747 0.773333
55 SON 0.505495 0.805195
56 SRP 0.505155 0.805195
57 F0P 0.504505 0.915493
58 KH3 0.5 0.866667
59 HY8 0.5 0.890411
60 CA0 0.5 0.769231
61 AMO 0.5 0.805195
62 54H 0.5 0.681818
63 ADX 0.5 0.694118
64 5AL 0.5 0.779221
65 VMS 0.5 0.681818
66 N37 0.495495 0.9
67 HZ2 0.495413 0.890411
68 NVA LMS 0.49505 0.707865
69 AHX 0.49505 0.753086
70 TSB 0.494949 0.689655
71 53H 0.494949 0.674157
72 G5A 0.494737 0.712644
73 45A 0.494382 0.74359
74 ABM 0.494382 0.74359
75 A2D 0.494382 0.74359
76 ZAS 0.494253 0.808219
77 A6D 0.490196 0.759494
78 GEK 0.49 0.956522
79 8QN 0.49 0.779221
80 GAP 0.489583 0.769231
81 A3S 0.48913 0.884058
82 AN2 0.48913 0.734177
83 S4M 0.488889 0.831169
84 SRA 0.488636 0.746835
85 EU9 0.486486 0.825
86 LAD 0.485437 0.810127
87 52H 0.484848 0.674157
88 V2G 0.484536 0.753086
89 BA3 0.483516 0.74359
90 AP2 0.483516 0.759494
91 A12 0.483516 0.759494
92 AOC 0.483146 0.842857
93 NEC 0.483146 0.788732
94 Y3J 0.481481 0.768116
95 VRT 0.479167 0.861111
96 50T 0.478723 0.734177
97 AP5 0.478261 0.74359
98 ADP 0.478261 0.74359
99 5AS 0.478261 0.655556
100 B4P 0.478261 0.74359
101 Q34 0.477876 0.866667
102 Q2M 0.477876 0.916667
103 A3N 0.477778 0.830986
104 YSA 0.476636 0.712644
105 XAH 0.476636 0.768293
106 8LH 0.474747 0.759494
107 V47 0.474747 0.882353
108 0XU 0.473684 0.897059
109 AT4 0.473118 0.7375
110 ADP MG 0.473118 0.763158
111 ADP BEF 0.473118 0.763158
112 J4G 0.471154 0.818182
113 WAQ 0.471154 0.807692
114 NSS 0.470588 0.712644
115 8LE 0.469388 0.75
116 5AD 0.468354 0.791045
117 AU1 0.468085 0.725
118 M33 0.468085 0.734177
119 MAO 0.467391 0.797468
120 NB8 0.466667 0.775
121 A3G 0.466667 0.871429
122 N5O 0.466667 0.857143
123 TXA 0.466667 0.759494
124 3AM 0.465909 0.727273
125 Q2V 0.465517 0.902778
126 QA7 0.465347 0.75
127 8X1 0.465347 0.707865
128 DAL AMP 0.465347 0.779221
129 8LQ 0.465347 0.782051
130 A3T 0.463158 0.842857
131 ATP 0.463158 0.74359
132 ACP 0.463158 0.746835
133 HEJ 0.463158 0.74359
134 7D7 0.4625 0.785714
135 QXP 0.460784 0.697674
136 9ZA 0.460784 0.740741
137 9ZD 0.460784 0.740741
138 APR 0.458333 0.766234
139 5FA 0.458333 0.74359
140 PRX 0.458333 0.746835
141 APC 0.458333 0.759494
142 AQP 0.458333 0.74359
143 AR6 0.458333 0.766234
144 F2R 0.457627 0.75
145 R2V 0.457143 0.697674
146 IOT 0.456897 0.761905
147 N5A 0.456522 0.855072
148 PAJ 0.456311 0.722892
149 4AD 0.456311 0.794872
150 WSA 0.45614 0.72093
151 HQG 0.455446 0.75641
152 NWQ 0.454545 0.782609
153 Q2P 0.453782 0.866667
154 8PZ 0.453704 0.712644
155 FA5 0.453704 0.805195
156 AGS 0.453608 0.728395
157 APC MG 0.453608 0.766234
158 RBY 0.453608 0.782051
159 ATP MG 0.453608 0.763158
160 AD9 0.453608 0.725
161 ADV 0.453608 0.782051
162 NVA 2AD 0.453608 0.849315
163 ADP PO3 0.453608 0.763158
164 PTJ 0.45283 0.731707
165 MHZ 0.452632 0.797468
166 00A 0.451923 0.740741
167 A3P 0.451613 0.74026
168 YLP 0.451327 0.771084
169 7MD 0.45045 0.768293
170 ALF ADP 0.45 0.707317
171 BEF ADP 0.44898 0.74359
172 2VA 0.447917 0.819444
173 H1Q 0.447917 0.753247
174 LEU LMS 0.447619 0.724138
175 QXG 0.447619 0.689655
176 OOB 0.446602 0.779221
177 ACQ 0.444444 0.746835
178 T99 0.444444 0.7375
179 TAT 0.444444 0.7375
180 ANP 0.444444 0.725
181 P5A 0.443396 0.719101
182 7D5 0.443182 0.708861
183 A1R 0.442308 0.7625
184 YLC 0.439655 0.790123
185 2AM 0.438202 0.717949
186 DLL 0.438095 0.779221
187 ARG AMP 0.4375 0.759036
188 KY2 0.436893 0.84
189 D3Y 0.436893 0.859155
190 A22 0.436893 0.734177
191 ANP MG 0.435644 0.734177
192 VO4 ADP 0.435644 0.725
193 ATF 0.435644 0.716049
194 MYR AMP 0.435185 0.746988
195 80F 0.434426 0.75
196 SO8 0.434343 0.808219
197 OAD 0.433962 0.769231
198 3UK 0.433962 0.769231
199 TAD 0.433628 0.765432
200 25A 0.432692 0.74359
201 6YZ 0.431373 0.746835
202 9SN 0.431193 0.731707
203 TYM 0.431034 0.805195
204 PR8 0.429907 0.8
205 B5V 0.429907 0.759494
206 KYB 0.428571 0.84
207 ADQ 0.428571 0.746835
208 YLB 0.42735 0.771084
209 1ZZ 0.425926 0.746988
210 9K8 0.425926 0.67033
211 3OD 0.425926 0.769231
212 FYA 0.425926 0.779221
213 PPS 0.425743 0.674419
214 JNT 0.424528 0.746835
215 B1U 0.423423 0.638298
216 MAP 0.423077 0.707317
217 4YB 0.421053 0.735632
218 A2P 0.421053 0.727273
219 9X8 0.420561 0.75
220 ADP BMA 0.420561 0.746835
221 OZV 0.419048 0.74359
222 5SV 0.419048 0.731707
223 YLA 0.416667 0.771084
224 3NZ 0.416667 0.824324
225 NX8 0.415842 0.875
226 KL2 0.41573 0.692308
227 8Q2 0.415254 0.688889
228 A3R 0.415094 0.7625
229 B5M 0.414414 0.75
230 B5Y 0.414414 0.75
231 LPA AMP 0.413793 0.768293
232 48N 0.413793 0.753086
233 AYB 0.413223 0.761905
234 ACK 0.413043 0.710526
235 QQY 0.413043 0.696203
236 JB6 0.412844 0.7625
237 BIS 0.412844 0.719512
238 K2H 0.411215 0.797297
239 PAP 0.41 0.730769
240 KY5 0.409091 0.887324
241 DQV 0.408696 0.75641
242 OVE 0.408602 0.7125
243 4UV 0.40708 0.75
244 AMP DBH 0.40708 0.746835
245 3AD 0.406977 0.852941
246 OMR 0.40678 0.738095
247 AF3 ADP 3PG 0.40678 0.743902
248 K38 0.405405 0.797297
249 LAQ 0.405172 0.768293
250 K2K 0.40367 0.875
251 7C5 0.403509 0.789474
252 7MC 0.403361 0.75
253 K3K 0.401786 0.797297
254 KOY 0.401709 0.847222
255 NWZ 0.4 0.861111
256 4UU 0.4 0.75
Similar Ligands (3D)
Ligand no: 1; Ligand: M3L; Similar ligands found: 189
No: Ligand Similarity coefficient
1 NPI 0.9598
2 CIR 0.9583
3 ARG 0.9547
4 1PS 0.9494
5 DHH 0.9481
6 ABH 0.9458
7 GGB 0.9446
8 6HN 0.9439
9 DAR 0.9422
10 IAR 0.9417
11 ILO 0.9402
12 S2C 0.9386
13 TZP 0.9362
14 EXY 0.9340
15 RGP 0.9318
16 4JK 0.9300
17 WT2 0.9300
18 HAR 0.9279
19 ZZU 0.9260
20 NMM 0.9249
21 26P 0.9248
22 ENW 0.9248
23 LXP 0.9235
24 VUR 0.9214
25 5AB 0.9198
26 4DI 0.9197
27 Z70 0.9193
28 API 0.9190
29 9J6 0.9185
30 NOT 0.9183
31 AHL 0.9157
32 XRX 0.9141
33 IJ6 0.9132
34 6CL 0.9132
35 R10 0.9132
36 PML 0.9131
37 KPC 0.9130
38 PA5 0.9127
39 FB6 0.9127
40 3CX 0.9083
41 HPO 0.9081
42 5OY 0.9067
43 2NP 0.9055
44 F98 0.9049
45 NFZ 0.9047
46 2JJ 0.9046
47 4TP 0.9044
48 KAP 0.9042
49 ENV 0.9037
50 MF3 0.9029
51 A5P 0.9026
52 JX7 0.9023
53 2FM 0.9021
54 TEG 0.9013
55 2OR 0.9010
56 RED 0.9004
57 LPA 0.9002
58 1OV 0.8996
59 GVA 0.8996
60 DA2 0.8990
61 DEZ 0.8988
62 DXP 0.8983
63 S6P 0.8979
64 3KJ 0.8975
65 1HS 0.8967
66 XI7 0.8963
67 IPE 0.8957
68 FOM 0.8956
69 GHQ 0.8953
70 PAN 0.8945
71 PMV 0.8944
72 P3S 0.8943
73 NNH 0.8940
74 XRS 0.8940
75 DNN 0.8927
76 DA3 0.8921
77 HSA 0.8920
78 HE8 0.8912
79 E4P 0.8904
80 HRG 0.8903
81 R52 0.8901
82 R5P 0.8901
83 6FG 0.8899
84 8AC 0.8892
85 ALY 0.8891
86 19N 0.8890
87 GGG 0.8890
88 ATX 0.8888
89 D53 0.8883
90 6C9 0.8878
91 SB7 0.8874
92 OCA 0.8872
93 6C5 0.8869
94 KNA 0.8869
95 CLT 0.8869
96 DKA 0.8869
97 011 0.8869
98 6C4 0.8861
99 5KJ 0.8859
100 LUQ 0.8858
101 DMA 0.8848
102 N8C 0.8847
103 I58 0.8841
104 6PG 0.8839
105 EIP 0.8836
106 LL2 0.8835
107 F6R 0.8834
108 58X 0.8828
109 FXY 0.8827
110 11X 0.8827
111 9YT 0.8826
112 QFJ 0.8825
113 OJD 0.8822
114 IPR 0.8819
115 P93 0.8819
116 UN1 0.8818
117 2MR 0.8816
118 M6R 0.8813
119 5TO 0.8812
120 AGP 0.8810
121 6C8 0.8809
122 DHM 0.8807
123 G6Q 0.8802
124 BCH 0.8800
125 OOG 0.8797
126 DX5 0.8794
127 37E 0.8791
128 RES 0.8782
129 S0A 0.8776
130 2J3 0.8775
131 AOY 0.8774
132 5SP 0.8772
133 DST 0.8771
134 4FE 0.8770
135 5RP 0.8768
136 JM2 0.8760
137 7XA 0.8760
138 DIA 0.8751
139 GRQ 0.8751
140 L06 0.8748
141 1X4 0.8744
142 STV 0.8739
143 Q06 0.8739
144 KPA 0.8737
145 TX4 0.8734
146 KPV 0.8733
147 JF5 0.8732
148 5PV 0.8728
149 4TB 0.8727
150 1KJ 0.8727
151 DED 0.8725
152 9GB 0.8719
153 G6P 0.8715
154 SPD 0.8715
155 4U7 0.8714
156 5DL 0.8713
157 3GC 0.8712
158 6MW 0.8711
159 S7D 0.8710
160 VGS 0.8703
161 0L1 0.8697
162 PRO GLY 0.8697
163 SLZ 0.8696
164 5LD 0.8692
165 11C 0.8681
166 DER 0.8674
167 F6P 0.8669
168 AHN 0.8668
169 M5P 0.8667
170 3VQ 0.8660
171 OKP 0.8656
172 STX 0.8655
173 I2E 0.8653
174 IJ1 0.8653
175 LX1 0.8629
176 A51 0.8627
177 C82 0.8626
178 HLP 0.8626
179 64Z 0.8625
180 D9Z 0.8619
181 VFM 0.8614
182 JKK 0.8611
183 SB9 0.8607
184 DI9 0.8601
185 JGY 0.8588
186 GLY GLY GLY 0.8566
187 BVS 0.8562
188 DZA 0.8538
189 PNP 0.8514
Ligand no: 2; Ligand: SAH; Similar ligands found: 15
No: Ligand Similarity coefficient
1 HCE 0.9148
2 GMD 0.9105
3 IDP 0.8930
4 GDP 0.8927
5 2EL 0.8907
6 GDP MG 0.8895
7 CUU 0.8893
8 BIG 0.8840
9 M7G 0.8830
10 DAT 0.8738
11 UC5 0.8671
12 4CT 0.8669
13 DTP 0.8653
14 GNH 0.8616
15 OS3 0.8593
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2H21; Ligand: SAM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2h21.bio4) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2H21; Ligand: SAM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2h21.bio4) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2H21; Ligand: SAM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2h21.bio4) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2H21; Ligand: SAM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2h21.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2H21; Ligand: SAM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 2h21.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2H21; Ligand: SAM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2h21.bio3) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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