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
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: 197
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 SXZ 0.692308 0.916667
6 DSH 0.692308 0.914286
7 DTA 0.666667 0.857143
8 3DH 0.662338 0.869565
9 S8M 0.655556 0.901408
10 SFG 0.635294 0.954545
11 SA8 0.62069 0.915493
12 EEM 0.617977 0.890411
13 MTA 0.615385 0.869565
14 SAI 0.613636 0.955882
15 S7M 0.586957 0.916667
16 36A 0.586538 0.90411
17 K15 0.583333 0.878378
18 RAB 0.573333 0.84058
19 ADN 0.573333 0.84058
20 XYA 0.573333 0.84058
21 62X 0.572917 0.855263
22 5CD 0.571429 0.852941
23 0UM 0.5625 0.876712
24 5N5 0.558442 0.84058
25 A4D 0.551282 0.867647
26 SAM 0.537634 0.916667
27 SSA 0.536842 0.712644
28 SMM 0.536842 0.88
29 KB1 0.534653 0.902778
30 A5D 0.532609 0.857143
31 SIB 0.53125 0.928571
32 EP4 0.530864 0.819444
33 DSZ 0.530612 0.732558
34 GSU 0.53 0.752941
35 AMP 0.529412 0.763158
36 A 0.529412 0.763158
37 5CA 0.525773 0.712644
38 ME8 0.524752 0.8125
39 M2T 0.52439 0.821918
40 6RE 0.523256 0.824324
41 GJV 0.522727 0.813333
42 AAT 0.515789 0.863014
43 LSS 0.515152 0.696629
44 KAA 0.514852 0.727273
45 J7C 0.511364 0.835616
46 A5A 0.510417 0.697674
47 SON 0.505495 0.805195
48 SRP 0.505155 0.805195
49 5AL 0.5 0.779221
50 VMS 0.5 0.681818
51 KH3 0.5 0.866667
52 ADX 0.5 0.694118
53 CA0 0.5 0.769231
54 AMP MG 0.5 0.74359
55 AMO 0.5 0.805195
56 54H 0.5 0.681818
57 AHX 0.49505 0.753086
58 TSB 0.494949 0.689655
59 53H 0.494949 0.674157
60 G5A 0.494737 0.712644
61 A2D 0.494382 0.74359
62 ABM 0.494382 0.74359
63 ZAS 0.494253 0.808219
64 A6D 0.490196 0.759494
65 8QN 0.49 0.779221
66 GEK 0.49 0.956522
67 GAP 0.489583 0.769231
68 A3S 0.48913 0.884058
69 AN2 0.48913 0.734177
70 S4M 0.488889 0.831169
71 SRA 0.488636 0.746835
72 LAD 0.485437 0.810127
73 52H 0.484848 0.674157
74 A12 0.483516 0.759494
75 BA3 0.483516 0.74359
76 AP2 0.483516 0.759494
77 AOC 0.483146 0.842857
78 NEC 0.483146 0.788732
79 Y3J 0.481481 0.768116
80 NVA LMS 0.480392 0.696629
81 VRT 0.479167 0.861111
82 50T 0.478723 0.734177
83 5AS 0.478261 0.655556
84 B4P 0.478261 0.74359
85 ADP 0.478261 0.74359
86 AP5 0.478261 0.74359
87 A3N 0.477778 0.830986
88 YSA 0.476636 0.712644
89 XAH 0.476636 0.768293
90 0XU 0.473684 0.897059
91 WAQ 0.471154 0.807692
92 NSS 0.470588 0.712644
93 5AD 0.468354 0.791045
94 ADP MG 0.468085 0.734177
95 AU1 0.468085 0.725
96 M33 0.468085 0.734177
97 MAO 0.467391 0.797468
98 TXA 0.466667 0.759494
99 A3G 0.466667 0.871429
100 NB8 0.466667 0.775
101 3AM 0.465909 0.727273
102 DAL AMP 0.465347 0.779221
103 ATP 0.463158 0.74359
104 ADP BEF 0.463158 0.716049
105 A3T 0.463158 0.842857
106 BEF ADP 0.463158 0.716049
107 ACP 0.463158 0.746835
108 7D7 0.4625 0.785714
109 LEU LMS 0.461538 0.677778
110 APC 0.458333 0.759494
111 AQP 0.458333 0.74359
112 APR 0.458333 0.766234
113 PRX 0.458333 0.746835
114 AR6 0.458333 0.766234
115 5FA 0.458333 0.74359
116 IOT 0.456897 0.761905
117 4AD 0.456311 0.794872
118 PAJ 0.456311 0.722892
119 WSA 0.45614 0.72093
120 FA5 0.453704 0.805195
121 YAP 0.453704 0.794872
122 RBY 0.453608 0.782051
123 ADV 0.453608 0.782051
124 ADP PO3 0.453608 0.763158
125 AD9 0.453608 0.725
126 SAP 0.453608 0.728395
127 AGS 0.453608 0.728395
128 PTJ 0.45283 0.731707
129 MHZ 0.452632 0.797468
130 00A 0.451923 0.740741
131 A3P 0.451613 0.74026
132 YLP 0.451327 0.771084
133 7MD 0.45045 0.768293
134 ALF ADP 0.45 0.707317
135 ADP ALF 0.45 0.707317
136 ATP MG 0.44898 0.734177
137 2VA 0.447917 0.819444
138 OOB 0.446602 0.779221
139 ANP 0.444444 0.725
140 ACQ 0.444444 0.746835
141 TAT 0.444444 0.7375
142 P5A 0.443396 0.719101
143 7D5 0.443182 0.708861
144 ARG AMP 0.442478 0.759036
145 A1R 0.442308 0.7625
146 YLC 0.439655 0.790123
147 2AM 0.438202 0.717949
148 DLL 0.438095 0.779221
149 A22 0.436893 0.734177
150 D3Y 0.436893 0.859155
151 TYR AMP 0.436364 0.782051
152 ATF 0.435644 0.716049
153 MYR AMP 0.435185 0.746988
154 SO8 0.434343 0.808219
155 3UK 0.433962 0.769231
156 OAD 0.433962 0.769231
157 TAD 0.433628 0.765432
158 25A 0.432692 0.74359
159 ANP MG 0.431373 0.707317
160 VO4 ADP 0.431373 0.734177
161 ADP VO4 0.431373 0.734177
162 9SN 0.431193 0.731707
163 TYM 0.431034 0.805195
164 PR8 0.429907 0.8
165 ADQ 0.428571 0.746835
166 YLB 0.42735 0.771084
167 3OD 0.425926 0.769231
168 FYA 0.425926 0.779221
169 1ZZ 0.425926 0.746988
170 PPS 0.425743 0.674419
171 NVA 2AD 0.424242 0.808219
172 MAP 0.423077 0.707317
173 A2P 0.421053 0.727273
174 4YB 0.421053 0.735632
175 ADP BMA 0.420561 0.746835
176 5SV 0.419048 0.731707
177 3NZ 0.416667 0.824324
178 YLA 0.416667 0.771084
179 48N 0.413793 0.753086
180 LPA AMP 0.413793 0.768293
181 AYB 0.413223 0.761905
182 QQY 0.413043 0.696203
183 ACK 0.413043 0.710526
184 JB6 0.412844 0.7625
185 BIS 0.412844 0.719512
186 PAP 0.41 0.730769
187 OVE 0.408602 0.7125
188 4UV 0.40708 0.75
189 AMP DBH 0.40708 0.746835
190 3AD 0.406977 0.852941
191 AF3 ADP 3PG 0.40678 0.743902
192 OMR 0.40678 0.738095
193 LAQ 0.405172 0.768293
194 A A 0.40367 0.74359
195 7C5 0.403509 0.789474
196 7MC 0.403361 0.75
197 4UU 0.4 0.75
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2H21; Ligand: SAM; Similar sites found: 52
This union binding pocket(no: 1) in the query (biounit: 2h21.bio4) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4G86 BNT 0.007503 0.44516 1.76056
2 5V22 SAH 0.00007409 0.45106 2.0202
3 3N71 SFG 0.0000004063 0.48955 2.72727
4 2W5Z SAH 0.0001235 0.41455 3.125
5 5JLB SAH 0.00004082 0.51673 3.22581
6 4FMU 0UM 0.00001542 0.49631 3.23741
7 4OKD GLC GLC GLC 0.02858 0.40758 3.40909
8 4C1Q SAH 0.00001235 0.46306 3.42857
9 3BMO AX4 0.01558 0.41655 3.47222
10 1MT6 SAH 0.000001932 0.61046 3.57143
11 5AYF C7H 0.00001052 0.52667 3.80228
12 5AYF SAM 0.000009943 0.52429 3.80228
13 3M54 SAH 0.000003968 0.47201 3.83142
14 2F69 SAH 0.000002357 0.4709 3.83142
15 4J8O SAH 0.000002542 0.47042 3.83142
16 5VAC SAH 0.00003549 0.44793 3.93013
17 5VBC SAH 0.0000297 0.44352 3.93013
18 5VA6 SAH 0.00003329 0.44224 3.93013
19 5VAH SAH 0.00004046 0.43973 3.93013
20 5M5G VAL MET LEU PRO GLY ARG GLY VAL PRO 0.00001955 0.52138 4.09091
21 5M5G SAH 0.0002381 0.43239 4.09091
22 5CZY SAM 0.00009203 0.40974 4.09091
23 1SQL GUN 0.03515 0.40108 4.10959
24 4YNM SAM 0.00002073 0.46288 4.42478
25 4AU7 SAH 0.0009236 0.45461 4.45344
26 1YTM OXD 0.02796 0.40504 4.54545
27 2POC UD1 0.02292 0.40476 4.63215
28 4NVQ SAH 0.000005286 0.46266 5.26316
29 4NVQ 2OD 0.000005268 0.45713 5.26316
30 5T0K SAM 0.000009586 0.47571 5.33808
31 5JIY SAM 0.000005061 0.47735 5.47445
32 5CPR SAM 0.0007328 0.4398 5.59701
33 4K30 NLG 0.02085 0.40686 5.625
34 2R3A SAM 0.0000622 0.44711 6.33333
35 5HQ8 SAH 0.00000008526 0.53195 7.87037
36 5CCM SAM 0.00000003253 0.64438 7.94393
37 5CCM 4ZX 0.00000005037 0.64438 7.94393
38 4Z4P SAH 0.00001575 0.5357 9.03614
39 3OOI SAM 0.00004527 0.46469 9.05172
40 3HNA SAH 0.00000272 0.57806 9.40767
41 3SWC SAH 0.000006798 0.55243 9.47368
42 2RFI SAH 0.00000612 0.47527 9.47368
43 5TUZ 7L6 0.000007818 0.53696 10.3448
44 5TUZ SAM 0.000007818 0.53696 10.3448
45 3TG5 SAH 0.0000002726 0.61648 10.6236
46 3S7D SAH 0.0000001862 0.521 10.6236
47 5KJK 6T1 0.00000003242 0.64957 10.7226
48 5KJK SAM 0.00000003242 0.64957 10.7226
49 1TLG GAL 0.0118 0.41035 12
50 3F9W SAH 0.00002537 0.49385 16.2651
51 3QXY SAM 0.00000005041 0.53978 26.2806
52 3KMT SAH 0.000007512 0.55736 27.7311
Pocket No.: 2; Query (leader) PDB : 2H21; Ligand: SAM; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2H21; Ligand: SAM; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2H21; Ligand: SAM; Similar sites found: 8
This union binding pocket(no: 4) in the query (biounit: 2h21.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5EVY SAL 0.03121 0.40056 2.28311
2 3NOJ PYR 0.02769 0.42075 2.52101
3 4RL4 PPV 0.03217 0.40916 2.83019
4 1KTG AMP 0.02065 0.40844 4.34783
5 3R4S SIA 0.01817 0.40382 4.77273
6 4MTI 2DX 0.02823 0.40177 5.21739
7 3BIB PSF 0.01837 0.41887 6.89655
8 1LNX URI 0.0297 0.4007 8.64198
Pocket No.: 5; Query (leader) PDB : 2H21; Ligand: SAM; Similar sites found: 4
This union binding pocket(no: 5) in the query (biounit: 2h21.bio2) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4M6T SAM 0.02609 0.4069 3.82514
2 5TCI 79V 0.004868 0.40571 3.98551
3 1D8C SOR 0.01041 0.43488 4.09091
4 2CJU PHX 0.01667 0.41217 5.78512
Pocket No.: 6; Query (leader) PDB : 2H21; Ligand: SAM; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback