Receptor
PDB id Resolution Class Description Source Keywords
3DMH 1.55 Å EC: 2.1.1.- T. THERMOPHILUS 16S RRNA N2 G1207 METHYLTRANSFERASE (RSMC) I WITH ADOMET AND GUANOSINE THERMUS THERMOPHILUS MONOMETHYLTRANSERASE 16S RRNA METHYLTRANSFERASE N2 G1207 METHYLTRANSFERASE S-ADENOSYL-L-HOMOCYSTEINE TRANSLATION METHYLTRANSFERASE TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF THE THERMUS THERMOPHILUS 16 S METHYLTRANSFERASE RSMC IN COMPLEX WITH COFACTOR AND SUBSTRATE GUANOSINE. J.BIOL.CHEM. V. 283 26548 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GMP A:385;
Valid;
none;
submit data
283.241 C10 H13 N5 O5 c1nc2...
SAM A:384;
Valid;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
SO4 A:382;
A:383;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3DMH 1.55 Å EC: 2.1.1.- T. THERMOPHILUS 16S RRNA N2 G1207 METHYLTRANSFERASE (RSMC) I WITH ADOMET AND GUANOSINE THERMUS THERMOPHILUS MONOMETHYLTRANSERASE 16S RRNA METHYLTRANSFERASE N2 G1207 METHYLTRANSFERASE S-ADENOSYL-L-HOMOCYSTEINE TRANSLATION METHYLTRANSFERASE TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF THE THERMUS THERMOPHILUS 16 S METHYLTRANSFERASE RSMC IN COMPLEX WITH COFACTOR AND SUBSTRATE GUANOSINE. J.BIOL.CHEM. V. 283 26548 2008
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 60 families.
1 3DMG - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 3DMH - SAM C15 H22 N6 O5 S C[S@@+](CC....
3 3DMF - SAM C15 H22 N6 O5 S C[S@@+](CC....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 54 families.
1 3DMG - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 3DMH - SAM C15 H22 N6 O5 S C[S@@+](CC....
3 3DMF - SAM C15 H22 N6 O5 S C[S@@+](CC....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 47 families.
1 3DMG - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 3DMH - SAM C15 H22 N6 O5 S C[S@@+](CC....
3 3DMF - SAM C15 H22 N6 O5 S C[S@@+](CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GMP; Similar ligands found: 112
No: Ligand ECFP6 Tc MDL keys Tc
1 GMP 1 1
2 G 0.732394 0.866667
3 5GP 0.732394 0.866667
4 3GP 0.704225 0.853333
5 GDP 0.684211 0.88
6 GNH 0.675325 0.868421
7 GP3 0.671053 0.857143
8 GP2 0.662338 0.846154
9 GTP 0.658228 0.88
10 2GP 0.657534 0.866667
11 GSP 0.641975 0.835443
12 G2P 0.641975 0.846154
13 ALF 5GP 0.6375 0.802469
14 GMV 0.6375 0.857143
15 GPG 0.635294 0.87013
16 G1R 0.62963 0.868421
17 GCP 0.62963 0.857143
18 GAV 0.626506 0.846154
19 GKE 0.625 0.87013
20 GDC 0.625 0.87013
21 GDD 0.625 0.87013
22 GNP 0.621951 0.857143
23 9GM 0.621951 0.857143
24 ALF GDP 0.593023 0.802469
25 GDP AF3 0.593023 0.802469
26 GDP ALF 0.593023 0.802469
27 G4P 0.588235 0.866667
28 G2R 0.586207 0.846154
29 G3D 0.583333 0.866667
30 P2G 0.576923 0.815789
31 SGP 0.576923 0.78481
32 G G 0.565217 0.833333
33 GFB 0.565217 0.846154
34 GDR 0.565217 0.846154
35 GKD 0.56383 0.87013
36 P1G 0.5625 0.805195
37 0O2 0.561798 0.866667
38 YGP 0.56044 0.792683
39 G3A 0.55914 0.857143
40 6CK 0.55914 0.825
41 Y9Z 0.554348 0.817073
42 G5P 0.553191 0.857143
43 NOS 0.549296 0.940298
44 GTG 0.548387 0.825
45 JB2 0.547368 0.846154
46 GDX 0.541667 0.857143
47 GPD 0.541667 0.814815
48 U2G 0.54 0.848101
49 GCP G 0.538462 0.828947
50 GDP 7MG 0.536842 0.822785
51 35G 0.53012 0.84
52 C2E 0.53012 0.828947
53 PCG 0.53012 0.84
54 CG2 0.529412 0.848101
55 5GP 5GP 0.52381 0.815789
56 MG7 0.520548 0.957143
57 JB3 0.514852 0.835443
58 A G 0.504762 0.844156
59 G A A A 0.504762 0.857143
60 U A G G 0.5 0.844156
61 AKW 0.495146 0.783133
62 FEG 0.495146 0.77381
63 NGD 0.495146 0.846154
64 ZGP 0.490385 0.764706
65 G U 0.490385 0.835443
66 G U34 0.490385 0.825
67 GH3 0.488889 0.855263
68 DG 0.487805 0.797468
69 DGP 0.487805 0.797468
70 2MD 0.481132 0.785714
71 G C 0.481132 0.835443
72 BGO 0.480769 0.8125
73 GPX 0.478261 0.828947
74 XTS 0.472973 0.913043
75 DGI 0.471264 0.810127
76 MGD 0.46789 0.785714
77 CAG 0.46789 0.776471
78 TPG 0.45614 0.741573
79 FE9 0.455357 0.684211
80 4BW 0.454545 0.828947
81 1YD 0.454545 0.828947
82 G G G RPC 0.453704 0.7875
83 GGM 0.453704 0.792683
84 SNI 0.453333 0.898551
85 PGD 0.451327 0.814815
86 MD1 0.451327 0.785714
87 DGT 0.450549 0.810127
88 APC G U 0.45045 0.797468
89 DBG 0.443478 0.835443
90 G1R G1R 0.443478 0.835443
91 13A 0.441558 0.768293
92 GPC 0.441441 0.795181
93 PGD O 0.439655 0.75
94 DG DG 0.43299 0.802469
95 G4M 0.430894 0.797619
96 G G G C 0.429825 0.802469
97 A G C C 0.426087 0.822785
98 1YC 0.421569 0.802632
99 AD3 0.421053 0.882353
100 4UR 0.416667 0.828947
101 G C C C 0.411765 0.8125
102 XYA 0.410959 0.882353
103 RAB 0.410959 0.882353
104 ADN 0.410959 0.882353
105 G1G 0.408696 0.814815
106 1DA 0.407895 0.882353
107 AC2 0.407895 0.797297
108 IMP 0.406977 0.84
109 A G U 0.404762 0.825
110 3ZE 0.404494 0.772152
111 MZR 0.402778 0.838235
112 CFE 0.4 0.857143
Ligand no: 2; Ligand: SAM; Similar ligands found: 202
No: Ligand ECFP6 Tc MDL keys Tc
1 SAM 1 1
2 SMM 0.792683 0.96
3 S4M 0.6875 0.909091
4 S7M 0.670455 0.945946
5 M2T 0.636364 0.878378
6 GEK 0.612903 0.931507
7 SAI 0.571429 0.878378
8 ADN 0.565789 0.773333
9 RAB 0.565789 0.773333
10 XYA 0.565789 0.773333
11 5CD 0.564103 0.783784
12 EP4 0.5625 0.826667
13 SA8 0.56044 0.945205
14 SFG 0.555556 0.875
15 5X8 0.555556 0.888889
16 5N5 0.551282 0.773333
17 A4D 0.544304 0.797297
18 EEM 0.542553 0.945946
19 SAH 0.537634 0.916667
20 DTA 0.536585 0.789474
21 62X 0.535354 0.884615
22 MTA 0.53012 0.875
23 3DH 0.517647 0.849315
24 5AL 0.510417 0.743902
25 54H 0.510204 0.673913
26 VMS 0.510204 0.673913
27 0UM 0.51 0.857143
28 AMP 0.505747 0.707317
29 LMS 0.505747 0.666667
30 A 0.505747 0.707317
31 ABM 0.505618 0.753086
32 A5A 0.505155 0.688889
33 SON 0.5 0.746988
34 SSA 0.5 0.684783
35 6RE 0.5 0.78481
36 K15 0.5 0.883117
37 5AD 0.5 0.75
38 SRP 0.5 0.746988
39 LSS 0.49505 0.706522
40 CA0 0.494624 0.714286
41 A12 0.494505 0.705882
42 AP2 0.494505 0.705882
43 ME8 0.490385 0.841463
44 TSB 0.49 0.681319
45 53H 0.49 0.666667
46 DAL AMP 0.49 0.765432
47 5CA 0.49 0.684783
48 ACP 0.489362 0.694118
49 ADP 0.48913 0.690476
50 5AS 0.48913 0.648936
51 J7C 0.488889 0.772152
52 A2D 0.488889 0.690476
53 ZAS 0.488636 0.769231
54 9ZD 0.485149 0.729412
55 9ZA 0.485149 0.729412
56 8QN 0.485149 0.743902
57 GAP 0.484536 0.73494
58 AN2 0.483871 0.682353
59 A3S 0.483871 0.813333
60 A7D 0.483871 0.851351
61 GJV 0.483516 0.775
62 SRA 0.483146 0.694118
63 LAD 0.480769 0.752941
64 KAA 0.480769 0.698925
65 GSU 0.480769 0.722222
66 AMO 0.480392 0.746988
67 DSZ 0.480392 0.703297
68 52H 0.48 0.666667
69 M33 0.478723 0.722892
70 BA3 0.478261 0.690476
71 MAO 0.478261 0.82716
72 NEC 0.477778 0.75
73 AOC 0.477778 0.776316
74 DSH 0.477778 0.842105
75 SXZ 0.47619 0.894737
76 AHX 0.475728 0.701149
77 NVA LMS 0.475728 0.736264
78 Y3J 0.47561 0.706667
79 G5A 0.474227 0.684783
80 A3T 0.473684 0.8
81 B4P 0.473118 0.690476
82 AP5 0.473118 0.690476
83 A3N 0.472527 0.766234
84 KB1 0.471698 0.833333
85 PRX 0.46875 0.73494
86 APC 0.46875 0.705882
87 AT4 0.468085 0.686047
88 PAJ 0.466019 0.712644
89 4AD 0.466019 0.759036
90 RBY 0.463918 0.72619
91 ADP PO3 0.463918 0.728395
92 ADV 0.463918 0.72619
93 ADX 0.463158 0.666667
94 MHZ 0.463158 0.82716
95 AU1 0.463158 0.674419
96 YAP 0.462963 0.738095
97 TXA 0.462264 0.72619
98 NB8 0.462264 0.72093
99 A3G 0.461538 0.802632
100 VRT 0.459184 0.842105
101 XAH 0.458716 0.715909
102 YSA 0.458716 0.684783
103 HEJ 0.458333 0.690476
104 50T 0.458333 0.682353
105 ATP 0.458333 0.690476
106 LEU LMS 0.457143 0.717391
107 7D7 0.45679 0.723684
108 KH3 0.455357 0.871795
109 ACQ 0.454545 0.694118
110 AR6 0.453608 0.710843
111 APR 0.453608 0.710843
112 AQP 0.453608 0.690476
113 5FA 0.453608 0.690476
114 NSS 0.451923 0.703297
115 FA5 0.449541 0.746988
116 A5D 0.44898 0.789474
117 AD9 0.44898 0.674419
118 AGS 0.44898 0.678161
119 SAP 0.44898 0.678161
120 PTJ 0.448598 0.72093
121 YLB 0.448276 0.758621
122 YLP 0.447368 0.738636
123 8X1 0.446602 0.680851
124 D3Y 0.446602 0.792208
125 ADP ALF 0.445545 0.678161
126 ALF ADP 0.445545 0.678161
127 3AM 0.444444 0.674699
128 MYR AMP 0.444444 0.776471
129 OAD 0.443396 0.73494
130 2VA 0.443299 0.779221
131 S8M 0.442308 0.831169
132 OOB 0.442308 0.722892
133 TYR AMP 0.441441 0.759036
134 6YZ 0.441176 0.694118
135 ADP VO4 0.441176 0.702381
136 VO4 ADP 0.441176 0.702381
137 T99 0.44 0.686047
138 TAT 0.44 0.686047
139 ANP 0.44 0.674419
140 WAQ 0.439252 0.75
141 B5Y 0.436364 0.717647
142 8PZ 0.436364 0.684783
143 F0P 0.435897 0.844156
144 YLC 0.435897 0.755814
145 AAT 0.435644 0.797468
146 1ZZ 0.435185 0.755814
147 9K8 0.435185 0.663158
148 3OD 0.435185 0.73494
149 NVA 2AD 0.434343 0.855263
150 00A 0.433962 0.689655
151 DLL 0.433962 0.722892
152 ARG AMP 0.433628 0.727273
153 7MD 0.433628 0.715909
154 ATF 0.431373 0.666667
155 SO8 0.43 0.792208
156 3UK 0.429907 0.714286
157 A6D 0.429907 0.72619
158 9X8 0.429907 0.717647
159 F2R 0.429752 0.7
160 5SV 0.428571 0.741176
161 AMP DBH 0.428571 0.714286
162 TYM 0.42735 0.746988
163 WSA 0.42735 0.692308
164 9SN 0.427273 0.681818
165 AHZ 0.426087 0.755814
166 P5A 0.425926 0.691489
167 B5V 0.425926 0.705882
168 PR8 0.425926 0.744186
169 A A 0.425926 0.710843
170 3NZ 0.425926 0.807692
171 A1R 0.424528 0.709302
172 2A5 0.424242 0.674419
173 7MC 0.423729 0.719101
174 B5M 0.423423 0.717647
175 7D5 0.422222 0.658824
176 JB6 0.422018 0.709302
177 FYA 0.422018 0.722892
178 AYB 0.421488 0.75
179 A22 0.419048 0.682353
180 MAP 0.419048 0.659091
181 2AM 0.417582 0.666667
182 TAD 0.417391 0.712644
183 A3P 0.416667 0.686747
184 ADP BMA 0.416667 0.714286
185 25A 0.415094 0.690476
186 YLA 0.413223 0.719101
187 8Q2 0.411765 0.663158
188 A3R 0.411215 0.709302
189 ADQ 0.411215 0.694118
190 48N 0.410256 0.72093
191 0XU 0.41 0.824324
192 GA7 0.408696 0.72619
193 7D3 0.40625 0.643678
194 PAP 0.405941 0.678571
195 DQV 0.405172 0.702381
196 OVE 0.404255 0.662791
197 4UV 0.403509 0.697674
198 AF3 ADP 3PG 0.403361 0.712644
199 3AD 0.402299 0.783784
200 CMP 0.402062 0.691358
201 2BA 0.402062 0.682927
202 7C5 0.4 0.731707
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DMH; 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: 3dmh.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3DMH; Ligand: GMP; 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: 3dmh.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
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