Receptor
PDB id Resolution Class Description Source Keywords
4OQE 2.2 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF THE TYLM1 N,N-DIMETHYLTRANSFERASE IN CO SAH AND TDP-FUC3NME STREPTOMYCES FRADIAE SAM METHYLTRANSFERASE N-METHYLTRANSFERASE S-ADENOSYLMETHIOTRANSFERASE
Ref.: PRODUCTION OF A NOVEL N-MONOMETHYLATED DIDEOXYSUGAR BIOCHEMISTRY V. 53 1105 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MMF B:301;
A:301;
Valid;
Valid;
none;
none;
submit data
561.371 C17 H29 N3 O14 P2 C[C@@...
SAH B:300;
A:300;
Valid;
Valid;
none;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3PFG 1.35 Å EC: 2.-.-.- X-RAY CRYSTAL STRUCTURE THE N,N-DIMETHYLTRANSFERASE TYLM1 FR STREPTOMYCES FRADIAE IN COMPLEX WITH SAM AND DTDP-PHENOL STREPTOMYCES FRADIAE NN-DIMETHYLTRANSFERASE SAM BINDING DTDP-LINKED SUGAR BINDTRANSFERASE
Ref.: MOLECULAR ARCHITECTURE OF TYLM1 FROM STREPTOMYCES F AN N,N-DIMETHYLTRANSFERASE INVOLVED IN THE PRODUCTI DTDP-D-MYCAMINOSE . BIOCHEMISTRY V. 50 780 2011
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 307 families.
1 6M81 - TLO C16 H20 N2 O11 P2 CC1=CN(C(=....
2 4OQE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 6M83 - TLO C16 H20 N2 O11 P2 CC1=CN(C(=....
4 4OQD - QDM C18 H31 N3 O14 P2 C[C@@H]1[C....
5 3PX2 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 3PFH - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 6M82 - TLO C16 H20 N2 O11 P2 CC1=CN(C(=....
8 3PX3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
9 3PFG - SAM C15 H22 N6 O5 S C[S@@+](CC....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 275 families.
1 6M81 - TLO C16 H20 N2 O11 P2 CC1=CN(C(=....
2 4OQE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 6M83 - TLO C16 H20 N2 O11 P2 CC1=CN(C(=....
4 4OQD - QDM C18 H31 N3 O14 P2 C[C@@H]1[C....
5 3PX2 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 3PFH - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 6M82 - TLO C16 H20 N2 O11 P2 CC1=CN(C(=....
8 3PX3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
9 3PFG - SAM C15 H22 N6 O5 S C[S@@+](CC....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 212 families.
1 6M81 - TLO C16 H20 N2 O11 P2 CC1=CN(C(=....
2 4OQE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
3 6M83 - TLO C16 H20 N2 O11 P2 CC1=CN(C(=....
4 4OQD - QDM C18 H31 N3 O14 P2 C[C@@H]1[C....
5 3PX2 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 3PFH - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 6M82 - TLO C16 H20 N2 O11 P2 CC1=CN(C(=....
8 3PX3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
9 3PFG - SAM C15 H22 N6 O5 S C[S@@+](CC....
10 5BSZ - THM C10 H14 N2 O5 CC1=CN(C(=....
11 3BXO - SAM C15 H22 N6 O5 S C[S@@+](CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MMF; Similar ligands found: 61
No: Ligand ECFP6 Tc MDL keys Tc
1 MMF 1 1
2 FNF 0.83871 0.986667
3 1YF 0.83871 0.986667
4 TRH 0.802198 0.973333
5 18T 0.802198 0.973333
6 1JB 0.802198 0.973333
7 T3Q 0.784946 0.973684
8 T3F 0.784946 0.973684
9 QDM 0.770833 0.961039
10 QUH 0.754902 0.973684
11 FUH 0.754902 0.973684
12 0FX 0.731959 0.973684
13 4TG 0.72 0.986667
14 T46 0.704082 0.973333
15 DAU 0.701031 0.947368
16 TDX 0.690722 0.96
17 3R2 0.673469 0.935065
18 0N2 0.67 0.961039
19 TTP 0.659341 0.907895
20 TYD 0.651685 0.907895
21 DWN 0.627451 0.948052
22 3YN 0.627451 0.947368
23 TLO 0.6 0.909091
24 JHZ 0.598131 0.924051
25 AKM 0.598131 0.925
26 TMP 0.595506 0.894737
27 TQP 0.58871 0.879518
28 7SG 0.58871 0.879518
29 9RC 0.563107 0.802326
30 T4K 0.559055 0.891566
31 T5K 0.559055 0.891566
32 TTP MG 0.535354 0.881579
33 TBD 0.50505 0.873418
34 T5A 0.5 0.857143
35 DT DT DT 0.495327 0.907895
36 DT DT PST 0.477876 0.8625
37 0DN 0.477778 0.779221
38 DT DT DT DT DT 0.473214 0.909091
39 THM 0.47191 0.815789
40 LLT 0.47191 0.815789
41 AZD 0.462264 0.851852
42 ATY 0.457143 0.909091
43 THP 0.454545 0.881579
44 UFP 0.453608 0.825
45 5HU 0.44898 0.883117
46 T3P 0.4375 0.857143
47 TPE 0.434783 0.910256
48 BRU 0.434343 0.825
49 D3T 0.432692 0.883117
50 DUT 0.432692 0.868421
51 ATM 0.432692 0.839506
52 5IU 0.43 0.825
53 FDM 0.43 0.8375
54 NYM 0.43 0.896104
55 DT ME6 DT 0.428571 0.886076
56 TXS 0.424242 0.7625
57 DUD 0.421569 0.868421
58 4TA 0.419847 0.823529
59 T3S 0.415842 0.78481
60 BVP 0.40566 0.858974
61 ABT 0.4 0.831325
Ligand no: 2; Ligand: SAH; Similar ligands found: 231
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 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 XYA 0.573333 0.84058
20 ADN 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 A 0.529412 0.763158
36 LMS 0.529412 0.694118
37 AMP 0.529412 0.763158
38 5CA 0.525773 0.712644
39 ME8 0.524752 0.8125
40 M2T 0.52439 0.821918
41 6RE 0.523256 0.824324
42 GJV 0.522727 0.813333
43 OZP 0.518519 0.915493
44 AAT 0.515789 0.863014
45 LSS 0.515152 0.696629
46 KAA 0.514852 0.727273
47 J7C 0.511364 0.835616
48 KG4 0.51087 0.769231
49 A5A 0.510417 0.697674
50 SON 0.505495 0.805195
51 SRP 0.505155 0.805195
52 F0P 0.504505 0.915493
53 ADX 0.5 0.694118
54 5AL 0.5 0.779221
55 54H 0.5 0.681818
56 VMS 0.5 0.681818
57 KH3 0.5 0.866667
58 HY8 0.5 0.890411
59 AMO 0.5 0.805195
60 CA0 0.5 0.769231
61 N37 0.495495 0.9
62 HZ2 0.495413 0.890411
63 AHX 0.49505 0.753086
64 NVA LMS 0.49505 0.707865
65 TSB 0.494949 0.689655
66 53H 0.494949 0.674157
67 G5A 0.494737 0.712644
68 ABM 0.494382 0.74359
69 A2D 0.494382 0.74359
70 45A 0.494382 0.74359
71 ZAS 0.494253 0.808219
72 A6D 0.490196 0.759494
73 GEK 0.49 0.956522
74 8QN 0.49 0.779221
75 GAP 0.489583 0.769231
76 A3S 0.48913 0.884058
77 AN2 0.48913 0.734177
78 S4M 0.488889 0.831169
79 SRA 0.488636 0.746835
80 LAD 0.485437 0.810127
81 52H 0.484848 0.674157
82 AP2 0.483516 0.759494
83 A12 0.483516 0.759494
84 BA3 0.483516 0.74359
85 NEC 0.483146 0.788732
86 AOC 0.483146 0.842857
87 Y3J 0.481481 0.768116
88 VRT 0.479167 0.861111
89 50T 0.478723 0.734177
90 5AS 0.478261 0.655556
91 ADP 0.478261 0.74359
92 AP5 0.478261 0.74359
93 B4P 0.478261 0.74359
94 A3N 0.477778 0.830986
95 YSA 0.476636 0.712644
96 XAH 0.476636 0.768293
97 8LH 0.474747 0.759494
98 0XU 0.473684 0.897059
99 AT4 0.473118 0.7375
100 ADP MG 0.473118 0.763158
101 J4G 0.471154 0.818182
102 WAQ 0.471154 0.807692
103 NSS 0.470588 0.712644
104 8LE 0.469388 0.75
105 5AD 0.468354 0.791045
106 M33 0.468085 0.734177
107 AU1 0.468085 0.725
108 MAO 0.467391 0.797468
109 NB8 0.466667 0.775
110 A3G 0.466667 0.871429
111 TXA 0.466667 0.759494
112 N5O 0.466667 0.857143
113 3AM 0.465909 0.727273
114 8X1 0.465347 0.707865
115 8LQ 0.465347 0.782051
116 DAL AMP 0.465347 0.779221
117 ACP 0.463158 0.746835
118 ATP 0.463158 0.74359
119 A3T 0.463158 0.842857
120 HEJ 0.463158 0.74359
121 7D7 0.4625 0.785714
122 LEU LMS 0.461538 0.688889
123 9ZD 0.460784 0.740741
124 9ZA 0.460784 0.740741
125 APR 0.458333 0.766234
126 AQP 0.458333 0.74359
127 APC 0.458333 0.759494
128 AR6 0.458333 0.766234
129 PRX 0.458333 0.746835
130 5FA 0.458333 0.74359
131 F2R 0.457627 0.75
132 IOT 0.456897 0.761905
133 N5A 0.456522 0.855072
134 4AD 0.456311 0.794872
135 PAJ 0.456311 0.722892
136 WSA 0.45614 0.72093
137 HQG 0.455446 0.75641
138 FA5 0.453704 0.805195
139 8PZ 0.453704 0.712644
140 YAP 0.453704 0.794872
141 NVA 2AD 0.453608 0.849315
142 ATP MG 0.453608 0.763158
143 AD9 0.453608 0.725
144 SAP 0.453608 0.728395
145 AGS 0.453608 0.728395
146 ADP PO3 0.453608 0.763158
147 APC MG 0.453608 0.766234
148 ADV 0.453608 0.782051
149 RBY 0.453608 0.782051
150 PTJ 0.45283 0.731707
151 MHZ 0.452632 0.797468
152 00A 0.451923 0.740741
153 A3P 0.451613 0.74026
154 YLP 0.451327 0.771084
155 7MD 0.45045 0.768293
156 ALF ADP 0.45 0.707317
157 ADP ALF 0.45 0.707317
158 2VA 0.447917 0.819444
159 H1Q 0.447917 0.753247
160 OOB 0.446602 0.779221
161 ANP 0.444444 0.725
162 ACQ 0.444444 0.746835
163 TAT 0.444444 0.7375
164 T99 0.444444 0.7375
165 P5A 0.443396 0.719101
166 7D5 0.443182 0.708861
167 A1R 0.442308 0.7625
168 YLC 0.439655 0.790123
169 2AM 0.438202 0.717949
170 DLL 0.438095 0.779221
171 ARG AMP 0.4375 0.759036
172 A22 0.436893 0.734177
173 D3Y 0.436893 0.859155
174 ATF 0.435644 0.716049
175 MYR AMP 0.435185 0.746988
176 80F 0.434426 0.75
177 SO8 0.434343 0.808219
178 3UK 0.433962 0.769231
179 OAD 0.433962 0.769231
180 TAD 0.433628 0.765432
181 25A 0.432692 0.74359
182 ADP VO4 0.431373 0.734177
183 VO4 ADP 0.431373 0.734177
184 6YZ 0.431373 0.746835
185 9SN 0.431193 0.731707
186 TYM 0.431034 0.805195
187 PR8 0.429907 0.8
188 B5V 0.429907 0.759494
189 ADQ 0.428571 0.746835
190 YLB 0.42735 0.771084
191 FYA 0.425926 0.779221
192 9K8 0.425926 0.67033
193 1ZZ 0.425926 0.746988
194 3OD 0.425926 0.769231
195 PPS 0.425743 0.674419
196 B1U 0.423423 0.638298
197 MAP 0.423077 0.707317
198 4YB 0.421053 0.735632
199 A2P 0.421053 0.727273
200 ADP BMA 0.420561 0.746835
201 9X8 0.420561 0.75
202 TYR AMP 0.419643 0.794872
203 5SV 0.419048 0.731707
204 OZV 0.419048 0.74359
205 3NZ 0.416667 0.824324
206 YLA 0.416667 0.771084
207 8Q2 0.415254 0.688889
208 A3R 0.415094 0.7625
209 B5M 0.414414 0.75
210 B5Y 0.414414 0.75
211 LPA AMP 0.413793 0.768293
212 48N 0.413793 0.753086
213 AYB 0.413223 0.761905
214 ACK 0.413043 0.710526
215 QQY 0.413043 0.696203
216 BIS 0.412844 0.719512
217 JB6 0.412844 0.7625
218 PAP 0.41 0.730769
219 DQV 0.408696 0.75641
220 OVE 0.408602 0.7125
221 AMP DBH 0.40708 0.746835
222 4UV 0.40708 0.75
223 3AD 0.406977 0.852941
224 OMR 0.40678 0.738095
225 AF3 ADP 3PG 0.40678 0.743902
226 LAQ 0.405172 0.768293
227 A A 0.40367 0.74359
228 7C5 0.403509 0.789474
229 7MC 0.403361 0.75
230 KOY 0.401709 0.847222
231 4UU 0.4 0.75
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3PFG; Ligand: SAM; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 3pfg.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
1 3JWH SAH 18.894
Pocket No.: 2; Query (leader) PDB : 3PFG; 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: 3pfg.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3PFG; Ligand: TLO; Similar sites found with APoc: 1
This union binding pocket(no: 3) in the query (biounit: 3pfg.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
1 3JWH SAH 18.894
Pocket No.: 4; Query (leader) PDB : 3PFG; Ligand: TLO; 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: 3pfg.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
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