Receptor
PDB id Resolution Class Description Source Keywords
2YCJ 1.96 Å EC: 2.-.-.- METHYLTRANSFERASE BOUND WITH METHYLTETRAHYDROFOLATE CARBOXYDOTHERMUS HYDROGENOFORMANS TRANSFERASE
Ref.: STRUCTURAL BASIS FOR ELECTRON AND METHYL-GROUP TRAN A METHYLTRANSFERASE SYSTEM OPERATING IN THE REDUCTI ACETYL-COA PATHWAY J.MOL.BIOL. V. 411 96 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C2F A:3000;
Valid;
none;
submit data
459.456 C20 H25 N7 O6 C[N@@...
GOL A:1268;
A:1269;
A:1270;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:1264;
A:1265;
A:1266;
A:1267;
A:1271;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
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
2YCJ 1.96 Å EC: 2.-.-.- METHYLTRANSFERASE BOUND WITH METHYLTETRAHYDROFOLATE CARBOXYDOTHERMUS HYDROGENOFORMANS TRANSFERASE
Ref.: STRUCTURAL BASIS FOR ELECTRON AND METHYL-GROUP TRAN A METHYLTRANSFERASE SYSTEM OPERATING IN THE REDUCTI ACETYL-COA PATHWAY J.MOL.BIOL. V. 411 96 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 2YCJ - C2F C20 H25 N7 O6 C[N@@]1[C@....
2 2YCK - THG C19 H23 N7 O6 c1cc(ccc1C....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 211 families.
1 2OGY Kd = 33.2 uM C2F C20 H25 N7 O6 C[N@@]1[C@....
2 2E7F Kd = 0.79 uM C2F C20 H25 N7 O6 C[N@@]1[C@....
3 2YCJ - C2F C20 H25 N7 O6 C[N@@]1[C@....
4 2YCK - THG C19 H23 N7 O6 c1cc(ccc1C....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 4O1E - C2F C20 H25 N7 O6 C[N@@]1[C@....
2 4O1F - THG C19 H23 N7 O6 c1cc(ccc1C....
3 2E7F Kd = 0.79 uM C2F C20 H25 N7 O6 C[N@@]1[C@....
4 2YCJ - C2F C20 H25 N7 O6 C[N@@]1[C@....
5 2YCK - THG C19 H23 N7 O6 c1cc(ccc1C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: C2F; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 C2F 1 1
2 FFO 0.739583 0.957747
3 TLL 0.635514 0.972603
4 THG 0.623762 0.887324
5 1YJ 0.623762 0.887324
6 THH 0.571429 0.84
7 MEF 0.555556 0.848101
8 FON 0.550459 0.957747
9 THF 0.509091 0.905405
10 1YA 0.486726 0.929577
11 9L9 0.460784 0.819444
12 3TZ 0.456897 0.696203
13 DHF 0.454545 0.887324
14 DZF 0.446429 0.756757
15 GHC 0.446429 0.658537
16 29D 0.444444 0.75
17 28Z 0.444444 0.75
18 29C 0.444444 0.75
19 83A 0.442478 0.74026
20 GHW 0.428571 0.666667
21 FOL 0.421053 0.77027
22 MHF 0.420168 0.848101
23 LYA 0.414414 0.701299
24 NHS 0.40708 0.712329
25 21V 0.405172 0.813333
26 DDF 0.405172 0.813333
27 TMF 0.403361 0.833333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YCJ; Ligand: C2F; Similar sites found: 198
This union binding pocket(no: 1) in the query (biounit: 2ycj.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WGC SIA GAL BGC 0.007677 0.44824 None
2 2XRH NIO 0.00231 0.44025 None
3 1WGC SIA GAL BGC 0.01183 0.42924 None
4 3RF4 FUN 0.003025 0.41621 None
5 2VKL MLT 0.02187 0.41544 None
6 2EB5 OXL 0.006861 0.41271 1.49813
7 1G0V NAG 0.004313 0.46767 1.84502
8 2J0W ASP 0.003147 0.43418 1.84502
9 1YHM AHD 0.003491 0.41936 1.84502
10 1KTC NGA 0.003839 0.41202 1.84502
11 4WX0 HXD 0.0009546 0.40729 1.90114
12 1NU4 MLA 0.008591 0.4456 2.06186
13 2OWZ CIT 0.003625 0.42477 2.21402
14 3B8I OXL 0.01473 0.42432 2.21402
15 2CW6 3HG 0.01066 0.42367 2.21402
16 4E28 9MZ 0.008436 0.4088 2.21402
17 1HQL GLA MBG 0.01376 0.40517 2.21402
18 4B16 NAG 0.008112 0.43768 2.25564
19 1NF8 BOG 0.004186 0.42858 2.41546
20 1SOW OXL 0.02206 0.40807 2.58303
21 4LWA Q13 0.01146 0.40706 2.58303
22 1RQH PYR 0.01332 0.40582 2.58303
23 1SS4 CIT 0.00009671 0.55999 2.61438
24 1SS4 GSH 0.0003241 0.52603 2.61438
25 4N7U 2JA 0.007875 0.43014 2.63158
26 1VR0 3SL 0.002194 0.41632 2.83401
27 1PR9 NAP 0.003337 0.42184 2.86885
28 3TKA CTN 0.001344 0.49215 2.95203
29 1KC7 PPR 0.01842 0.4006 2.95203
30 3KJI ADP 0.0008332 0.41909 3.14961
31 4AF5 CIT 0.006781 0.41293 3.15789
32 2Y7P SAL 0.005959 0.40428 3.21101
33 2QGI UDP 0.008019 0.40419 3.22581
34 1P72 THM 0.004139 0.41069 3.29341
35 4OYA 1VE 0.005734 0.45211 3.32103
36 1Z44 NPO 0.02148 0.42401 3.32103
37 3O03 GCO 0.01248 0.42029 3.32103
38 2R00 OEG 0.007214 0.41788 3.32103
39 3UH0 TSB 0.003191 0.40967 3.32103
40 1GPJ CIT 0.008656 0.40831 3.32103
41 3LTW HLZ 0.009858 0.40584 3.32103
42 1PEA ACM 0.01842 0.40536 3.32103
43 3L24 GOA 0.02813 0.40283 3.32103
44 1WRA PC 0.0158 0.40244 3.32103
45 2YIV YIV 0.02286 0.40091 3.32103
46 4RJK PYR 0.01682 0.40722 3.3275
47 4F8L GAL 0.03565 0.41199 3.44828
48 3QDY A2G GAL 0.00816 0.42207 3.4965
49 3QDV NDG 0.007467 0.41721 3.4965
50 3QDW NDG 0.00915 0.41321 3.4965
51 3QDW A2G 0.02329 0.4069 3.4965
52 3QDV A2G 0.02618 0.40438 3.4965
53 3QDY CBS 0.01486 0.40365 3.4965
54 1JGS SAL 0.02527 0.42016 3.62319
55 1HFA PIO 0.01365 0.45126 3.69004
56 2YD6 FLC 0.01344 0.42979 3.69004
57 3T7V MD0 0.01394 0.40763 3.69004
58 1A5Z OXM 0.01857 0.40519 3.69004
59 1NML CIT 0.006172 0.40366 3.69004
60 4DN8 BMA 0.008224 0.40928 3.84615
61 1ZZ7 S0H 0.002832 0.41738 4.0404
62 2YVF FAD 0.001126 0.465 4.05904
63 2YVF NAD 0.001173 0.465 4.05904
64 4WBD ADP 0.003871 0.43011 4.05904
65 2WQP WQP 0.003544 0.4127 4.05904
66 2Q8H TF4 0.01897 0.41131 4.05904
67 4LIT AKG 0.006408 0.40829 4.05904
68 2W92 NGT 0.01553 0.4061 4.05904
69 2W3L DRO 0.02312 0.40705 4.16667
70 3ACC 5GP 0.004214 0.40521 4.41989
71 3VPD BUA 0.001476 0.49691 4.42804
72 4O8A 2OP 0.002814 0.45209 4.42804
73 3U1T MLI 0.00326 0.43349 4.42804
74 3VPD CIT 0.0113 0.43026 4.42804
75 3IHB TRS 0.008932 0.41387 4.42804
76 2ZJ5 ADP 0.005162 0.41223 4.42804
77 3IHB GLU 0.0118 0.4082 4.42804
78 1SQ5 PAU 0.005212 0.40664 4.42804
79 2GDZ NAD 0.006926 0.40566 4.42804
80 3SCH TB6 0.005618 0.41649 4.54545
81 3VHZ L2P GLC MAN SGA 0.02281 0.41268 4.58015
82 2QLX RM4 0.0158 0.40244 4.62963
83 3MAG 3MA 0.006067 0.44417 4.79705
84 1Y1A GSH 0.01176 0.44176 4.79705
85 1TDF NAP 0.007305 0.43617 4.79705
86 1WDA BAG 0.0009932 0.42979 4.79705
87 1I0Z OXM 0.009285 0.42662 4.79705
88 3L6R MLI 0.00504 0.42493 4.79705
89 1TDF FAD 0.008531 0.41862 4.79705
90 2BGM NAJ 0.02602 0.40499 4.79705
91 3CQ5 PMP 0.003995 0.40612 4.87805
92 1XE7 GUN 0.005762 0.43681 4.92611
93 2VQ5 LDP 0.006552 0.43407 4.97512
94 2VQ5 HBA 0.006099 0.42119 4.97512
95 2G36 TRP 0.009121 0.40184 5
96 1JN2 SFP 0.02216 0.41567 5.06329
97 3S9K CIT 0.007471 0.44769 5.08475
98 1Y75 NAG 0.001343 0.42466 5.08475
99 1AJ0 PH2 0.000139 0.47206 5.16605
100 1AJ0 SAN 0.0000343 0.47069 5.16605
101 4QVH FLC 0.0165 0.43141 5.16605
102 1NOW IFG 0.00573 0.40497 5.16605
103 2OKK ABU 0.01916 0.40455 5.16605
104 3UBW 6SP 0.00005447 0.56527 5.36398
105 2XI7 XI7 0.001434 0.48756 5.43478
106 2IUW AKG 0.003489 0.40842 5.46218
107 3CBG FER 0.005018 0.43976 5.53506
108 1O9U ADZ 0.006778 0.43334 5.53506
109 1RYI GOA 0.04014 0.40825 5.53506
110 3CBG 4FE 0.03743 0.4033 5.53506
111 1BTN I3P 0.000413 0.52813 5.66038
112 3GM5 CIT 0.003415 0.4259 5.66038
113 3U7Y FLC 0.01732 0.43591 5.67686
114 1C3V PDC 0.003997 0.41689 5.71429
115 4NTX AMR 0.0071 0.40375 5.88235
116 2Q1A 2KT 0.0009125 0.45082 5.90406
117 3HZL 6PC 0.003759 0.44592 5.90406
118 3ZPG 5GP 0.01284 0.41968 5.90406
119 2ZWS PLM 0.02682 0.41876 5.90406
120 4JRB PGT 0.002568 0.40374 5.90406
121 1X8X TYR 0.004068 0.40095 5.90406
122 4K7O EKZ 0.005435 0.42345 5.95238
123 4NC7 I3C 0.005603 0.42285 6.06061
124 3E6J DR2 0.03335 0.40243 6.11354
125 1DL7 NCH 0.04078 0.40878 6.25
126 9LDB OXM 0.00108 0.48266 6.27306
127 9LDT OXM 0.002097 0.46788 6.27306
128 3I7S PYR 0.000933 0.46637 6.27306
129 1R37 NAD 0.003538 0.42206 6.27306
130 1CKN GTP 0.002534 0.41386 6.27306
131 1CKM GTP 0.003319 0.40927 6.27306
132 2VDJ HSE 0.003039 0.44227 6.64207
133 2HFK E4H 0.002396 0.42031 6.64207
134 1C7R PA5 0.001725 0.41508 6.64207
135 3SIX GDP 0.001573 0.41156 6.64207
136 1JAC AMG 0.007297 0.44005 6.76692
137 1SC3 MLI 0.006845 0.42567 6.81818
138 2Q09 DI6 0.004361 0.40463 6.97115
139 1V7R CIT 0.003632 0.45562 6.98925
140 4M5P MLA 0.006205 0.44367 7.01107
141 4M5P 23W 0.02198 0.40172 7.01107
142 2JBH 5GP 0.005255 0.40145 7.11111
143 1EYE PMM 0.00009326 0.49545 7.14286
144 2BZ1 TAU 0.01535 0.43195 7.14286
145 1YAG ATP 0.002994 0.41071 7.2
146 2QCX PF1 0.007914 0.40443 7.22433
147 4C1K PEP 0.001899 0.42441 7.25191
148 1XX4 BAM 0.0007278 0.48089 7.27969
149 4R33 TRP 0.001515 0.43533 7.38007
150 4R33 SAH 0.001515 0.43533 7.38007
151 4LHM AZZ 0.001652 0.43299 7.38007
152 4CIB 7UZ 0.005146 0.41229 7.38007
153 4BT5 23B 0.002171 0.41649 7.393
154 4ME6 ADP 0.001325 0.43701 7.74908
155 4TMK T5A 0.03996 0.41736 7.74908
156 1M1B SPV 0.007768 0.40477 7.74908
157 2X2T GAL NGA 0.02754 0.40329 7.74908
158 3I51 45C 0.002339 0.40523 7.77778
159 4W6Z ETF 0.003674 0.43839 8.11808
160 2B7N NTM 0.001514 0.43458 8.11808
161 1H8P PC 0.02533 0.40509 8.25688
162 4GYW UDP 0.0003538 0.46013 8.48709
163 1OIK AKG 0.002443 0.43223 8.48709
164 4N7C AEF 0.01238 0.40724 8.52273
165 1GU3 BGC BGC BGC BGC BGC 0.004215 0.41038 8.72483
166 4M51 BEZ 0.0146 0.41013 8.85609
167 2VMD MBG 0.01817 0.41224 8.94942
168 1Z45 GAL 0.002889 0.41702 9.22509
169 1UUY PPI 0.0123 0.4206 9.58084
170 1AUA BOG 0.005683 0.40511 9.5941
171 4DQ2 BTX 0.0003094 0.45641 9.7561
172 4G28 0W8 0.000918 0.43113 9.80392
173 1NX4 AKG 0.006046 0.40935 9.9631
174 1II5 GLU 0.004914 0.41313 10.3004
175 2BO4 FLC 0.007835 0.41626 10.3321
176 2VEG PMM 0.0001759 0.49547 10.5096
177 1Y2W NAG 0.003465 0.42563 10.5634
178 2C31 ADP 0.008453 0.43342 10.7011
179 2C31 TZD 0.008716 0.43342 10.7011
180 3NNF AKG 0.01058 0.4045 10.7011
181 3UEC ALA ARG TPO LYS 0.006368 0.42034 10.9589
182 2ZE3 AKG 0.001302 0.43732 11.4391
183 1OGZ EQU 0.0008359 0.42164 12
184 1UW1 ADP 0.003494 0.41935 12.5
185 1Y9Q MED 0.002079 0.43527 13.0208
186 2F01 BTN 0.01256 0.423 13.3858
187 2F01 BTQ 0.01256 0.423 13.3858
188 3BLI PYR 0.001064 0.45545 15.4982
189 3DGB MUC 0.001686 0.41045 15.8672
190 2Y5S 78H 0.005019 0.41558 16.6052
191 1AD4 HH2 0.001146 0.44028 18.4211
192 2BMB PMM 0.0006165 0.44641 18.4502
193 1Y7P RIP 0.006529 0.41365 18.8341
194 3TL1 JRO 0.01791 0.40215 18.8679
195 1X54 4AD 0.0008007 0.43399 19.1882
196 3H22 B53 0.00002795 0.52668 20.2952
197 3TYZ PAB 0.0006147 0.4712 21.0332
198 4F4S EFO 0.004651 0.40864 22.3684
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