Receptor
PDB id Resolution Class Description Source Keywords
4IWN 1.73 Å EC: 2.1.1.- CRYSTAL STRUCTURE OF A PUTATIVE METHYLTRANSFERASE CMOA IN CO A NOVEL SAM DERIVATIVE ESCHERICHIA COLI PUTATIVE TRNA MODIFICATION ENZYME SCM-SAH TRANSFERASE
Ref.: S-ADENOSYL-S-CARBOXYMETHYL-L-HOMOCYSTEINE: A NOVEL FOUND IN THE PUTATIVE TRNA-MODIFYING ENZYME CMOA. ACTA CRYSTALLOGR.,SECT.D V. 69 1090 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MPD A:302;
B:302;
 Invalid;
Invalid;
 none;
none;
 submit data
118.174 C6 H14 O2 C[C@@...
GEK B:301;
A:301;
 Valid;
Valid;
 none;
none;
 submit data
442.447 C16 H22 N6 O7 S c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4IWN 1.73 Å EC: 2.1.1.- CRYSTAL STRUCTURE OF A PUTATIVE METHYLTRANSFERASE CMOA IN CO A NOVEL SAM DERIVATIVE ESCHERICHIA COLI PUTATIVE TRNA MODIFICATION ENZYME SCM-SAH TRANSFERASE
Ref.: S-ADENOSYL-S-CARBOXYMETHYL-L-HOMOCYSTEINE: A NOVEL FOUND IN THE PUTATIVE TRNA-MODIFYING ENZYME CMOA. ACTA CRYSTALLOGR.,SECT.D V. 69 1090 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 57 families.
1 4IWN - GEK C16 H22 N6 O7 S c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 50 families.
1 4IWN - GEK C16 H22 N6 O7 S c1nc(c2c(n....
2 1IM8 - SAI C14 H20 N6 O5 Se c1nc(c2c(n....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 44 families.
1 4IWN - GEK C16 H22 N6 O7 S c1nc(c2c(n....
2 1IM8 - SAI C14 H20 N6 O5 Se c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GEK; Similar ligands found: 170
No: Ligand ECFP6 Tc MDL keys Tc
1 GEK 1 1
2 S7M 0.62766 0.931507
3 SAM 0.612903 0.931507
4 M2T 0.571429 0.837838
5 S4M 0.549451 0.846154
6 SMM 0.545455 0.894737
7 RAB 0.52439 0.805556
8 XYA 0.52439 0.805556
9 ADN 0.52439 0.805556
10 5CD 0.52381 0.816901
11 A4D 0.52381 0.830986
12 EP4 0.523256 0.786667
13 5N5 0.511905 0.805556
14 4AD 0.509615 0.810127
15 5X8 0.505155 0.927536
16 DTA 0.5 0.821918
17 SA8 0.494949 0.878378
18 SAI 0.49 0.915493
19 SAH 0.49 0.956522
20 SFG 0.489796 0.913043
21 3DH 0.483516 0.833333
22 5AL 0.480392 0.772152
23 EEM 0.480392 0.88
24 AMP MG 0.478723 0.7375
25 NEC 0.478723 0.756757
26 MTA 0.477778 0.833333
27 A2D 0.473684 0.7375
28 A 0.473118 0.734177
29 ZAS 0.473118 0.8
30 AMP 0.473118 0.734177
31 SRP 0.471154 0.797468
32 GAP 0.470588 0.78481
33 A7D 0.469388 0.887324
34 SON 0.469388 0.797468
35 SRA 0.468085 0.719512
36 6RE 0.468085 0.815789
37 NSS 0.46729 0.747126
38 CA0 0.464646 0.7625
39 BA3 0.463918 0.7375
40 A12 0.463918 0.753086
41 AP2 0.463918 0.753086
42 ME8 0.463636 0.804878
43 DSH 0.463158 0.876712
44 62X 0.462963 0.822785
45 DAL AMP 0.462264 0.794872
46 G5A 0.460784 0.727273
47 50T 0.46 0.707317
48 ADP 0.459184 0.7375
49 AP5 0.459184 0.7375
50 5AS 0.459184 0.67033
51 B4P 0.459184 0.7375
52 K15 0.458716 0.844156
53 J7C 0.458333 0.802632
54 ABM 0.458333 0.716049
55 8QN 0.457944 0.772152
56 LAD 0.454545 0.802469
57 AN2 0.454545 0.728395
58 AMO 0.453704 0.797468
59 0UM 0.453704 0.842105
60 PAJ 0.453704 0.717647
61 GJV 0.453608 0.805195
62 AGS 0.45098 0.722892
63 AD9 0.45098 0.719512
64 SAP 0.45098 0.722892
65 SXZ 0.45045 0.905405
66 ADP MG 0.45 0.75
67 NVA LMS 0.449541 0.730337
68 MAO 0.44898 0.768293
69 AOC 0.447917 0.808219
70 A5A 0.447619 0.712644
71 KB1 0.446429 0.866667
72 ACP 0.445545 0.740741
73 ADP BEF 0.445545 0.731707
74 BEF ADP 0.445545 0.731707
75 ATP 0.445545 0.7375
76 SSA 0.443396 0.727273
77 A3N 0.443299 0.797297
78 PRX 0.441176 0.719512
79 APR 0.441176 0.759494
80 AR6 0.441176 0.759494
81 APC 0.441176 0.753086
82 AQP 0.441176 0.7375
83 5FA 0.441176 0.7375
84 54H 0.439252 0.696629
85 VMS 0.439252 0.696629
86 52H 0.439252 0.688889
87 YAP 0.438596 0.7875
88 NB8 0.4375 0.768293
89 3OD 0.4375 0.7625
90 PTJ 0.4375 0.72619
91 RBY 0.436893 0.775
92 ADP PO3 0.436893 0.779221
93 ADV 0.436893 0.775
94 DLL 0.436364 0.772152
95 ADX 0.435644 0.709302
96 M33 0.435644 0.728395
97 MHZ 0.435644 0.768293
98 AU1 0.435644 0.719512
99 5CA 0.435185 0.727273
100 A22 0.435185 0.728395
101 TSB 0.435185 0.704545
102 53H 0.435185 0.688889
103 A3G 0.43299 0.835616
104 ATP MG 0.432692 0.75
105 OAD 0.432432 0.7625
106 3AM 0.431579 0.7
107 OOB 0.431193 0.772152
108 5SV 0.431193 0.705882
109 5AD 0.430233 0.757143
110 ADP VO4 0.429907 0.75
111 VO4 ADP 0.429907 0.75
112 ANP MG 0.429907 0.722892
113 ACQ 0.428571 0.740741
114 KAA 0.428571 0.741573
115 GSU 0.428571 0.767442
116 LSS 0.427273 0.711111
117 DSZ 0.427273 0.747126
118 Y3J 0.426966 0.736111
119 FA5 0.426087 0.797468
120 A3S 0.425743 0.847222
121 7D7 0.425287 0.753425
122 YLP 0.425 0.764706
123 TXA 0.424779 0.753086
124 AHX 0.423423 0.746988
125 A5D 0.423077 0.821918
126 TYR AMP 0.422414 0.797468
127 MYR AMP 0.421053 0.761905
128 2AM 0.421053 0.691358
129 ADP ALF 0.420561 0.722892
130 ALF ADP 0.420561 0.722892
131 KH3 0.420168 0.833333
132 LEU LMS 0.419643 0.711111
133 VRT 0.419048 0.826667
134 S8M 0.418182 0.864865
135 25A 0.418182 0.7375
136 A3T 0.417476 0.808219
137 AHZ 0.416667 0.761905
138 ARG AMP 0.416667 0.77381
139 WAQ 0.415929 0.8
140 ANP 0.415094 0.719512
141 TAT 0.415094 0.731707
142 YLB 0.414634 0.764706
143 ADQ 0.414414 0.740741
144 48N 0.413223 0.746988
145 1ZZ 0.412281 0.741176
146 JB6 0.412281 0.756098
147 AAT 0.411215 0.828947
148 PLP AAD 0.410853 0.711111
149 00A 0.410714 0.73494
150 XAH 0.410256 0.761905
151 YSA 0.410256 0.727273
152 NVA 2AD 0.409524 0.8
153 25L 0.408696 0.728395
154 OVE 0.408163 0.686747
155 ATF 0.407407 0.710843
156 A6D 0.40708 0.753086
157 3UK 0.40708 0.7625
158 ADP BMA 0.40708 0.7625
159 A3P 0.405941 0.734177
160 SO8 0.40566 0.776316
161 9SN 0.405172 0.72619
162 2VA 0.403846 0.786667
163 A A 0.403509 0.7375
164 P5A 0.403509 0.733333
165 PR8 0.403509 0.792683
166 7C5 0.403361 0.782051
167 YLC 0.403226 0.783133
168 A1R 0.401786 0.756098
169 AYB 0.401575 0.755814
170 FYA 0.4 0.75
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4IWN; Ligand: GEK; Similar sites found: 216
This union binding pocket(no: 1) in the query (biounit: 4iwn.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1LSS NAD 0.00008021 0.4826 None
2 2HMT NAI 0.0004418 0.44736 None
3 5XKR BZE 0.01129 0.4161 None
4 4N49 SAM 0.001138 0.43403 1.74672
5 5JAQ NAI 0.01032 0.40635 1.74672
6 2JHP SAH 0.0008289 0.45222 2.18341
7 3CH6 NAP 0.01348 0.41688 2.18341
8 1ZX5 LFR 0.01834 0.40886 2.18341
9 3GEG NAD 0.0009232 0.40743 2.18341
10 4XNV BUR 0.03155 0.40481 2.18341
11 4A3X LAT 0.0195 0.41398 2.20264
12 4POO SAM 0.0003435 0.44137 2.5
13 5KVA SAM 0.0006997 0.4317 2.51799
14 3S1S SAH 0.0001003 0.46965 2.62009
15 4LH7 1X8 0.008651 0.43887 2.62009
16 4FC7 COA 0.007026 0.4165 2.62009
17 4RDH AMP 0.006537 0.41558 2.62009
18 5ITV NAI 0.005775 0.40824 2.62009
19 4X7Y SAH 0.01054 0.40785 2.62009
20 5EZ7 FAD 0.01167 0.40403 2.62009
21 2HK9 ATR 0.02138 0.40235 2.62009
22 2ZWI C5P 0.02364 0.40018 2.62009
23 2PXX SAH 0.0000004587 0.58389 2.7907
24 2VDV SAM 0.000001131 0.59593 2.84553
25 5F2K SAH 0.000002457 0.55161 3.05677
26 5F2K OCA 0.000002457 0.55161 3.05677
27 1KYZ SAH 0.00002198 0.51714 3.05677
28 2BZG SAH 0.0001307 0.48313 3.05677
29 4E70 N7I 0.00009542 0.43282 3.05677
30 1KYZ FER 0.0005924 0.41718 3.05677
31 3FWY ADP 0.009061 0.40554 3.05677
32 4OUE IPT 0.02938 0.40449 3.05677
33 5N5D SAM 0.0001648 0.44759 3.09735
34 3HVJ 705 0.00001769 0.42622 3.16742
35 3MQ2 SAH 0.00005339 0.50566 3.21101
36 5IL1 SAM 0.0003072 0.46683 3.49345
37 5K7U SAM 0.0003398 0.46491 3.49345
38 5KXE 6Y2 0.01626 0.41778 3.49345
39 1Y8Q ATP 0.002545 0.41268 3.49345
40 3JWH SAH 0.00000001437 0.69518 3.68664
41 2UYQ SAM 0.000003633 0.61891 3.93013
42 5JJR SAH 0.00004798 0.50225 3.93013
43 1BC5 SAH 0.0001924 0.45817 3.93013
44 3TKA SAM 0.0003685 0.45468 3.93013
45 4MO2 FDA 0.008889 0.40714 3.93013
46 4GLW 0XT 0.02501 0.40283 3.93013
47 3BGD SAH 0.0003479 0.44774 4.23077
48 3BGD PM6 0.0004535 0.42023 4.23077
49 4AZT SAM 0.00000006938 0.62697 4.36681
50 4AZW SAM 0.000000304 0.59157 4.36681
51 5DNK SAH 0.0000001737 0.49989 4.36681
52 3PT9 SAH 0.0002286 0.47247 4.36681
53 2HNK SAH 0.0002938 0.45883 4.36681
54 3C6K MTA 0.0006328 0.45528 4.36681
55 1UWK NAD 0.00129 0.45168 4.36681
56 1YXM ADE 0.003816 0.44183 4.36681
57 1V59 NAD 0.01147 0.41174 4.36681
58 1R6D DAU 0.01579 0.40829 4.36681
59 1R6D NAD 0.01639 0.40829 4.36681
60 3A27 SAM 0.00001535 0.52399 4.80349
61 5JGL SAM 0.0000007876 0.51848 4.80349
62 1KPG SAH 0.00001805 0.50477 4.80349
63 1SQF SAM 0.00005507 0.49962 4.80349
64 2ZIF SAM 0.00008561 0.4862 4.80349
65 3FPF TNA 0.00005065 0.40603 4.80349
66 3FPF MTA 0.00005065 0.40603 4.80349
67 4RL4 PPV 0.04138 0.40025 5.18868
68 4KRG SAH 0.00000005063 0.64128 5.24017
69 5F8F SFG 0.000001367 0.58437 5.24017
70 1KPH SAH 0.00002254 0.50078 5.24017
71 5BW4 SAM 0.00001105 0.4782 5.24017
72 1U2Z SAH 0.00009481 0.47063 5.24017
73 3FZG SAM 0.00005951 0.50922 5.5
74 5DX1 SFG 0.0000005684 0.56563 5.67686
75 5DWQ SFG 0.0000007884 0.55744 5.67686
76 5DX0 SFG 0.0000009449 0.55659 5.67686
77 5DX8 SFG 0.0000008303 0.55406 5.67686
78 5DXA SFG 0.000001144 0.54842 5.67686
79 3VSE SAH 0.00004738 0.52629 5.67686
80 1Q0S SAH 0.0004299 0.43771 5.67686
81 2IZ1 ATR 0.01041 0.42767 5.67686
82 4D7E FAD 0.003134 0.42552 5.67686
83 1P7T PYR 0.02093 0.40491 5.67686
84 1ZGA SAH 0.00001835 0.53917 5.88235
85 4XUC SAM 0.00001153 0.52661 5.9633
86 4XUC 43G 0.00001153 0.52661 5.9633
87 5X62 SAH 0.00000001704 0.66249 6.11354
88 3GWZ SAH 0.00000539 0.56413 6.11354
89 5E72 SAM 0.000001579 0.53558 6.11354
90 3GXO SAH 0.00002454 0.52686 6.11354
91 4R6W SAH 0.0000001824 0.50803 6.11354
92 5ULP KB1 0.000007481 0.5069 6.11354
93 2PX8 SAH 0.0001419 0.48157 6.11354
94 5CUQ NSC 0.0001134 0.48148 6.11354
95 3LKZ SFG 0.0001459 0.47623 6.11354
96 3L9W AMP 0.0001442 0.42176 6.11354
97 3L9W GSH 0.0005397 0.41231 6.11354
98 4R6W PC 0.0000006515 0.40258 6.11354
99 4Y7E BMA BMA BMA 0.01825 0.4009 6.35838
100 3OU2 SAH 0.000002293 0.51847 6.42202
101 5T67 JHZ 0.00002137 0.53016 6.55022
102 5T67 SAH 0.00001796 0.52715 6.55022
103 3TKY SAH 0.000003547 0.50813 6.55022
104 1G60 SAM 0.00002878 0.50656 6.55022
105 1QAN SAH 0.00002005 0.50288 6.55022
106 1NW5 SAM 0.0002058 0.46981 6.55022
107 3P9C SAH 0.00002528 0.44325 6.55022
108 3VYW SAM 0.001265 0.4321 6.55022
109 3RKR NAP 0.005565 0.43127 6.55022
110 4LWP SAH 0.0000004683 0.59055 6.9869
111 5MW4 5JU 0.00002074 0.52444 6.9869
112 3QOX SAH 0.0000125 0.50631 6.9869
113 1X87 NAD 0.001432 0.42281 6.9869
114 4UCI SAM 0.001698 0.40852 6.9869
115 1P1C SAH 0.0007318 0.43464 7.03518
116 2EJU SAH 0.000001792 0.56496 7.42358
117 1JG3 ADN 0.00003917 0.50612 7.42358
118 4KIB SAH 0.000001802 0.50321 7.42358
119 4BLW SAH 0.0002429 0.43767 7.42358
120 4BLW AMP 0.0001828 0.40956 7.42358
121 4DMG SAM 0.00000393 0.57819 7.86026
122 5E1M SAH 0.00000929 0.53061 7.86026
123 5E1M PRO PRO LYS ARG ILE ALA 0.00000929 0.53061 7.86026
124 3EVG SAH 0.00002637 0.51367 7.86026
125 1G55 SAH 0.0000258 0.5086 8.29694
126 4RPL FAD 0.009061 0.42609 8.29694
127 4RPL 3UC 0.01127 0.42357 8.29694
128 5GM1 SAH 0.00000003251 0.61112 8.41751
129 4JLS 3ZE 0.01966 0.41382 8.55263
130 5XVK SAH 0.00002781 0.49223 8.73362
131 2DPM SAM 0.000095 0.47496 8.73362
132 5XLX SAH 0.0003438 0.4297 8.73362
133 3H8V ATP 0.005006 0.41356 8.73362
134 3LCV SAM 0.00003028 0.49073 8.8968
135 1FP1 SAH 0.0000003871 0.6095 9.17031
136 1XTP SAI 0.000002998 0.55514 9.17031
137 5FTW SAH 0.0000122 0.51708 9.17031
138 2P41 SAH 0.00003193 0.51002 9.17031
139 5XVQ SAH 0.00005699 0.4796 9.17031
140 1UAY ADN 0.0009094 0.45966 9.17031
141 1Q9I TEO 0.0178 0.40874 9.17031
142 5U8U FAD 0.0326 0.40098 9.17031
143 3H2B SAH 0.000001245 0.56524 9.35961
144 1XCL SAH 0.0001182 0.4278 9.3617
145 5HJM MTA 0.000004656 0.54059 9.60699
146 5THY SAH 0.000006664 0.52816 9.60699
147 3Q87 SAM 0.0000243 0.49461 9.60699
148 1DL5 SAH 0.00002439 0.47248 9.60699
149 2OBF F83 0.00003154 0.40297 9.60699
150 2OBF SAH 0.00003154 0.40297 9.60699
151 2OG2 MLI 0.01499 0.40165 9.60699
152 4NEC SAH 0.0000006019 0.6007 10.0437
153 5MPT SAH 0.000004055 0.54937 10.0437
154 3PFG TLO 0.0000002092 0.46413 10.0437
155 3PFG SAM 0.002745 0.46176 10.0437
156 1V5F FAD 0.02223 0.40812 10.0437
157 4YNU FAD 0.01737 0.40095 10.0437
158 3P2E SAH 0.0000197 0.50831 10.2222
159 1L1E SAH 0.00001115 0.51874 10.4803
160 1TPY SAH 0.00002385 0.49977 10.4803
161 5LOG SAH 0.00007771 0.46032 10.4803
162 2PT9 S4M 0.0007521 0.42312 10.4803
163 4PIO AVI 0.00006589 0.4234 10.917
164 4PIO SAH 0.00005638 0.42104 10.917
165 4YMH SAH 0.00002514 0.50384 11.3537
166 2Q28 ADP 0.001046 0.43942 11.3537
167 2REG CHT 0.01064 0.4061 11.3537
168 1R18 SAH 0.000002147 0.543 11.8943
169 4II2 ATP 0.002362 0.42065 12.2271
170 3LST SAH 0.000006131 0.5615 12.6638
171 1XDS SAM 0.000008951 0.5538 13.1004
172 5L95 AMP 0.002312 0.40313 13.75
173 2A14 SAH 0.00002603 0.4982 14.4105
174 1V6A TRE 0.01909 0.41496 14.4105
175 3BXO SAM 0.000000002231 0.72279 14.8472
176 2YX1 SFG 0.000003426 0.4776 14.8472
177 3A25 SAM 0.000191 0.47589 15.7205
178 3C3Y SAH 0.0005455 0.45159 15.7205
179 5THZ SAH 0.00001609 0.50186 15.8025
180 1F3L SAH 0.00000008558 0.60084 16.5939
181 2AOT SAH 0.000002108 0.57574 17.0306
182 1JQD SAH 0.00001182 0.46553 17.0306
183 1JQD HSM 0.0000834 0.45119 17.0306
184 4DCM SAM 0.00001134 0.54223 17.9039
185 1QZZ SAM 0.00004716 0.51995 18.7773
186 3DXY SAM 0.000006563 0.5675 18.8073
187 3GCZ SAM 0.00001906 0.51986 19.6507
188 3MB5 SAM 0.00001613 0.50182 19.6507
189 1I1N SAH 0.000003154 0.49592 19.9115
190 2PWY SAH 0.000007746 0.51474 20.524
191 2ZFU SAH 0.0000007269 0.56872 21.3953
192 1I9G SAM 0.00005967 0.48802 21.3974
193 2WA2 SAM 0.00001594 0.52921 22.2707
194 4KRI SAH 0.00000003768 0.62291 23.1441
195 4A6D SAM 0.00001831 0.51501 24.0175
196 2XVM SAH 0.00000003984 0.66408 24.1206
197 5MGZ SAH 0.0000000118 0.65227 24.4541
198 4PNE SAH 0.00000003855 0.60812 24.4541
199 4OBW SAM 0.0000001934 0.60741 24.4541
200 5E8J SAH 0.0000008657 0.60137 24.4541
201 5E9W SAH 0.000000839 0.49641 24.4541
202 5GWX SAM 0.000004043 0.5029 25.7642
203 5GWX SAR 0.000004043 0.5029 25.7642
204 1VE3 SAM 0.00000001597 0.65499 25.9912
205 5KOK SAH 0.000001844 0.5579 27.0742
206 5KOK S9T 0.000002171 0.46473 27.0742
207 5KOK R9T 0.000006975 0.45414 27.0742
208 4GQB 0XU 0.000002192 0.52799 27.2727
209 1Z3C SA8 0.0000014 0.49474 28.821
210 5FA8 SAM 0.000001114 0.54889 29.1925
211 3G2O SAM 0.00000008169 0.62385 29.6943
212 5FA5 MTA 0.00005465 0.51092 30
213 3T7S SAM 0.00000008835 0.62236 30.5677
214 5JE0 AZ8 0.00000009021 0.61 30.5677
215 5JE0 SAH 0.00000009021 0.61 30.5677
216 1L3I SAH 0.000008309 0.48952 38.0208
Pocket No.: 2; Query (leader) PDB : 4IWN; Ligand: GEK; 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: 4iwn.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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