Receptor
PDB id Resolution Class Description Source Keywords
1XVA 2.2 Å EC: 2.1.1.20 METHYLTRANSFERASE ESCHERICHIA COLI METHYLTRANSFERASE
Ref.: CRYSTAL STRUCTURE OF GLYCINE N-METHYLTRANSFERASE FR LIVER. BIOCHEMISTRY V. 35 11985 1996
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:294;
B:294;
Invalid;
Invalid;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
SAM A:293;
B:293;
Valid;
Valid;
none;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1XVA 2.2 Å EC: 2.1.1.20 METHYLTRANSFERASE ESCHERICHIA COLI METHYLTRANSFERASE
Ref.: CRYSTAL STRUCTURE OF GLYCINE N-METHYLTRANSFERASE FR LIVER. BIOCHEMISTRY V. 35 11985 1996
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1XVA - SAM C15 H22 N6 O5 S C[S@@+](CC....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1XVA - SAM C15 H22 N6 O5 S C[S@@+](CC....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1XVA - SAM C15 H22 N6 O5 S C[S@@+](CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SAM; Similar ligands found: 192
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 XYA 0.565789 0.773333
9 ADN 0.565789 0.773333
10 RAB 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 AMP MG 0.511364 0.710843
25 5AL 0.510417 0.743902
26 VMS 0.510204 0.673913
27 54H 0.510204 0.673913
28 0UM 0.51 0.857143
29 A 0.505747 0.707317
30 AMP 0.505747 0.707317
31 ABM 0.505618 0.753086
32 A5A 0.505155 0.688889
33 DAL AMP 0.50505 0.765432
34 NVA LMS 0.504951 0.725275
35 K15 0.5 0.883117
36 6RE 0.5 0.78481
37 5AD 0.5 0.75
38 SSA 0.5 0.684783
39 SON 0.5 0.746988
40 SRP 0.5 0.746988
41 LSS 0.49505 0.706522
42 CA0 0.494624 0.714286
43 A12 0.494505 0.705882
44 AP2 0.494505 0.705882
45 ME8 0.490385 0.841463
46 5CA 0.49 0.684783
47 TSB 0.49 0.681319
48 53H 0.49 0.666667
49 ACP 0.489362 0.694118
50 5AS 0.48913 0.648936
51 ADP 0.48913 0.690476
52 A2D 0.488889 0.690476
53 J7C 0.488889 0.772152
54 ZAS 0.488636 0.769231
55 8QN 0.485149 0.743902
56 GAP 0.484536 0.73494
57 AN2 0.483871 0.682353
58 A3S 0.483871 0.813333
59 A7D 0.483871 0.851351
60 GJV 0.483516 0.775
61 SRA 0.483146 0.694118
62 LAD 0.480769 0.752941
63 KAA 0.480769 0.698925
64 GSU 0.480769 0.722222
65 AMO 0.480392 0.746988
66 DSZ 0.480392 0.703297
67 52H 0.48 0.666667
68 ADP MG 0.478723 0.702381
69 M33 0.478723 0.722892
70 MAO 0.478261 0.82716
71 BA3 0.478261 0.690476
72 AOC 0.477778 0.776316
73 DSH 0.477778 0.842105
74 NEC 0.477778 0.75
75 SXZ 0.47619 0.894737
76 AHX 0.475728 0.701149
77 Y3J 0.47561 0.706667
78 G5A 0.474227 0.684783
79 A3T 0.473684 0.8
80 ADP BEF 0.473684 0.686047
81 BEF ADP 0.473684 0.686047
82 B4P 0.473118 0.690476
83 AP5 0.473118 0.690476
84 A3N 0.472527 0.766234
85 KB1 0.471698 0.833333
86 LEU LMS 0.471154 0.706522
87 APC 0.46875 0.705882
88 PRX 0.46875 0.73494
89 PAJ 0.466019 0.712644
90 4AD 0.466019 0.759036
91 RBY 0.463918 0.72619
92 ADP PO3 0.463918 0.728395
93 ADV 0.463918 0.72619
94 ADX 0.463158 0.666667
95 MHZ 0.463158 0.82716
96 AU1 0.463158 0.674419
97 YAP 0.462963 0.738095
98 TXA 0.462264 0.72619
99 NB8 0.462264 0.72093
100 A3G 0.461538 0.802632
101 VRT 0.459184 0.842105
102 ATP MG 0.459184 0.702381
103 YSA 0.458716 0.684783
104 XAH 0.458716 0.715909
105 50T 0.458333 0.682353
106 ATP 0.458333 0.690476
107 7D7 0.45679 0.723684
108 ANP MG 0.455446 0.678161
109 KH3 0.455357 0.871795
110 ACQ 0.454545 0.694118
111 AQP 0.453608 0.690476
112 5FA 0.453608 0.690476
113 AR6 0.453608 0.710843
114 APR 0.453608 0.710843
115 NSS 0.451923 0.703297
116 FA5 0.449541 0.746988
117 AGS 0.44898 0.678161
118 SAP 0.44898 0.678161
119 A5D 0.44898 0.789474
120 AD9 0.44898 0.674419
121 PTJ 0.448598 0.72093
122 YLB 0.448276 0.758621
123 YLP 0.447368 0.738636
124 D3Y 0.446602 0.792208
125 ADP ALF 0.445545 0.678161
126 ALF ADP 0.445545 0.678161
127 TYR AMP 0.445455 0.746988
128 MYR AMP 0.444444 0.776471
129 3AM 0.444444 0.674699
130 OAD 0.443396 0.73494
131 2VA 0.443299 0.779221
132 OOB 0.442308 0.722892
133 S8M 0.442308 0.831169
134 ADP VO4 0.441176 0.702381
135 VO4 ADP 0.441176 0.702381
136 ANP 0.44 0.674419
137 TAT 0.44 0.686047
138 WAQ 0.439252 0.75
139 ARG AMP 0.438596 0.727273
140 YLC 0.435897 0.755814
141 AAT 0.435644 0.797468
142 3OD 0.435185 0.73494
143 1ZZ 0.435185 0.755814
144 NVA 2AD 0.434343 0.815789
145 DLL 0.433962 0.722892
146 00A 0.433962 0.689655
147 7MD 0.433628 0.715909
148 ATF 0.431373 0.666667
149 SO8 0.43 0.792208
150 3UK 0.429907 0.714286
151 A6D 0.429907 0.72619
152 5SV 0.428571 0.741176
153 AMP DBH 0.428571 0.714286
154 WSA 0.42735 0.692308
155 TYM 0.42735 0.746988
156 9SN 0.427273 0.681818
157 AHZ 0.426087 0.755814
158 A A 0.425926 0.710843
159 3NZ 0.425926 0.807692
160 P5A 0.425926 0.691489
161 PR8 0.425926 0.744186
162 A1R 0.424528 0.709302
163 2A5 0.424242 0.674419
164 7MC 0.423729 0.719101
165 7D5 0.422222 0.658824
166 FYA 0.422018 0.722892
167 JB6 0.422018 0.709302
168 AYB 0.421488 0.75
169 PLP AAD 0.419355 0.764045
170 A22 0.419048 0.682353
171 MAP 0.419048 0.659091
172 2AM 0.417582 0.666667
173 TAD 0.417391 0.712644
174 A3P 0.416667 0.686747
175 ADP BMA 0.416667 0.714286
176 25A 0.415094 0.690476
177 YLA 0.413223 0.719101
178 ADQ 0.411215 0.694118
179 48N 0.410256 0.72093
180 0XU 0.41 0.824324
181 NAD IBO 0.406504 0.717647
182 7D3 0.40625 0.643678
183 PAP 0.405941 0.678571
184 OVE 0.404255 0.662791
185 4UV 0.403509 0.697674
186 ALF ADP 3PG 0.403361 0.712644
187 AF3 ADP 3PG 0.403361 0.712644
188 LA8 ALF 3PG 0.403361 0.712644
189 3AD 0.402299 0.783784
190 CMP 0.402062 0.691358
191 2BA 0.402062 0.682927
192 7C5 0.4 0.731707
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1XVA; Ligand: SAM; Similar sites found: 194
This union binding pocket(no: 1) in the query (biounit: 1xva.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1O9U ADZ 0.01789 0.42015 1.71233
2 4IVG ANP 0.004176 0.41893 1.71233
3 1R6D DAU 0.009669 0.40672 1.71233
4 1R6D NAD 0.0113 0.40488 1.71233
5 1SQ5 PAU 0.01086 0.40152 1.71233
6 2YC5 6BC 0.001354 0.42281 1.75439
7 1EB9 HBA 0.002784 0.41096 1.9084
8 1SS4 GSH 0.0004128 0.5327 1.96078
9 1SS4 CIT 0.01529 0.47207 1.96078
10 4G87 UD1 0.002343 0.42527 2.05479
11 2XK9 XK9 0.001558 0.4194 2.05479
12 1KOL NAD 0.002295 0.4158 2.05479
13 1N1G BCP 0.002317 0.41447 2.05479
14 4DEM YS4 0.02809 0.40293 2.05479
15 1BDB NAD 0.01671 0.40784 2.16606
16 1M5B BN1 0.003333 0.42737 2.28137
17 2ZWS PLM 0.001131 0.50208 2.39726
18 1T26 NAI 0.002501 0.45045 2.39726
19 1T26 GBD 0.002501 0.45045 2.39726
20 3I0O ADP 0.0006514 0.44035 2.39726
21 4C12 ADP 0.002276 0.43053 2.39726
22 2YPO PHE 0.0006139 0.42818 2.39726
23 3FC4 EDO 0.003494 0.42428 2.39726
24 2J07 HDF 0.004148 0.4182 2.39726
25 2J07 FAD 0.004148 0.4182 2.39726
26 1RZM E4P 0.0128 0.41434 2.39726
27 1REO FAD 0.003202 0.41389 2.39726
28 2Z9V PXM 0.009534 0.40388 2.39726
29 4J7H TRH 0.001316 0.40145 2.39726
30 2CKM AA7 0.008687 0.40003 2.39726
31 3D3W NAP 0.002135 0.41067 2.45902
32 1Y9Q MED 0.004702 0.42811 2.60417
33 2DTX BMA 0.002446 0.41814 2.65152
34 4K5S PM0 0.004543 0.41672 2.73973
35 2F2U M77 0.002881 0.41513 2.73973
36 4HA6 FAD 0.005268 0.40991 2.73973
37 4K5S FAD 0.002729 0.40951 2.73973
38 4MP8 MLI 0.003775 0.40915 2.73973
39 4MP8 NAD 0.003775 0.40915 2.73973
40 1CSI OAA 0.004371 0.40897 2.73973
41 1CSI CMX 0.004371 0.40897 2.73973
42 3NKS FAD 0.003818 0.40897 2.73973
43 1VDC FAD 0.007315 0.40812 2.73973
44 1U1J MET 0.0312 0.40798 2.73973
45 2YBQ UP2 0.004421 0.40557 2.73973
46 3OND ADN 0.009213 0.40436 2.73973
47 3OND NAD 0.009213 0.40436 2.73973
48 4R33 SAH 0.003852 0.40421 2.73973
49 4R33 TRP 0.003852 0.40421 2.73973
50 3NFZ 3NF 0.004316 0.40374 2.73973
51 3IB8 AMP 0.000367 0.4019 2.73973
52 3SJ7 NDP 0.002646 0.40466 2.77778
53 2PT9 2MH 0.00067 0.43243 2.80374
54 4AT0 FAD 0.0007027 0.44618 3.08219
55 3F3E LEU 0.0004893 0.44113 3.08219
56 2QA1 FAD 0.001469 0.42154 3.08219
57 1H6W SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.01169 0.40168 3.08219
58 3TN7 NJP 0.003912 0.40145 3.11284
59 3IU9 T07 0.01604 0.40184 3.125
60 1G0N NDP 0.005867 0.40329 3.18021
61 1HDR NAD 0.008318 0.40684 3.27869
62 1KTC NGA 0.0003618 0.46308 3.42466
63 3T31 FAD 0.0007623 0.45023 3.42466
64 3T31 DCQ 0.0008424 0.45023 3.42466
65 4USQ FAD 0.000557 0.43528 3.42466
66 2YVF NAD 0.002581 0.43456 3.42466
67 2YVF FAD 0.002473 0.43456 3.42466
68 1DLJ UGA 0.001638 0.43423 3.42466
69 3P3N AKG 0.01006 0.41332 3.42466
70 4GYW UDP 0.002282 0.41226 3.42466
71 1DLJ NAI 0.009011 0.40633 3.42466
72 1ME8 RVP 0.03072 0.40039 3.42466
73 2JBH 5GP 0.008038 0.40218 3.55556
74 1Z44 NPO 0.004915 0.46693 3.76712
75 1V35 NAI 0.0003545 0.45093 3.76712
76 2Q09 DI6 0.002408 0.42332 3.76712
77 1FL2 FAD 0.003296 0.41447 3.76712
78 2HGZ PBF 0.001472 0.4072 3.76712
79 4KS1 2H8 0.009005 0.4013 3.76712
80 1BTN I3P 0.02223 0.4273 3.77358
81 1A27 NAP 0.00299 0.40421 3.80623
82 1SG4 CO8 0.00209 0.40524 3.84615
83 3ZPG 5GP 0.001513 0.47413 4.10959
84 4RJK PYR 0.007671 0.43134 4.10959
85 3NYQ AMP 0.0007808 0.42875 4.10959
86 3NYQ MCA 0.0007143 0.42875 4.10959
87 1WVG CXY 0.0006643 0.41521 4.10959
88 1LVL FAD 0.004738 0.41161 4.10959
89 2BJK NAD 0.008561 0.4091 4.10959
90 2NP9 YE1 0.003546 0.40423 4.10959
91 3DAG FEG 0.002578 0.40057 4.10959
92 3O03 NAP 0.01474 0.40258 4.12371
93 2AE2 PTO 0.002695 0.41766 4.23077
94 2AE2 NAP 0.002695 0.41766 4.23077
95 1DR1 NAP 0.001941 0.41957 4.2328
96 1DR1 HBI 0.001941 0.41957 4.2328
97 2RHW C0E 0.01191 0.40882 4.24028
98 3ZLM ANP 0.0009424 0.40238 4.25532
99 2Q37 3AL 0.007018 0.41467 4.41989
100 3WO0 ALA 0.001404 0.42346 4.45205
101 3WO0 ADP 0.001404 0.42346 4.45205
102 3K37 BCZ 0.01456 0.4124 4.45205
103 4QN7 G39 0.003235 0.4093 4.45205
104 1F1V DHY 0.00573 0.40812 4.45205
105 4O1M NAD 0.003595 0.40141 4.45205
106 3I28 34N 0.0003476 0.4566 4.79452
107 2RDT 2RD 0.004511 0.42783 4.79452
108 1I0Z OXM 0.01276 0.42756 4.79452
109 2TPL HPP 0.0005822 0.42258 4.79452
110 1TDF FAD 0.005778 0.4111 4.79452
111 2RDT FMN 0.01346 0.4027 4.79452
112 1SOW NAD 0.003942 0.40261 4.79452
113 3K9W ADE 0.031 0.40611 4.81283
114 3K9W 4PS 0.031 0.40611 4.81283
115 2X61 NGA GAL SIA 0.01197 0.40606 5.03876
116 2C7G FAD 0.002612 0.43066 5.13699
117 2C7G ODP 0.002491 0.43066 5.13699
118 2P1O IHP 0.001616 0.41352 5.13699
119 2P1O NLA 0.001616 0.41352 5.13699
120 2J7T 274 0.001967 0.40913 5.13699
121 3MAG 3MA 0.04435 0.40655 5.13699
122 1ZK7 FAD 0.007352 0.40633 5.13699
123 4NE2 SH2 0.003981 0.40607 5.13699
124 4CKU P2F 0.0084 0.40586 5.13699
125 2G86 UMP 0.01021 0.40349 5.13699
126 1N6B DMZ 0.005971 0.40196 5.13699
127 1I2B USQ 0.01501 0.40089 5.13699
128 1I2B NAD 0.01501 0.40089 5.13699
129 1I2B UPG 0.01501 0.40089 5.13699
130 2YHW BM3 0.00298 0.40425 5.24781
131 4FWE FAD 0.0004841 0.44816 5.47945
132 2IXB A2G 0.001621 0.42353 5.47945
133 4M51 BEZ 0.02385 0.40746 5.47945
134 2QLX RM4 0.007082 0.42629 5.55556
135 3CQD ATP 0.002003 0.41908 5.82192
136 1IYE PGU 0.00227 0.40974 5.82192
137 3S7O LBV 0.00245 0.40858 5.82192
138 1U7Z PMT 0.00417 0.40299 5.82192
139 3S9K CIT 0.001151 0.51391 5.9322
140 1MZV AMP 0.006322 0.40178 5.95745
141 1G7V PAI 0.00262 0.41705 5.98592
142 2NX1 RP5 0.002067 0.40692 5.99251
143 2NX1 PEP 0.00209 0.40675 5.99251
144 1TFZ 869 0.0006175 0.41225 6.16438
145 3DGB MUC 0.002604 0.41206 6.16438
146 2Q2V NAD 0.0007989 0.4284 6.27451
147 1XE7 GUN 0.006065 0.44383 6.40394
148 1K97 CIR 0.03236 0.40044 6.50685
149 1K97 ASP 0.03236 0.40044 6.50685
150 1NVV GNP 0.007498 0.41242 6.62651
151 2J8Z NAP 0.001501 0.4132 6.84932
152 2AQJ FAD 0.01013 0.41023 6.84932
153 4HZX G39 0.004103 0.40997 6.84932
154 2AQJ TRP 0.01218 0.40645 6.84932
155 1Q3Q ANP 0.0121 0.40588 6.84932
156 1R27 MGD 0.004706 0.4046 6.84932
157 4P4T GDP 0.001753 0.40118 6.84932
158 4CS4 ANP 0.004699 0.40572 6.93431
159 4CS4 AXZ 0.007164 0.40497 6.93431
160 1G8S MET 0.009712 0.41401 6.95652
161 1V7R CIT 0.005163 0.45598 6.98925
162 3VPD ANP 0.001488 0.40165 7.11744
163 4JWX 1N4 0.01155 0.40039 7.14286
164 2IZ1 ATR 0.007206 0.41981 7.19178
165 1XHL NDP 0.001449 0.41793 7.19178
166 3PLN U5P 0.006733 0.41019 7.19178
167 4BJZ P3A 0.01036 0.41607 7.53425
168 4BJZ FAD 0.01036 0.41607 7.53425
169 2PP3 LGT 0.001368 0.41783 7.87671
170 4NAT ADP 0.03047 0.4015 8.125
171 2RGH FAD 0.003653 0.41283 8.21918
172 1L3I SAH 0.001545 0.40974 8.33333
173 3FS8 TDR 0.02632 0.40053 8.42491
174 2YB9 HA0 0.001333 0.41644 8.56164
175 3F81 STT 0.007893 0.43808 9.28962
176 1H82 FAD 0.0007624 0.45189 9.58904
177 1H82 GZZ 0.0008789 0.45189 9.58904
178 4M5P MLA 0.04022 0.40882 9.58904
179 1ULE GLA GAL NAG 0.01301 0.42024 10
180 2E2R 2OH 0.002221 0.41392 10.6557
181 1TIW FAD 0.003918 0.40964 10.9589
182 1TIW TFB 0.003918 0.40964 10.9589
183 1FIQ SAL 0.001469 0.41772 11.6438
184 1FIQ MTE 0.001738 0.41242 11.6438
185 1PEA ACM 0.005914 0.43679 11.9863
186 2Q8H TF4 0.01779 0.42026 11.9863
187 1QO0 BMD 0.008652 0.41626 11.9863
188 2WGC SIA GAL BGC 0.04991 0.411 12.2807
189 5RHN 8BR 0.000362 0.40813 15.6522
190 4IAE 1DX 0.004523 0.41721 15.873
191 4KCT PYR 0.004353 0.41294 17.4658
192 1Q0H FOM 0.01054 0.40051 24.6575
193 3PFG SAM 0.00001179 0.50366 26.2357
194 1TUV VK3 0.01878 0.41908 29.8246
Pocket No.: 2; Query (leader) PDB : 1XVA; 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: 1xva.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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