Receptor
PDB id Resolution Class Description Source Keywords
4RV9 2.2 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF MTMC IN COMPLEX WITH SAH STREPTOMYCES ARGILLACEUS METHYLTRANSFERASE TRANSFERASE
Ref.: STRUCTURAL INSIGHT INTO MTMC, A BIFUNCTIONAL KETOREDUCTASE-METHYLTRANSFERASE INVOLVED IN THE ASS THE MITHRAMYCIN TRISACCHARIDE CHAIN. BIOCHEMISTRY V. 54 2481 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:504;
Invalid;
none;
submit data
35.453 Cl [Cl-]
ZN A:501;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
ACT A:503;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
SAH A:502;
Valid;
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
4RVG 2.3 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF MTMC IN COMPLEX WITH SAM AND TDP STREPTOMYCES ARGILLACEUS C-METHYLTRANSFERASE TDP-4-KETO-D-OLIVOSE TRANSFERASE
Ref.: STRUCTURAL INSIGHT INTO MTMC, A BIFUNCTIONAL KETOREDUCTASE-METHYLTRANSFERASE INVOLVED IN THE ASS THE MITHRAMYCIN TRISACCHARIDE CHAIN. BIOCHEMISTRY V. 54 2481 2015
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 4RVD - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 4RVG - SAM C15 H22 N6 O5 S C[S@@+](CC....
3 4RV9 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 4RVH - 3YN C16 H24 N2 O14 P2 C[C@@H]1C(....
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 4RVD - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 4RVG - SAM C15 H22 N6 O5 S C[S@@+](CC....
3 4RV9 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 4RVH - 3YN C16 H24 N2 O14 P2 C[C@@H]1C(....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 166 families.
1 4RVD - SAM C15 H22 N6 O5 S C[S@@+](CC....
2 4RVG - SAM C15 H22 N6 O5 S C[S@@+](CC....
3 4RV9 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
4 4RVH - 3YN C16 H24 N2 O14 P2 C[C@@H]1C(....
5 4E33 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 4E2W - JHZ C17 H27 N3 O13 P2 C[C@@H]1C(....
7 4E2Z - JHZ C17 H27 N3 O13 P2 C[C@@H]1C(....
8 4E30 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
9 4E2X - SAH C14 H20 N6 O5 S c1nc(c2c(n....
10 4E32 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
11 4E2Y - SAH C14 H20 N6 O5 S c1nc(c2c(n....
12 4E31 - JHZ C17 H27 N3 O13 P2 C[C@@H]1C(....
13 3NDI - SAM C15 H22 N6 O5 S C[S@@+](CC....
14 3NDJ - SAH C14 H20 N6 O5 S c1nc(c2c(n....
15 5T6B - SAH C14 H20 N6 O5 S c1nc(c2c(n....
16 5T67 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
17 5T64 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SAH; Similar ligands found: 197
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 SXZ 0.692308 0.916667
6 DSH 0.692308 0.914286
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 ADN 0.573333 0.84058
20 XYA 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 AMP 0.529412 0.763158
36 A 0.529412 0.763158
37 5CA 0.525773 0.712644
38 ME8 0.524752 0.8125
39 M2T 0.52439 0.821918
40 6RE 0.523256 0.824324
41 GJV 0.522727 0.813333
42 AAT 0.515789 0.863014
43 LSS 0.515152 0.696629
44 KAA 0.514852 0.727273
45 J7C 0.511364 0.835616
46 A5A 0.510417 0.697674
47 SON 0.505495 0.805195
48 SRP 0.505155 0.805195
49 5AL 0.5 0.779221
50 VMS 0.5 0.681818
51 KH3 0.5 0.866667
52 ADX 0.5 0.694118
53 CA0 0.5 0.769231
54 AMP MG 0.5 0.74359
55 AMO 0.5 0.805195
56 54H 0.5 0.681818
57 AHX 0.49505 0.753086
58 TSB 0.494949 0.689655
59 53H 0.494949 0.674157
60 G5A 0.494737 0.712644
61 A2D 0.494382 0.74359
62 ABM 0.494382 0.74359
63 ZAS 0.494253 0.808219
64 A6D 0.490196 0.759494
65 8QN 0.49 0.779221
66 GEK 0.49 0.956522
67 GAP 0.489583 0.769231
68 A3S 0.48913 0.884058
69 AN2 0.48913 0.734177
70 S4M 0.488889 0.831169
71 SRA 0.488636 0.746835
72 LAD 0.485437 0.810127
73 52H 0.484848 0.674157
74 A12 0.483516 0.759494
75 BA3 0.483516 0.74359
76 AP2 0.483516 0.759494
77 AOC 0.483146 0.842857
78 NEC 0.483146 0.788732
79 Y3J 0.481481 0.768116
80 NVA LMS 0.480392 0.696629
81 VRT 0.479167 0.861111
82 50T 0.478723 0.734177
83 5AS 0.478261 0.655556
84 B4P 0.478261 0.74359
85 ADP 0.478261 0.74359
86 AP5 0.478261 0.74359
87 A3N 0.477778 0.830986
88 YSA 0.476636 0.712644
89 XAH 0.476636 0.768293
90 0XU 0.473684 0.897059
91 WAQ 0.471154 0.807692
92 NSS 0.470588 0.712644
93 5AD 0.468354 0.791045
94 ADP MG 0.468085 0.734177
95 AU1 0.468085 0.725
96 M33 0.468085 0.734177
97 MAO 0.467391 0.797468
98 TXA 0.466667 0.759494
99 A3G 0.466667 0.871429
100 NB8 0.466667 0.775
101 3AM 0.465909 0.727273
102 DAL AMP 0.465347 0.779221
103 ATP 0.463158 0.74359
104 ADP BEF 0.463158 0.716049
105 A3T 0.463158 0.842857
106 BEF ADP 0.463158 0.716049
107 ACP 0.463158 0.746835
108 7D7 0.4625 0.785714
109 LEU LMS 0.461538 0.677778
110 APC 0.458333 0.759494
111 AQP 0.458333 0.74359
112 APR 0.458333 0.766234
113 PRX 0.458333 0.746835
114 AR6 0.458333 0.766234
115 5FA 0.458333 0.74359
116 IOT 0.456897 0.761905
117 4AD 0.456311 0.794872
118 PAJ 0.456311 0.722892
119 WSA 0.45614 0.72093
120 FA5 0.453704 0.805195
121 YAP 0.453704 0.794872
122 RBY 0.453608 0.782051
123 ADV 0.453608 0.782051
124 ADP PO3 0.453608 0.763158
125 AD9 0.453608 0.725
126 SAP 0.453608 0.728395
127 AGS 0.453608 0.728395
128 PTJ 0.45283 0.731707
129 MHZ 0.452632 0.797468
130 00A 0.451923 0.740741
131 A3P 0.451613 0.74026
132 YLP 0.451327 0.771084
133 7MD 0.45045 0.768293
134 ALF ADP 0.45 0.707317
135 ADP ALF 0.45 0.707317
136 ATP MG 0.44898 0.734177
137 2VA 0.447917 0.819444
138 OOB 0.446602 0.779221
139 ANP 0.444444 0.725
140 ACQ 0.444444 0.746835
141 TAT 0.444444 0.7375
142 P5A 0.443396 0.719101
143 7D5 0.443182 0.708861
144 ARG AMP 0.442478 0.759036
145 A1R 0.442308 0.7625
146 YLC 0.439655 0.790123
147 2AM 0.438202 0.717949
148 DLL 0.438095 0.779221
149 A22 0.436893 0.734177
150 D3Y 0.436893 0.859155
151 TYR AMP 0.436364 0.782051
152 ATF 0.435644 0.716049
153 MYR AMP 0.435185 0.746988
154 SO8 0.434343 0.808219
155 3UK 0.433962 0.769231
156 OAD 0.433962 0.769231
157 TAD 0.433628 0.765432
158 25A 0.432692 0.74359
159 ANP MG 0.431373 0.707317
160 VO4 ADP 0.431373 0.734177
161 ADP VO4 0.431373 0.734177
162 9SN 0.431193 0.731707
163 TYM 0.431034 0.805195
164 PR8 0.429907 0.8
165 ADQ 0.428571 0.746835
166 YLB 0.42735 0.771084
167 3OD 0.425926 0.769231
168 FYA 0.425926 0.779221
169 1ZZ 0.425926 0.746988
170 PPS 0.425743 0.674419
171 NVA 2AD 0.424242 0.808219
172 MAP 0.423077 0.707317
173 A2P 0.421053 0.727273
174 4YB 0.421053 0.735632
175 ADP BMA 0.420561 0.746835
176 5SV 0.419048 0.731707
177 3NZ 0.416667 0.824324
178 YLA 0.416667 0.771084
179 48N 0.413793 0.753086
180 LPA AMP 0.413793 0.768293
181 AYB 0.413223 0.761905
182 QQY 0.413043 0.696203
183 ACK 0.413043 0.710526
184 JB6 0.412844 0.7625
185 BIS 0.412844 0.719512
186 PAP 0.41 0.730769
187 OVE 0.408602 0.7125
188 4UV 0.40708 0.75
189 AMP DBH 0.40708 0.746835
190 3AD 0.406977 0.852941
191 AF3 ADP 3PG 0.40678 0.743902
192 OMR 0.40678 0.738095
193 LAQ 0.405172 0.768293
194 A A 0.40367 0.74359
195 7C5 0.403509 0.789474
196 7MC 0.403361 0.75
197 4UU 0.4 0.75
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RVG; Ligand: TYD; Similar sites found: 44
This union binding pocket(no: 1) in the query (biounit: 4rvg.bio1) has 44 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4AZW SAM 0.000002939 0.40124 1.40845
2 5HJM MTA 0.002329 0.44868 1.42045
3 4YUW 4JU 0.01114 0.40003 1.97368
4 5E1M PRO PRO LYS ARG ILE ALA 0.00008033 0.41841 2.07469
5 5E1M SAH 0.00008033 0.41841 2.07469
6 3OFK SAH 0.00006627 0.51068 2.31481
7 5JE8 NAD 0.008566 0.40833 2.31788
8 1KPH SAH 0.00001342 0.40156 2.43902
9 1KPG SAH 0.00001496 0.4004 2.43902
10 5K8V 6RE 0.001376 0.40986 2.49307
11 3TLJ SAH 0.01262 0.40622 2.68097
12 4OPC PGT 0.01136 0.40095 2.8169
13 4OPC FDA 0.009959 0.40012 2.8169
14 1IM8 SAI 0.000001403 0.41384 2.86885
15 3GFB NAD 0.009246 0.40204 3.14286
16 4LYQ MAN BMA BMA 0.0251 0.41973 3.28639
17 1JQD SAH 0.0000414 0.41027 3.42466
18 1XDS SAM 0.0005765 0.49515 3.47594
19 3VYW SAM 0.01213 0.41249 3.57143
20 4RL4 PPV 0.03766 0.42435 4.24528
21 4OBW SAM 0.0005256 0.48292 5.05837
22 1Y8Q ATP 0.0001746 0.48378 5.20231
23 4PIO SAH 0.0001087 0.40737 5.26316
24 4PIO AVI 0.0001402 0.40088 5.26316
25 3GDH SAH 0.003905 0.42566 5.39419
26 3VC1 GST 0.0001275 0.42795 5.44872
27 3VC1 SAH 0.0001275 0.42795 5.44872
28 4Y2H 49K 0.0003784 0.40973 7.10227
29 4Y2H SAH 0.0006124 0.40314 7.10227
30 5DM1 SAH 0.0001618 0.41863 7.11611
31 5DM1 5D7 0.0002139 0.4173 7.11611
32 4K28 NAD 0.006508 0.4134 8.17844
33 4R6W PC 0.00006988 0.45198 9.30233
34 4R6W SAH 0.000006792 0.44431 9.30233
35 3EGV SAH 0.0001798 0.50985 10.2041
36 4M73 SAH 0.0000902 0.42021 10.9792
37 4M73 M72 0.0004497 0.40181 10.9792
38 4DMG SAM 0.006649 0.44589 12.2137
39 2VDV SAM 0.001047 0.48216 15.0407
40 5N53 8NB 0.001638 0.49719 15.8974
41 4QTU SAM 0.00009087 0.51389 16.8269
42 5WSY 7UC 0.04609 0.40918 19.0751
43 5DLY 5D7 0.0004433 0.40736 24.4361
44 5DLY SAH 0.000318 0.40649 24.4361
Pocket No.: 2; Query (leader) PDB : 4RVG; Ligand: SAM; Similar sites found: 46
This union binding pocket(no: 2) in the query (biounit: 4rvg.bio1) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4AZW SAM 0.000002664 0.40989 1.40845
2 5HJM MTA 0.002521 0.44511 1.42045
3 4YUW 4JU 0.01146 0.40266 1.97368
4 4YUW S4M 0.01161 0.40202 1.97368
5 5E1M SAH 0.00008133 0.4256 2.07469
6 5E1M PRO PRO LYS ARG ILE ALA 0.00008133 0.4256 2.07469
7 1L1E SAH 0.00001065 0.40322 2.09059
8 3OFK SAH 0.00005848 0.51068 2.31481
9 1KPG SAH 0.00001282 0.40931 2.43902
10 1KPH SAH 0.00001615 0.40738 2.43902
11 5K8V 6RE 0.0009338 0.41967 2.49307
12 3TLJ SAH 0.01204 0.40533 2.68097
13 4OPC PGT 0.009065 0.40781 2.8169
14 4OPC FDA 0.007573 0.40779 2.8169
15 1IM8 SAI 0.000001231 0.4234 2.86885
16 4LYQ MAN BMA BMA 0.02936 0.41442 3.28639
17 1JQD SAH 0.00003758 0.41891 3.42466
18 1XDS SAM 0.0005219 0.49515 3.47594
19 3VYW SAM 0.01107 0.41249 3.57143
20 1TPY SAH 0.00001698 0.407 3.83275
21 2FK8 SAM 0.000008499 0.40685 4.40252
22 4OBW SAM 0.0004211 0.48527 5.05837
23 1Y8Q ATP 0.0003686 0.46761 5.20231
24 4PIO SAH 0.00008993 0.41652 5.26316
25 4PIO AVI 0.0001243 0.40876 5.26316
26 3GDH SAH 0.003668 0.42489 5.39419
27 3TPV ADE 0.01694 0.40983 5.39906
28 3VC1 GST 0.0001118 0.43685 5.44872
29 3VC1 SAH 0.0001118 0.43685 5.44872
30 4Y2H 49K 0.0003476 0.41769 7.10227
31 4Y2H SAH 0.000538 0.41152 7.10227
32 5DM1 SAH 0.00015 0.42691 7.11611
33 5DM1 5D7 0.0001973 0.42568 7.11611
34 4R6W PC 0.00006104 0.45911 9.30233
35 4R6W SAH 0.000006461 0.45289 9.30233
36 3EGV SAH 0.0001684 0.50892 10.2041
37 4M73 SAH 0.00008924 0.42811 10.9792
38 4M73 M72 0.0004192 0.40963 10.9792
39 4DMG SAM 0.006112 0.44589 12.2137
40 1I7M CG 0.04057 0.41056 13.4328
41 2VDV SAM 0.0009855 0.48137 15.0407
42 5N53 8NB 0.001507 0.49719 15.8974
43 4QTU SAM 0.0000807 0.51389 16.8269
44 5WSY 7UC 0.04301 0.40918 19.0751
45 5DLY SAH 0.0002919 0.41479 24.4361
46 5DLY 5D7 0.0004234 0.41478 24.4361
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