Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:504;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
SAM A:503;
Valid;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
ZN A:501;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
TYD A:502;
Valid;
none;
submit data
402.188 C10 H16 N2 O11 P2 CC1=C...
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 269 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 237 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 187 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: SAM; Similar ligands found: 202
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 ADN 0.565789 0.773333
9 RAB 0.565789 0.773333
10 XYA 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 5AL 0.510417 0.743902
25 54H 0.510204 0.673913
26 VMS 0.510204 0.673913
27 0UM 0.51 0.857143
28 AMP 0.505747 0.707317
29 LMS 0.505747 0.666667
30 A 0.505747 0.707317
31 ABM 0.505618 0.753086
32 A5A 0.505155 0.688889
33 SON 0.5 0.746988
34 SSA 0.5 0.684783
35 6RE 0.5 0.78481
36 K15 0.5 0.883117
37 5AD 0.5 0.75
38 SRP 0.5 0.746988
39 LSS 0.49505 0.706522
40 CA0 0.494624 0.714286
41 A12 0.494505 0.705882
42 AP2 0.494505 0.705882
43 ME8 0.490385 0.841463
44 TSB 0.49 0.681319
45 53H 0.49 0.666667
46 DAL AMP 0.49 0.765432
47 5CA 0.49 0.684783
48 ACP 0.489362 0.694118
49 ADP 0.48913 0.690476
50 5AS 0.48913 0.648936
51 J7C 0.488889 0.772152
52 A2D 0.488889 0.690476
53 ZAS 0.488636 0.769231
54 9ZD 0.485149 0.729412
55 9ZA 0.485149 0.729412
56 8QN 0.485149 0.743902
57 GAP 0.484536 0.73494
58 AN2 0.483871 0.682353
59 A3S 0.483871 0.813333
60 A7D 0.483871 0.851351
61 GJV 0.483516 0.775
62 SRA 0.483146 0.694118
63 LAD 0.480769 0.752941
64 KAA 0.480769 0.698925
65 GSU 0.480769 0.722222
66 AMO 0.480392 0.746988
67 DSZ 0.480392 0.703297
68 52H 0.48 0.666667
69 M33 0.478723 0.722892
70 BA3 0.478261 0.690476
71 MAO 0.478261 0.82716
72 NEC 0.477778 0.75
73 AOC 0.477778 0.776316
74 DSH 0.477778 0.842105
75 SXZ 0.47619 0.894737
76 AHX 0.475728 0.701149
77 NVA LMS 0.475728 0.736264
78 Y3J 0.47561 0.706667
79 G5A 0.474227 0.684783
80 A3T 0.473684 0.8
81 B4P 0.473118 0.690476
82 AP5 0.473118 0.690476
83 A3N 0.472527 0.766234
84 KB1 0.471698 0.833333
85 PRX 0.46875 0.73494
86 APC 0.46875 0.705882
87 AT4 0.468085 0.686047
88 PAJ 0.466019 0.712644
89 4AD 0.466019 0.759036
90 RBY 0.463918 0.72619
91 ADP PO3 0.463918 0.728395
92 ADV 0.463918 0.72619
93 ADX 0.463158 0.666667
94 MHZ 0.463158 0.82716
95 AU1 0.463158 0.674419
96 YAP 0.462963 0.738095
97 TXA 0.462264 0.72619
98 NB8 0.462264 0.72093
99 A3G 0.461538 0.802632
100 VRT 0.459184 0.842105
101 XAH 0.458716 0.715909
102 YSA 0.458716 0.684783
103 HEJ 0.458333 0.690476
104 50T 0.458333 0.682353
105 ATP 0.458333 0.690476
106 LEU LMS 0.457143 0.717391
107 7D7 0.45679 0.723684
108 KH3 0.455357 0.871795
109 ACQ 0.454545 0.694118
110 AR6 0.453608 0.710843
111 APR 0.453608 0.710843
112 AQP 0.453608 0.690476
113 5FA 0.453608 0.690476
114 NSS 0.451923 0.703297
115 FA5 0.449541 0.746988
116 A5D 0.44898 0.789474
117 AD9 0.44898 0.674419
118 AGS 0.44898 0.678161
119 SAP 0.44898 0.678161
120 PTJ 0.448598 0.72093
121 YLB 0.448276 0.758621
122 YLP 0.447368 0.738636
123 8X1 0.446602 0.680851
124 D3Y 0.446602 0.792208
125 ADP ALF 0.445545 0.678161
126 ALF ADP 0.445545 0.678161
127 3AM 0.444444 0.674699
128 MYR AMP 0.444444 0.776471
129 OAD 0.443396 0.73494
130 2VA 0.443299 0.779221
131 S8M 0.442308 0.831169
132 OOB 0.442308 0.722892
133 TYR AMP 0.441441 0.759036
134 6YZ 0.441176 0.694118
135 ADP VO4 0.441176 0.702381
136 VO4 ADP 0.441176 0.702381
137 T99 0.44 0.686047
138 TAT 0.44 0.686047
139 ANP 0.44 0.674419
140 WAQ 0.439252 0.75
141 B5Y 0.436364 0.717647
142 8PZ 0.436364 0.684783
143 F0P 0.435897 0.844156
144 YLC 0.435897 0.755814
145 AAT 0.435644 0.797468
146 1ZZ 0.435185 0.755814
147 9K8 0.435185 0.663158
148 3OD 0.435185 0.73494
149 NVA 2AD 0.434343 0.855263
150 00A 0.433962 0.689655
151 DLL 0.433962 0.722892
152 ARG AMP 0.433628 0.727273
153 7MD 0.433628 0.715909
154 ATF 0.431373 0.666667
155 SO8 0.43 0.792208
156 3UK 0.429907 0.714286
157 A6D 0.429907 0.72619
158 9X8 0.429907 0.717647
159 F2R 0.429752 0.7
160 5SV 0.428571 0.741176
161 AMP DBH 0.428571 0.714286
162 TYM 0.42735 0.746988
163 WSA 0.42735 0.692308
164 9SN 0.427273 0.681818
165 AHZ 0.426087 0.755814
166 P5A 0.425926 0.691489
167 B5V 0.425926 0.705882
168 PR8 0.425926 0.744186
169 A A 0.425926 0.710843
170 3NZ 0.425926 0.807692
171 A1R 0.424528 0.709302
172 2A5 0.424242 0.674419
173 7MC 0.423729 0.719101
174 B5M 0.423423 0.717647
175 7D5 0.422222 0.658824
176 JB6 0.422018 0.709302
177 FYA 0.422018 0.722892
178 AYB 0.421488 0.75
179 A22 0.419048 0.682353
180 MAP 0.419048 0.659091
181 2AM 0.417582 0.666667
182 TAD 0.417391 0.712644
183 A3P 0.416667 0.686747
184 ADP BMA 0.416667 0.714286
185 25A 0.415094 0.690476
186 YLA 0.413223 0.719101
187 8Q2 0.411765 0.663158
188 A3R 0.411215 0.709302
189 ADQ 0.411215 0.694118
190 48N 0.410256 0.72093
191 0XU 0.41 0.824324
192 GA7 0.408696 0.72619
193 7D3 0.40625 0.643678
194 PAP 0.405941 0.678571
195 DQV 0.405172 0.702381
196 OVE 0.404255 0.662791
197 4UV 0.403509 0.697674
198 AF3 ADP 3PG 0.403361 0.712644
199 3AD 0.402299 0.783784
200 CMP 0.402062 0.691358
201 2BA 0.402062 0.682927
202 7C5 0.4 0.731707
Ligand no: 2; Ligand: TYD; Similar ligands found: 87
No: Ligand ECFP6 Tc MDL keys Tc
1 TYD 1 1
2 TTP 0.884058 1
3 TMP 0.80597 0.985714
4 TLO 0.716049 0.945205
5 DAU 0.694118 0.932432
6 1JB 0.682353 0.932432
7 TRH 0.682353 0.932432
8 3R2 0.682353 0.92
9 18T 0.682353 0.932432
10 TDX 0.682353 0.945205
11 ATY 0.670886 0.945205
12 3YN 0.666667 0.932432
13 DWN 0.666667 0.907895
14 T3Q 0.666667 0.907895
15 T3F 0.666667 0.907895
16 TBD 0.662338 0.958904
17 T46 0.659091 0.932432
18 0N2 0.659091 0.896104
19 AZD 0.654321 0.907895
20 MMF 0.651685 0.907895
21 0FX 0.651685 0.907895
22 THM 0.641791 0.873239
23 LLT 0.641791 0.873239
24 QDM 0.637363 0.896104
25 JHZ 0.630435 0.884615
26 1YF 0.630435 0.92
27 AKM 0.630435 0.886076
28 FNF 0.630435 0.92
29 4TG 0.623656 0.92
30 DT DT DT 0.616279 0.917808
31 DUD 0.61039 0.957143
32 UFP 0.6 0.905405
33 0DN 0.6 0.833333
34 DT DT DT DT DT 0.582418 0.945205
35 QUH 0.58 0.907895
36 FUH 0.58 0.907895
37 T5A 0.572816 0.841463
38 BRU 0.571429 0.905405
39 5HU 0.571429 0.971831
40 DT DT PST 0.569892 0.87013
41 FDM 0.564103 0.918919
42 5IU 0.564103 0.905405
43 NYM 0.564103 0.958333
44 T3P 0.56 0.943662
45 THP 0.556962 0.971429
46 D3T 0.542169 0.971831
47 DUT 0.542169 0.957143
48 ATM 0.542169 0.894737
49 TXS 0.538462 0.789474
50 YYY 0.536585 0.891892
51 T3S 0.525 0.789474
52 BVP 0.52381 0.944444
53 ABT 0.521739 0.884615
54 D4D 0.506024 0.928571
55 7SG 0.504274 0.864198
56 TQP 0.504274 0.864198
57 T5K 0.5 0.853659
58 2DT 0.5 0.957747
59 TPE 0.5 0.894737
60 T4K 0.5 0.853659
61 DT ME6 DT 0.5 0.87013
62 4TA 0.486486 0.807229
63 DCP 0.477273 0.891892
64 8DD 0.473118 0.8125
65 AZZ 0.469136 0.779221
66 DU 0.469136 0.942857
67 UMP 0.469136 0.942857
68 8GD 0.467391 0.829268
69 WMJ 0.452632 0.761905
70 DUP 0.449438 0.930556
71 D4T 0.449438 0.928571
72 6U4 0.447917 0.848101
73 ADS THS THS THS 0.444444 0.758621
74 DDN 0.439024 0.942857
75 3DT 0.428571 0.835616
76 UC5 0.425287 0.943662
77 ID2 0.423077 0.8
78 DT MA7 DT 0.420635 0.797619
79 8DG 0.418367 0.829268
80 DUN 0.41573 0.930556
81 5GW 0.410526 0.878378
82 DCM 0.406977 0.878378
83 DC 0.406977 0.878378
84 DT DC 0.405405 0.833333
85 74W 0.4 0.732558
86 74X 0.4 0.732558
87 D4M 0.4 0.914286
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RVG; Ligand: TYD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4rvg.bio1) has 44 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4RVG; 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: 4rvg.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
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