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 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: 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
Ligand no: 2; Ligand: TYD; Similar ligands found: 88
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 18T 0.682353 0.932432
7 TDX 0.682353 0.945205
8 3R2 0.682353 0.92
9 1JB 0.682353 0.932432
10 TRH 0.682353 0.932432
11 ATY 0.670886 0.945205
12 3YN 0.666667 0.932432
13 DWN 0.666667 0.907895
14 T3F 0.666667 0.907895
15 T3Q 0.666667 0.907895
16 TBD 0.662338 0.958904
17 0N2 0.659091 0.896104
18 T46 0.659091 0.932432
19 AZD 0.654321 0.907895
20 MMF 0.651685 0.907895
21 0FX 0.651685 0.907895
22 LLT 0.641791 0.873239
23 THM 0.641791 0.873239
24 QDM 0.637363 0.896104
25 AKM 0.630435 0.886076
26 FNF 0.630435 0.92
27 JHZ 0.630435 0.884615
28 1YF 0.630435 0.92
29 4TG 0.623656 0.92
30 DUD 0.61039 0.957143
31 0DN 0.6 0.833333
32 UFP 0.6 0.905405
33 DT DT DT DT DT 0.582418 0.945205
34 QUH 0.58 0.907895
35 FUH 0.58 0.907895
36 T5A 0.572816 0.841463
37 5HU 0.571429 0.971831
38 BRU 0.571429 0.905405
39 FDM 0.564103 0.918919
40 NYM 0.564103 0.958333
41 5IU 0.564103 0.905405
42 DT DT PST 0.56383 0.881579
43 T3P 0.56 0.943662
44 THP 0.556962 0.971429
45 ATM 0.542169 0.894737
46 D3T 0.542169 0.971831
47 DUT 0.542169 0.957143
48 TXS 0.538462 0.789474
49 YYY 0.536585 0.891892
50 T3S 0.525 0.789474
51 BVP 0.52381 0.944444
52 ABT 0.521739 0.884615
53 DT DT DT 0.511364 0.878378
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 TPE 0.5 0.894737
59 DT ME6 DT 0.5 0.87013
60 T4K 0.5 0.853659
61 2DT 0.5 0.957747
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 UMP 0.469136 0.942857
67 DU 0.469136 0.942857
68 8GD 0.467391 0.829268
69 WMJ 0.452632 0.761905
70 D4T 0.449438 0.928571
71 DUP 0.449438 0.930556
72 6U4 0.447917 0.848101
73 DDN 0.439024 0.942857
74 3DT 0.428571 0.835616
75 UC5 0.425287 0.943662
76 ID2 0.423077 0.8
77 DT MA7 DT 0.420635 0.797619
78 8DG 0.418367 0.829268
79 DUN 0.41573 0.930556
80 DUT MG 0.413043 0.864865
81 5GW 0.410526 0.878378
82 DC 0.406977 0.878378
83 DCM 0.406977 0.878378
84 DT DC 0.405405 0.833333
85 ADS THS THS THS 0.403361 0.767442
86 74W 0.4 0.732558
87 D4M 0.4 0.914286
88 74X 0.4 0.732558
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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