Receptor
PDB id Resolution Class Description Source Keywords
4E32 1.5 Å EC: 2.1.1.- X-RAY STRUCTURE OF THE C-3'-METHYLTRANSFERASE TCAB9 IN COMPL ADENOSYL-L-HOMOCYSTEINE AND DTDP-SUGAR SUBSTRATE MICROMONOSPORA CHALCEA KIJANOSE TETRONITROSE TETRADEOXY SUGAR KETO SUGAR SUGAR METHYLATION TRANSFERASE
Ref.: PROBING THE CATALYTIC MECHANISM OF A C-3'-METHYLTRA INVOLVED IN THE BIOSYNTHESIS OF D-TETRONITROSE. PROTEIN SCI. V. 21 876 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DWN A:505;
Valid;
none;
submit data
529.33 C16 H25 N3 O13 P2 C[C@@...
EDO A:502;
A:503;
Invalid;
Invalid;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
SAH A:504;
Valid;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
ZN A:501;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3NDJ 1.5 Å EC: 2.1.1.- X-RAY STRUCTURE OF A C-3'-METHYLTRANSFERASE IN COMPLEX WITH ADENOSYL-L-HOMOCYSTEINE AND SUGAR PRODUCT MICROMONOSPORA CHALCEA S-ADENOSYL-L-HOMOCYSTEINE KIJANOSE TETRONITROSE TETRADEOXKETO SUGAR MICROMONOSPORA CHALCEA TCAB9 C-3-prime -METHYLTRANSSUGAR METHYLATION TRANSFERASE
Ref.: MOLECULAR ARCHITECTURE OF A C-3'-METHYLTRANSFERASE IN THE BIOSYNTHESIS OF D-TETRONITROSE. BIOCHEMISTRY V. 49 5891 2010
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 60 families.
1 4E33 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 4E2W - JHZ C17 H27 N3 O13 P2 C[C@@H]1C(....
3 4E2Z - JHZ C17 H27 N3 O13 P2 C[C@@H]1C(....
4 4E30 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
5 4E2X - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 4E32 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 4E2Y - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 4E31 - JHZ C17 H27 N3 O13 P2 C[C@@H]1C(....
9 3NDI - SAM C15 H22 N6 O5 S C[S@@+](CC....
10 3NDJ - SAH C14 H20 N6 O5 S c1nc(c2c(n....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 54 families.
1 4E33 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 4E2W - JHZ C17 H27 N3 O13 P2 C[C@@H]1C(....
3 4E2Z - JHZ C17 H27 N3 O13 P2 C[C@@H]1C(....
4 4E30 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
5 4E2X - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 4E32 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 4E2Y - SAH C14 H20 N6 O5 S c1nc(c2c(n....
8 4E31 - JHZ C17 H27 N3 O13 P2 C[C@@H]1C(....
9 3NDI - SAM C15 H22 N6 O5 S C[S@@+](CC....
10 3NDJ - SAH C14 H20 N6 O5 S c1nc(c2c(n....
11 5T6B - SAH C14 H20 N6 O5 S c1nc(c2c(n....
12 5T67 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
13 5T64 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
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: DWN; Similar ligands found: 59
No: Ligand ECFP6 Tc MDL keys Tc
1 DWN 1 1
2 3YN 0.822222 0.973333
3 0N2 0.755319 0.986842
4 JHZ 0.72449 0.974026
5 T46 0.683673 0.947368
6 TTP 0.674157 0.907895
7 T3F 0.673469 0.973684
8 T3Q 0.673469 0.973684
9 AKM 0.673267 0.949367
10 TYD 0.666667 0.907895
11 0FX 0.66 0.973684
12 3R2 0.653061 0.935065
13 TRH 0.653061 0.947368
14 18T 0.653061 0.947368
15 1JB 0.653061 0.947368
16 TDX 0.636364 0.934211
17 QDM 0.631068 0.935897
18 DAU 0.63 0.922078
19 MMF 0.627451 0.948052
20 TLO 0.612245 0.909091
21 1YF 0.609524 0.960526
22 FNF 0.609524 0.960526
23 TMP 0.609195 0.894737
24 4TG 0.603774 0.960526
25 FUH 0.566372 0.948052
26 QUH 0.566372 0.948052
27 DT DT DT 0.533981 0.907895
28 TBD 0.515464 0.873418
29 DT DT DT DT DT 0.509259 0.909091
30 T5A 0.508333 0.857143
31 DT DT PST 0.5 0.8625
32 T4K 0.496183 0.869048
33 T5K 0.496183 0.869048
34 0DN 0.488636 0.779221
35 7SG 0.48855 0.879518
36 TQP 0.48855 0.879518
37 THM 0.482759 0.815789
38 LLT 0.482759 0.815789
39 DT ME6 DT 0.471074 0.8625
40 NYM 0.46875 0.921053
41 ATY 0.466019 0.934211
42 UFP 0.463158 0.825
43 AZD 0.457143 0.851852
44 THP 0.44898 0.881579
45 T3P 0.446809 0.857143
46 BRU 0.443299 0.825
47 5HU 0.443299 0.883117
48 TPE 0.442478 0.935065
49 FDM 0.438776 0.8375
50 5IU 0.438776 0.825
51 4TA 0.4375 0.823529
52 TXS 0.43299 0.7625
53 ATM 0.427184 0.839506
54 DUT 0.427184 0.868421
55 D3T 0.427184 0.883117
56 T3S 0.424242 0.78481
57 DUD 0.415842 0.868421
58 BVP 0.413462 0.858974
59 ABT 0.40708 0.831325
Ligand no: 2; Ligand: SAH; Similar ligands found: 211
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 DSH 0.692308 0.914286
6 SXZ 0.692308 0.916667
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 ADN 0.573333 0.84058
19 RAB 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 SMM 0.536842 0.88
28 SSA 0.536842 0.712644
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 A 0.529412 0.763158
36 LMS 0.529412 0.694118
37 AMP 0.529412 0.763158
38 5CA 0.525773 0.712644
39 ME8 0.524752 0.8125
40 M2T 0.52439 0.821918
41 6RE 0.523256 0.824324
42 GJV 0.522727 0.813333
43 AAT 0.515789 0.863014
44 LSS 0.515152 0.696629
45 KAA 0.514852 0.727273
46 J7C 0.511364 0.835616
47 A5A 0.510417 0.697674
48 SON 0.505495 0.805195
49 SRP 0.505155 0.805195
50 F0P 0.504505 0.915493
51 54H 0.5 0.681818
52 VMS 0.5 0.681818
53 ADX 0.5 0.694118
54 CA0 0.5 0.769231
55 AMO 0.5 0.805195
56 5AL 0.5 0.779221
57 KH3 0.5 0.866667
58 NVA LMS 0.49505 0.707865
59 AHX 0.49505 0.753086
60 TSB 0.494949 0.689655
61 53H 0.494949 0.674157
62 G5A 0.494737 0.712644
63 ABM 0.494382 0.74359
64 A2D 0.494382 0.74359
65 ZAS 0.494253 0.808219
66 A6D 0.490196 0.759494
67 8QN 0.49 0.779221
68 GEK 0.49 0.956522
69 GAP 0.489583 0.769231
70 AN2 0.48913 0.734177
71 A3S 0.48913 0.884058
72 S4M 0.488889 0.831169
73 SRA 0.488636 0.746835
74 LAD 0.485437 0.810127
75 52H 0.484848 0.674157
76 A12 0.483516 0.759494
77 BA3 0.483516 0.74359
78 AP2 0.483516 0.759494
79 NEC 0.483146 0.788732
80 AOC 0.483146 0.842857
81 Y3J 0.481481 0.768116
82 VRT 0.479167 0.861111
83 50T 0.478723 0.734177
84 B4P 0.478261 0.74359
85 ADP 0.478261 0.74359
86 5AS 0.478261 0.655556
87 AP5 0.478261 0.74359
88 A3N 0.477778 0.830986
89 YSA 0.476636 0.712644
90 XAH 0.476636 0.768293
91 0XU 0.473684 0.897059
92 AT4 0.473118 0.7375
93 WAQ 0.471154 0.807692
94 NSS 0.470588 0.712644
95 5AD 0.468354 0.791045
96 AU1 0.468085 0.725
97 M33 0.468085 0.734177
98 MAO 0.467391 0.797468
99 TXA 0.466667 0.759494
100 NB8 0.466667 0.775
101 A3G 0.466667 0.871429
102 3AM 0.465909 0.727273
103 DAL AMP 0.465347 0.779221
104 8X1 0.465347 0.707865
105 A3T 0.463158 0.842857
106 ATP 0.463158 0.74359
107 HEJ 0.463158 0.74359
108 ACP 0.463158 0.746835
109 7D7 0.4625 0.785714
110 LEU LMS 0.461538 0.688889
111 9ZA 0.460784 0.740741
112 9ZD 0.460784 0.740741
113 5FA 0.458333 0.74359
114 AQP 0.458333 0.74359
115 AR6 0.458333 0.766234
116 APC 0.458333 0.759494
117 APR 0.458333 0.766234
118 PRX 0.458333 0.746835
119 F2R 0.457627 0.75
120 IOT 0.456897 0.761905
121 4AD 0.456311 0.794872
122 PAJ 0.456311 0.722892
123 WSA 0.45614 0.72093
124 YAP 0.453704 0.794872
125 8PZ 0.453704 0.712644
126 FA5 0.453704 0.805195
127 ADP PO3 0.453608 0.763158
128 ADV 0.453608 0.782051
129 NVA 2AD 0.453608 0.849315
130 SAP 0.453608 0.728395
131 AGS 0.453608 0.728395
132 RBY 0.453608 0.782051
133 AD9 0.453608 0.725
134 PTJ 0.45283 0.731707
135 MHZ 0.452632 0.797468
136 00A 0.451923 0.740741
137 A3P 0.451613 0.74026
138 YLP 0.451327 0.771084
139 7MD 0.45045 0.768293
140 ALF ADP 0.45 0.707317
141 ADP ALF 0.45 0.707317
142 2VA 0.447917 0.819444
143 OOB 0.446602 0.779221
144 ANP 0.444444 0.725
145 T99 0.444444 0.7375
146 ACQ 0.444444 0.746835
147 TAT 0.444444 0.7375
148 P5A 0.443396 0.719101
149 7D5 0.443182 0.708861
150 A1R 0.442308 0.7625
151 YLC 0.439655 0.790123
152 2AM 0.438202 0.717949
153 DLL 0.438095 0.779221
154 ARG AMP 0.4375 0.759036
155 A22 0.436893 0.734177
156 D3Y 0.436893 0.859155
157 ATF 0.435644 0.716049
158 MYR AMP 0.435185 0.746988
159 80F 0.434426 0.75
160 SO8 0.434343 0.808219
161 OAD 0.433962 0.769231
162 3UK 0.433962 0.769231
163 TAD 0.433628 0.765432
164 25A 0.432692 0.74359
165 6YZ 0.431373 0.746835
166 VO4 ADP 0.431373 0.734177
167 ADP VO4 0.431373 0.734177
168 9SN 0.431193 0.731707
169 TYM 0.431034 0.805195
170 B5V 0.429907 0.759494
171 PR8 0.429907 0.8
172 ADQ 0.428571 0.746835
173 YLB 0.42735 0.771084
174 9K8 0.425926 0.67033
175 1ZZ 0.425926 0.746988
176 FYA 0.425926 0.779221
177 3OD 0.425926 0.769231
178 PPS 0.425743 0.674419
179 MAP 0.423077 0.707317
180 A2P 0.421053 0.727273
181 4YB 0.421053 0.735632
182 9X8 0.420561 0.75
183 ADP BMA 0.420561 0.746835
184 TYR AMP 0.419643 0.794872
185 5SV 0.419048 0.731707
186 3NZ 0.416667 0.824324
187 YLA 0.416667 0.771084
188 8Q2 0.415254 0.688889
189 A3R 0.415094 0.7625
190 B5Y 0.414414 0.75
191 B5M 0.414414 0.75
192 48N 0.413793 0.753086
193 LPA AMP 0.413793 0.768293
194 AYB 0.413223 0.761905
195 ACK 0.413043 0.710526
196 QQY 0.413043 0.696203
197 BIS 0.412844 0.719512
198 JB6 0.412844 0.7625
199 PAP 0.41 0.730769
200 DQV 0.408696 0.75641
201 OVE 0.408602 0.7125
202 AMP DBH 0.40708 0.746835
203 4UV 0.40708 0.75
204 3AD 0.406977 0.852941
205 AF3 ADP 3PG 0.40678 0.743902
206 OMR 0.40678 0.738095
207 LAQ 0.405172 0.768293
208 A A 0.40367 0.74359
209 7C5 0.403509 0.789474
210 7MC 0.403361 0.75
211 4UU 0.4 0.75
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3NDJ; Ligand: SAH; 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: 3ndj.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3NDJ; Ligand: JHZ; 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: 3ndj.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
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