Receptor
PDB id Resolution Class Description Source Keywords
4E2X 1.4 Å EC: 2.1.1.- X-RAY STRUCTURE OF THE Y222F MUTANT OF TCAB9, A C-3'- METHYLTRANSFERASE, IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEIN MICROMONOSPORA CHALCEA KIJANOSE TETRONITROSE TETRADEOXY SUGAR SUGAR METHYLATIONTRANSFERASE
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
EDO A:502;
A:503;
A:504;
A:505;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
SAH A:506;
Valid;
none;
submit data
384.411 C14 H20 N6 O5 S c1nc(...
TYD A:507;
Valid;
none;
submit data
402.188 C10 H16 N2 O11 P2 CC1=C...
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: 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
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 : 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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