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Receptor
PDB id Resolution Class Description Source Keywords
1VCE 2.1 Å EC: 2.1.1.98 CRYSTAL STRUCTURE OF PROJECT ID PH0725 FROM PYROCOCCUS HORIK PYROCOCCUS HORIKOSHII TRANSFERASE STRUCTURAL GENOMICS RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI
Ref.: CRYSTAL STRUCTURE OF DIPHTHINE SYNTHASE FROM PYROCO HORIKOSHII OT3 TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAH A:1300;
Valid;
none;
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384.411 C14 H20 N6 O5 S c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1VCE 2.1 Å EC: 2.1.1.98 CRYSTAL STRUCTURE OF PROJECT ID PH0725 FROM PYROCOCCUS HORIK PYROCOCCUS HORIKOSHII TRANSFERASE STRUCTURAL GENOMICS RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI
Ref.: CRYSTAL STRUCTURE OF DIPHTHINE SYNTHASE FROM PYROCO HORIKOSHII OT3 TO BE PUBLISHED
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1VCE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1VCE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1VCE - SAH C14 H20 N6 O5 S c1nc(c2c(n....
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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1VCE; Ligand: SAH; Similar sites found with APoc: 106
This union binding pocket(no: 1) in the query (biounit: 1vce.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 3L9R L9R None
2 5N0O SAM 1.50943
3 6GEW SFG 1.50943
4 6GEW SAH 1.50943
5 3FXU TSU 1.50943
6 2AWN ADP 1.50943
7 5D9G GLU ASN LEU TYR PHE GLN 1.62602
8 5DYO FLU 1.83486
9 6MJF SAH 1.88679
10 5KJW 53C 1.88679
11 5XHA FRU 2.26415
12 5YJS SAL 2.26415
13 6F3M NAD 2.26415
14 4TWP AXI 2.26415
15 2C5S AMP 2.64151
16 3A23 GAL 2.64151
17 3ZF8 GDP 2.64151
18 3QSB 743 2.64151
19 1W8S FBP 2.6616
20 2VDF OCT 2.7668
21 4KBA 1QM 3.01887
22 5W4W 9WG 3.01887
23 5G48 1FL 3.01887
24 5VN0 FAD 3.01887
25 5OCG 9R5 3.1746
26 1GXU 2HP 3.2967
27 1C1X HFA 3.39623
28 1BW9 PPY 3.39623
29 4I3V NAD 3.39623
30 4NOS ITU 3.39623
31 3OQJ 3CX 3.50195
32 3SAO DBH 3.75
33 1KOR ARG 3.77358
34 1KOR ANP 3.77358
35 1OFL NGK GCD 3.77358
36 1KOR SIN 3.77358
37 1GPM AMP 3.77358
38 1CT9 AMP 4.15094
39 1LSH PLD 4.15094
40 1RYD GLC 4.15094
41 4A59 AMP 4.15094
42 2Z9I GLY ALA THR VAL 4.15094
43 3OCP CMP 4.31655
44 6GNO XDI 4.44444
45 1F9V ADP 4.5283
46 1RRC ADP 4.5283
47 4JNA FAD 4.5283
48 3UYK 0CX 4.5283
49 6FA4 D1W 4.62428
50 5CIC 51R 4.62963
51 2E0N SAH 4.6332
52 4MOB ADP 4.90566
53 4NAT 2W5 5
54 3TTZ 07N 5.05051
55 1MFI FHC 5.26316
56 2G30 ALA ALA PHE 5.81395
57 4YRI 4JH 6.03774
58 3LTW HLZ 6.03774
59 1Y7P RIP 6.27803
60 2OFD NGA 6.33803
61 2OG2 MLI 6.41509
62 3B9Q MLI 6.41509
63 5LXT GTP 6.41509
64 3E7S AT2 6.41509
65 4X6F 3XU 6.66667
66 4WOE ADP 6.79245
67 3H0L ADP 6.79245
68 4O9S 2RY 6.97674
69 4WO4 JLS 7
70 5IDB BMA 7.04225
71 5WL1 CUY 7.07071
72 5WL1 D3D 7.07071
73 3HUJ AGH 7.07071
74 4RF7 ARG 7.16981
75 2XG5 EC5 7.33945
76 2XG5 EC2 7.33945
77 2YKL NLD 7.54717
78 2Z3U CRR 7.92453
79 5A7Y SAH 7.92453
80 1K97 ASP 7.92453
81 1K97 CIR 7.92453
82 1UH4 GLC 8.30189
83 2CDC XYS 8.30189
84 4B5W PYR 8.59375
85 1LNX URI 8.64198
86 6EK3 OUL 9.04977
87 5NLM IOS 9.0566
88 1S7N COA 9.34066
89 3RWP ABQ 9.6463
90 4KP7 NAP 9.81132
91 4KP7 1UQ 9.81132
92 1KSK URA 10.6838
93 2QE0 NAP 11.6981
94 2NU8 COA 12.4528
95 3CBC DBS 12.6263
96 1EP2 ORO 12.8302
97 1YNS HPO 13.0268
98 5Y4R C2E 13.5849
99 1ZEI CRS 15.0943
100 2YBQ SAH 18.4906
101 2YBQ UP2 18.4906
102 1PJS SAH 19.6226
103 5HW4 SAM 21.7742
104 1V9A SAH 24.6862
105 2QBU SAH 28.0172
106 1CBF SAH 33.9623
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