Receptor
PDB id Resolution Class Description Source Keywords
6I5Y 1.9 Å EC: 6.1.1.1 CRYSTAL STRUCTURE OF E. COLI TYRRS IN COMPLEX WITH 5'-O-(N-L SULFAMOYL-ADENOSINE ESCHERICHIA COLI BL21(DE3) PROTEIN-INHIBITOR COMPLEX ROSSMANN FOLD TRNA AMINOACYLATIO
Ref.: COMPARATIVE ANALYSIS OF PYRIMIDINE SUBSTITUTED AMINOACYL-SULFAMOYL NUCLEOSIDES AS POTENTIAL INHIBI TARGETING CLASS I AMINOACYL-TRNA SYNTHETASES. EUR.J.MED.CHEM. V. 173 154 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
YSA A:501;
B:501;
 Valid;
Valid;
 none;
none;
 submit data
509.493 C19 H23 N7 O8 S c1cc(...
EDO A:502;
B:503;
B:502;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6HB5 1.88 Å EC: 6.1.1.1 CRYSTAL STRUCTURE OF E. COLI TYRRS IN COMPLEX WITH 5'-O-(N-L SULFAMOYL-CYTIDINE ESCHERICHIA COLI (STRAIN B / BL21-DE3)ORGANISM_TAXID: 469008 PROTEIN-INHIBITOR COMPLEX ROSSMANN FOLD TRNA AMINOACYLATIO
Ref.: COMPARATIVE ANALYSIS OF PYRIMIDINE SUBSTITUTED AMINOACYL-SULFAMOYL NUCLEOSIDES AS POTENTIAL INHIBI TARGETING CLASS I AMINOACYL-TRNA SYNTHETASES. EUR.J.MED.CHEM. V. 173 154 2019
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 6HB7 - Y3U C19 H24 N4 O10 S CN1C(=O)C=....
2 6HB6 - YSU C18 H22 N4 O10 S c1cc(ccc1C....
3 6HB5 - YSC C18 H23 N5 O9 S c1cc(ccc1C....
4 7AP3 - RRB C22 H27 N5 O9 S c1cc(ccc1C....
5 6I5Y - YSA C19 H23 N7 O8 S c1cc(ccc1C....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 1WQ4 - TYR C9 H11 N O3 c1cc(ccc1C....
2 2YXN - AZY C9 H10 N4 O3 c1cc(c(cc1....
3 1WQ3 - IYR C9 H10 I N O3 c1cc(c(cc1....
4 1X8X - TYR C9 H11 N O3 c1cc(ccc1C....
5 6HB7 - Y3U C19 H24 N4 O10 S CN1C(=O)C=....
6 6HB6 - YSU C18 H22 N4 O10 S c1cc(ccc1C....
7 6HB5 - YSC C18 H23 N5 O9 S c1cc(ccc1C....
8 7AP3 - RRB C22 H27 N5 O9 S c1cc(ccc1C....
9 6I5Y - YSA C19 H23 N7 O8 S c1cc(ccc1C....
10 1TYB - TYR C9 H11 N O3 c1cc(ccc1C....
11 4TS1 Kd = 11.6 uM TYR C9 H11 N O3 c1cc(ccc1C....
12 1TYD - TYR C9 H11 N O3 c1cc(ccc1C....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1WQ4 - TYR C9 H11 N O3 c1cc(ccc1C....
2 2YXN - AZY C9 H10 N4 O3 c1cc(c(cc1....
3 1WQ3 - IYR C9 H10 I N O3 c1cc(c(cc1....
4 1X8X - TYR C9 H11 N O3 c1cc(ccc1C....
5 1Y42 - TYR C9 H11 N O3 c1cc(ccc1C....
6 6HB7 - Y3U C19 H24 N4 O10 S CN1C(=O)C=....
7 6HB6 - YSU C18 H22 N4 O10 S c1cc(ccc1C....
8 6HB5 - YSC C18 H23 N5 O9 S c1cc(ccc1C....
9 7AP3 - RRB C22 H27 N5 O9 S c1cc(ccc1C....
10 6I5Y - YSA C19 H23 N7 O8 S c1cc(ccc1C....
11 1JIL ic50 = 4 nM 485 C17 H24 N2 O8 C[C@@H]1[C....
12 2PID - YSA C19 H23 N7 O8 S c1cc(ccc1C....
13 1TYB - TYR C9 H11 N O3 c1cc(ccc1C....
14 4TS1 Kd = 11.6 uM TYR C9 H11 N O3 c1cc(ccc1C....
15 1TYD - TYR C9 H11 N O3 c1cc(ccc1C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: YSA; Similar ligands found: 255
No: Ligand ECFP6 Tc MDL keys Tc
1 YSA 1 1
2 SSA 0.76087 0.952941
3 5CA 0.744681 0.952941
4 A5A 0.731183 0.940476
5 LSS 0.729167 0.931035
6 DSZ 0.729167 0.952941
7 GSU 0.72449 0.952941
8 KAA 0.707071 0.920455
9 WSA 0.700935 0.987952
10 VMS 0.697917 0.918605
11 54H 0.697917 0.918605
12 TSB 0.690722 0.929412
13 53H 0.690722 0.908046
14 52H 0.680412 0.908046
15 NSS 0.66 0.952941
16 NVA LMS 0.653465 0.920455
17 G5A 0.645833 0.952941
18 RRB 0.633027 0.964286
19 8X1 0.607843 0.920455
20 D3Y 0.607843 0.752941
21 8PZ 0.601852 0.97619
22 5AS 0.6 0.886364
23 B1U 0.581818 0.879121
24 P5A 0.579439 0.910112
25 8Q2 0.577586 0.965116
26 LMS 0.569892 0.939759
27 4YB 0.561404 0.953488
28 649 0.555556 0.954023
29 AHX 0.53211 0.806818
30 FA5 0.530973 0.835294
31 SON 0.53 0.793103
32 CA0 0.524752 0.781609
33 SLU 0.52381 0.94186
34 5AL 0.52381 0.790698
35 3NZ 0.522523 0.747126
36 AMP 0.520833 0.776471
37 A 0.520833 0.776471
38 5X8 0.519608 0.729412
39 AMP MG 0.515464 0.764706
40 SRP 0.514019 0.813953
41 LEU LMS 0.513514 0.855556
42 ABM 0.50505 0.758621
43 A2D 0.50505 0.8
44 45A 0.50505 0.758621
45 KG4 0.504854 0.781609
46 QA7 0.504587 0.764045
47 DLL 0.504505 0.811765
48 FYA 0.504425 0.811765
49 AN2 0.5 0.790698
50 XAH 0.5 0.78022
51 SRA 0.5 0.802326
52 AMO 0.495495 0.813953
53 V2G 0.495327 0.786517
54 ADX 0.495146 0.894118
55 AU1 0.495146 0.781609
56 AP2 0.49505 0.772727
57 A12 0.49505 0.772727
58 BA3 0.49505 0.8
59 AOC 0.494949 0.697674
60 NB8 0.491228 0.806818
61 8LQ 0.490909 0.793103
62 ADP 0.490196 0.77907
63 AP5 0.490196 0.8
64 B4P 0.490196 0.8
65 5CD 0.48913 0.682353
66 7MD 0.487395 0.78022
67 9ZD 0.486486 0.775281
68 9ZA 0.486486 0.775281
69 8QN 0.486486 0.790698
70 8LH 0.486239 0.772727
71 GAP 0.485981 0.761364
72 AT4 0.485437 0.793103
73 ADP MG 0.485437 0.776471
74 ADP BEF 0.485437 0.776471
75 YSC 0.482456 0.886364
76 LAD 0.482456 0.777778
77 WAQ 0.482456 0.775281
78 8LE 0.481481 0.764045
79 M33 0.480769 0.770115
80 ME8 0.478261 0.78022
81 TXA 0.478261 0.772727
82 5N5 0.478261 0.674419
83 DAL AMP 0.477477 0.770115
84 MAP 0.477477 0.764045
85 SAH 0.476636 0.712644
86 50T 0.47619 0.75
87 SFG 0.47619 0.697674
88 ATP 0.47619 0.77907
89 HEJ 0.47619 0.77907
90 ACP 0.47619 0.781609
91 3UK 0.473684 0.802326
92 OOB 0.473214 0.811765
93 RAB 0.472527 0.694118
94 ADN 0.472527 0.694118
95 XYA 0.472527 0.694118
96 ANP 0.472222 0.781609
97 AR6 0.471698 0.77907
98 APC 0.471698 0.772727
99 5FA 0.471698 0.77907
100 APR 0.471698 0.77907
101 AQP 0.471698 0.77907
102 PRX 0.471698 0.741573
103 9SN 0.470085 0.766667
104 B5V 0.469565 0.813953
105 3DH 0.469388 0.678161
106 RUZ 0.469027 0.929412
107 PAJ 0.469027 0.73913
108 4AD 0.469027 0.804598
109 TYM 0.467742 0.835294
110 AD9 0.46729 0.761364
111 ADV 0.46729 0.772727
112 SA8 0.46729 0.663043
113 APC MG 0.46729 0.758621
114 AGS 0.46729 0.804598
115 RBY 0.46729 0.772727
116 ADP PO3 0.46729 0.776471
117 ATP MG 0.46729 0.776471
118 B5Y 0.466102 0.804598
119 9K8 0.465517 0.778947
120 1ZZ 0.465517 0.723404
121 00A 0.464912 0.775281
122 7MC 0.464 0.763441
123 ANP MG 0.463636 0.790698
124 BEF ADP 0.462963 0.758621
125 H1Q 0.462264 0.767442
126 YSU 0.46087 0.895349
127 QXP 0.460177 0.852273
128 SMM 0.459459 0.680851
129 S7M 0.459459 0.684783
130 ACQ 0.458716 0.781609
131 T99 0.458716 0.793103
132 TAT 0.458716 0.793103
133 SAM 0.458716 0.684783
134 AMP DBH 0.458333 0.761364
135 A4D 0.457447 0.694118
136 A3S 0.457143 0.729412
137 J4G 0.456897 0.804598
138 Y3U 0.456897 0.875
139 R2V 0.456897 0.873563
140 ADQ 0.45614 0.781609
141 6RE 0.455446 0.67033
142 B5M 0.453782 0.804598
143 DTA 0.453608 0.729412
144 M2T 0.453608 0.666667
145 PTJ 0.452991 0.747253
146 YLC 0.452381 0.76087
147 YLB 0.452381 0.744681
148 JNT 0.452174 0.781609
149 YLP 0.451613 0.744681
150 A22 0.451327 0.790698
151 ATF 0.45045 0.752809
152 ALF ADP 0.45045 0.725275
153 VO4 ADP 0.45045 0.761364
154 SAI 0.449541 0.685393
155 RRW 0.449153 0.897727
156 RSN 0.449153 0.918605
157 MYR AMP 0.449153 0.705263
158 KB1 0.449153 0.673913
159 ADP BMA 0.448276 0.761364
160 OAD 0.448276 0.781609
161 QXG 0.448276 0.863636
162 25A 0.447368 0.8
163 OZV 0.447368 0.77907
164 J7C 0.446602 0.677778
165 A3N 0.446602 0.651685
166 6YZ 0.446429 0.781609
167 PR8 0.444444 0.769231
168 LAQ 0.443548 0.76087
169 0UM 0.443478 0.655914
170 A1R 0.443478 0.775281
171 EP4 0.443299 0.644444
172 HQG 0.442478 0.770115
173 EEM 0.441441 0.648936
174 3OD 0.440678 0.781609
175 48N 0.44 0.766667
176 KOY 0.44 0.744186
177 4UU 0.439024 0.784091
178 ARG AMP 0.439024 0.734043
179 DND 0.436508 0.793103
180 9X8 0.435897 0.784091
181 A3T 0.435185 0.697674
182 F2R 0.435115 0.744681
183 5SV 0.434783 0.709677
184 MTA 0.434343 0.678161
185 IOT 0.434109 0.736842
186 A3R 0.431034 0.775281
187 7C5 0.430894 0.719101
188 YLA 0.430769 0.744681
189 A7D 0.429907 0.701149
190 KMQ 0.429752 0.752809
191 NAD TDB 0.429688 0.8
192 NAD IBO 0.429688 0.8
193 JB6 0.428571 0.816092
194 BIS 0.428571 0.736264
195 LPA AMP 0.428571 0.741935
196 GJV 0.428571 0.663043
197 S4M 0.428571 0.645833
198 AYB 0.427481 0.736842
199 GA7 0.427419 0.772727
200 NWW 0.427083 0.642857
201 80F 0.425373 0.782609
202 NAX 0.425197 0.788889
203 25L 0.425 0.790698
204 DQV 0.424 0.811765
205 TAD 0.424 0.777778
206 K15 0.423729 0.642105
207 VRT 0.423423 0.696629
208 A3G 0.423077 0.72093
209 DSH 0.423077 0.677778
210 4UV 0.422764 0.784091
211 TXE 0.421875 0.775281
212 OMR 0.421875 0.715789
213 ALF ADP 3PG 0.421875 0.73913
214 V47 0.421053 0.705882
215 COD 0.421053 0.739583
216 ATP A 0.418033 0.788235
217 ATP A A A 0.418033 0.788235
218 ZAS 0.417476 0.693182
219 SXZ 0.416667 0.684783
220 67D 0.416667 0.931035
221 YLY 0.416058 0.736842
222 62X 0.415254 0.628866
223 EO7 0.415094 0.896552
224 A5D 0.414414 0.729412
225 EU9 0.414062 0.715789
226 TXD 0.414062 0.775281
227 NAI 0.414062 0.775281
228 6V0 0.414062 0.766667
229 D4F 0.413043 0.8
230 MHZ 0.412844 0.65625
231 KXW 0.412698 0.681319
232 A3P 0.411215 0.776471
233 MAO 0.411215 0.709677
234 AF3 ADP 3PG 0.410853 0.73913
235 AMP NAD 0.410448 0.790698
236 NAD 0.410448 0.811765
237 GEK 0.410256 0.727273
238 NEC 0.409524 0.636364
239 AHZ 0.409449 0.723404
240 2VA 0.409091 0.681818
241 3AM 0.407767 0.744186
242 Q34 0.407692 0.652632
243 BT5 0.407407 0.755319
244 CNA 0.406015 0.813953
245 AR6 AR6 0.404762 0.77907
246 AFH 0.404762 0.758242
247 A3D 0.404412 0.802326
248 5AD 0.404255 0.630952
249 KYE 0.403226 0.652632
250 4UW 0.403101 0.758242
251 7D5 0.401961 0.707865
252 GTA 0.401575 0.741935
253 K3E 0.4 0.677778
254 N37 0.4 0.704545
255 NAQ 0.4 0.766667
Similar Ligands (3D)
Ligand no: 1; Ligand: YSA; Similar ligands found: 3
No: Ligand Similarity coefficient
1 TYR AMP 0.9711
2 MSP 0.8658
3 MOD 0.8570
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6HB5; Ligand: YSC; 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: 6hb5.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6HB5; Ligand: YSC; 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: 6hb5.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
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