Receptor
PDB id Resolution Class Description Source Keywords
2J3L 2.3 Å EC: 6.1.1.15 PROLYL-TRNA SYNTHETASE FROM ENTEROCOCCUS FAECALIS COMPLEXED WITH A PROLYL-ADENYLATE ANALOGUE ('5'-O-(N-(L-PROLYL)- S ULFAMOYL)ADENOSINE) ENTEROCOCCUS FAECALIS BACTERIAL-TYPE PROLYL-TRNA SYNTHETASE CLASS II AMINOACYL- TSYNTHETASE EDITING TRANSLATION ATP + L-PROLINE + TRNA (PGIVES AMP + PPI + L-PROLYL-TRNA(PRO) LIGASE
Ref.: STRUCTURES OF TWO BACTERIAL PROLYL-TRNA SYNTHETASES AND WITHOUT A CIS-EDITING DOMAIN. STRUCTURE V. 14 1511 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
P5A A:1576;
B:1582;
 Valid;
Valid;
 none;
none;
 submit data
443.435 C15 H21 N7 O7 S c1nc(...
SO4 A:1566;
A:1567;
A:1568;
A:1569;
A:1570;
A:1571;
A:1572;
A:1573;
A:1574;
A:1575;
B:1571;
B:1572;
B:1573;
B:1574;
B:1575;
B:1576;
B:1577;
B:1578;
B:1579;
B:1580;
B:1581;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2J3M 2.3 Å EC: 6.1.1.15 PROLYL-TRNA SYNTHETASE FROM ENTEROCOCCUS FAECALIS COMPLEXED WITH ATP, MANGANESE AND PROLINOL ENTEROCOCCUS FAECALIS BACTERIAL-TYPE PROLYL-TRNA SYNTHETASE CLASS II AMINOACYL- TRNA SYNTHETASE EDITING TRANSLATION ATP + L-PROLINE + TRNA (PRO) GIVES AMP + PPI + L-PROLYL-TRNA(PRO) LIGASE
Ref.: STRUCTURES OF TWO BACTERIAL PROLYL-TRNA SYNTHETASES WITH AND WITHOUT A CIS-EDITING DOMAIN. STRUCTURE V. 14 1511 2006
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2J3L - P5A C15 H21 N7 O7 S c1nc(c2c(n....
2 2J3M - PRI C5 H9 N O C1C[C@H](N....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2J3L - P5A C15 H21 N7 O7 S c1nc(c2c(n....
2 2J3M - PRI C5 H9 N O C1C[C@H](N....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2J3L - P5A C15 H21 N7 O7 S c1nc(c2c(n....
2 2J3M - PRI C5 H9 N O C1C[C@H](N....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: P5A; Similar ligands found: 264
No: Ligand ECFP6 Tc MDL keys Tc
1 P5A 1 1
2 8X1 0.892857 0.94382
3 G5A 0.681319 0.954023
4 54H 0.663158 0.877778
5 VMS 0.663158 0.877778
6 A5A 0.659574 0.897727
7 SSA 0.652632 0.931818
8 52H 0.645833 0.868132
9 NSS 0.642857 0.910112
10 DSZ 0.642857 0.910112
11 TSB 0.639175 0.88764
12 5CA 0.639175 0.931818
13 53H 0.639175 0.868132
14 5AS 0.633333 0.910112
15 LSS 0.626263 0.89011
16 PR8 0.623762 0.853933
17 NVA LMS 0.62 0.901099
18 KAA 0.607843 0.988506
19 GSU 0.607843 0.931818
20 LMS 0.602273 0.896552
21 B1U 0.59434 0.822917
22 8PZ 0.584906 0.910112
23 YSA 0.579439 0.910112
24 SON 0.574468 0.777778
25 4YB 0.558559 0.911111
26 WSA 0.552632 0.920455
27 A 0.549451 0.741573
28 AMP 0.549451 0.741573
29 8Q2 0.547826 0.880435
30 AMP MG 0.543478 0.730337
31 649 0.53913 0.955056
32 CA0 0.536082 0.747253
33 45A 0.531915 0.725275
34 A2D 0.531915 0.744444
35 ABM 0.531915 0.725275
36 KG4 0.530612 0.747253
37 AT4 0.525773 0.758242
38 AOC 0.521277 0.666667
39 AP2 0.520833 0.758242
40 A12 0.520833 0.758242
41 BA3 0.520833 0.744444
42 ADX 0.520408 0.853933
43 AU1 0.520408 0.747253
44 V2G 0.519608 0.811111
45 8LE 0.519608 0.731183
46 5AL 0.519608 0.755556
47 AP5 0.515464 0.744444
48 ADP 0.515464 0.744444
49 B4P 0.515464 0.744444
50 QA7 0.514286 0.731183
51 SRA 0.510638 0.766667
52 ADP MG 0.510204 0.741573
53 AN2 0.510204 0.755556
54 ADP BEF 0.510204 0.741573
55 GAP 0.509804 0.766667
56 LEU LMS 0.509259 0.819149
57 SLU 0.508065 0.858696
58 M33 0.50505 0.736264
59 APC MG 0.504951 0.744444
60 XYA 0.5 0.681818
61 HEJ 0.5 0.744444
62 50T 0.5 0.717391
63 5CD 0.5 0.651685
64 ATP 0.5 0.744444
65 ACP 0.5 0.747253
66 ADN 0.5 0.681818
67 DAL AMP 0.5 0.736264
68 RAB 0.5 0.681818
69 9ZD 0.495327 0.741935
70 9ZA 0.495327 0.741935
71 8LH 0.495238 0.758242
72 SRP 0.495238 0.797753
73 ANP 0.495146 0.747253
74 5FA 0.49505 0.744444
75 APR 0.49505 0.744444
76 PRX 0.49505 0.747253
77 AR6 0.49505 0.744444
78 APC 0.49505 0.758242
79 AQP 0.49505 0.744444
80 3DH 0.494624 0.648352
81 4AD 0.490741 0.769231
82 A1R 0.490741 0.820225
83 A3R 0.490741 0.820225
84 AD9 0.490196 0.728261
85 ATP MG 0.490196 0.741573
86 ADP PO3 0.490196 0.741573
87 RBY 0.490196 0.758242
88 AGS 0.490196 0.769231
89 ADV 0.490196 0.758242
90 5N5 0.488636 0.681818
91 TXA 0.486486 0.73913
92 NB8 0.486486 0.771739
93 DLL 0.486239 0.755556
94 AHX 0.486239 0.791209
95 8LQ 0.485981 0.758242
96 ATF 0.485714 0.72043
97 ANP MG 0.485714 0.755556
98 BEF ADP 0.485437 0.725275
99 5X8 0.485149 0.696629
100 A4D 0.483146 0.681818
101 3UK 0.481818 0.747253
102 8QN 0.481481 0.755556
103 OOB 0.481481 0.755556
104 T99 0.480769 0.758242
105 ACQ 0.480769 0.747253
106 TAT 0.480769 0.758242
107 DTA 0.478261 0.696629
108 AMO 0.477064 0.777778
109 PAJ 0.477064 0.726316
110 3OD 0.473214 0.747253
111 9K8 0.473214 0.73
112 MTA 0.473118 0.648352
113 00A 0.472727 0.723404
114 A22 0.472222 0.736264
115 MAP 0.472222 0.731183
116 ALF ADP 0.471698 0.694737
117 VO4 ADP 0.471698 0.728261
118 H1Q 0.470588 0.733333
119 A3N 0.469388 0.659341
120 OAD 0.468468 0.747253
121 QXP 0.46789 0.835165
122 25A 0.46789 0.744444
123 EP4 0.467391 0.634409
124 6YZ 0.46729 0.747253
125 9SN 0.464912 0.715789
126 GJV 0.464646 0.706522
127 LAD 0.464286 0.842697
128 B5V 0.464286 0.73913
129 WAQ 0.464286 0.820225
130 6RE 0.463918 0.695652
131 ADQ 0.463636 0.747253
132 HQG 0.462963 0.736264
133 M2T 0.462366 0.638298
134 LAQ 0.462185 0.804348
135 B5Y 0.46087 0.731183
136 FA5 0.46087 0.777778
137 BIS 0.460177 0.741935
138 1ZZ 0.460177 0.765957
139 PTJ 0.460177 0.715789
140 ME8 0.460177 0.765957
141 JNT 0.459459 0.786517
142 LPA AMP 0.458333 0.784946
143 7MD 0.457627 0.844444
144 ARG AMP 0.457627 0.776596
145 XAH 0.456897 0.844444
146 MYR AMP 0.45614 0.747368
147 ADP BMA 0.455357 0.728261
148 9X8 0.455357 0.75
149 5SV 0.454545 0.752688
150 DND 0.454545 0.73913
151 NAX 0.454545 0.755319
152 J7C 0.454545 0.703297
153 OZV 0.454545 0.744444
154 YLY 0.453846 0.817204
155 AMP DBH 0.452991 0.691489
156 NX8 0.45283 0.733333
157 TXE 0.45082 0.76087
158 NWW 0.450549 0.613636
159 7C5 0.449153 0.670213
160 B5M 0.448276 0.731183
161 4UU 0.445378 0.731183
162 NEC 0.444444 0.644444
163 DSH 0.444444 0.761364
164 25L 0.443478 0.736264
165 SAH 0.443396 0.719101
166 4UW 0.442623 0.708333
167 6V0 0.442623 0.734043
168 QXG 0.442478 0.826087
169 SFG 0.442308 0.704545
170 TAD 0.441667 0.763441
171 4UV 0.440678 0.731183
172 OMR 0.439024 0.757895
173 ZAS 0.438776 0.681319
174 R2V 0.438596 0.835165
175 NWZ 0.438095 0.722222
176 G3A 0.436975 0.715789
177 139 0.436508 0.774194
178 KMQ 0.435897 0.72043
179 S4M 0.435644 0.723404
180 L3W 0.435484 0.73913
181 7MC 0.435484 0.826087
182 NAD TDB 0.435484 0.744444
183 NAD IBO 0.435484 0.744444
184 FYA 0.434783 0.775281
185 JB6 0.434783 0.8
186 YLP 0.434426 0.826087
187 48N 0.434426 0.734043
188 SA8 0.433962 0.688172
189 G5P 0.433333 0.715789
190 NWQ 0.43299 0.6
191 A4P 0.432 0.717172
192 MAO 0.431373 0.734043
193 UP5 0.430894 0.731183
194 TXD 0.430894 0.76087
195 NAI 0.430894 0.723404
196 N5O 0.43 0.715909
197 A3G 0.43 0.727273
198 SAI 0.429907 0.692308
199 DQV 0.429752 0.755556
200 GTA 0.429752 0.693878
201 3AM 0.428571 0.730337
202 IOT 0.428571 0.817204
203 TYM 0.427419 0.777778
204 AF3 ADP 3PG 0.427419 0.708333
205 ALF ADP 3PG 0.427419 0.708333
206 V47 0.427273 0.674157
207 S7M 0.427273 0.691489
208 SMM 0.427273 0.6875
209 AHZ 0.42623 0.71134
210 SAM 0.425926 0.691489
211 YLA 0.425197 0.826087
212 UPA 0.424 0.741935
213 4TC 0.424 0.734043
214 YLB 0.424 0.826087
215 YLC 0.424 0.824176
216 ATP A A A 0.423729 0.733333
217 ATP A 0.423729 0.733333
218 BT5 0.423077 0.797872
219 A7D 0.423077 0.727273
220 KOY 0.422764 0.692308
221 EEM 0.422018 0.65625
222 CNA 0.421875 0.758242
223 EO7 0.421569 0.857143
224 N5A 0.421569 0.693182
225 AR6 AR6 0.421488 0.725275
226 A5D 0.420561 0.696629
227 MHZ 0.419048 0.734043
228 F2R 0.418605 0.787234
229 2AM 0.418367 0.722222
230 A2P 0.417476 0.730337
231 A3P 0.417476 0.741573
232 A6D 0.417391 0.666667
233 AMP NAD 0.415385 0.736264
234 NAD 0.415385 0.755556
235 T5A 0.414062 0.75
236 594 0.413534 0.875
237 0UM 0.412281 0.736264
238 5AD 0.411111 0.602273
239 AYB 0.410853 0.817204
240 SXZ 0.410256 0.709677
241 AFH 0.409836 0.726316
242 GA7 0.409836 0.73913
243 A3S 0.409524 0.715909
244 A3D 0.409091 0.747253
245 7D5 0.408163 0.714286
246 D4F 0.407407 0.729167
247 KY2 0.40708 0.728261
248 NAJ PZO 0.406015 0.715789
249 OVE 0.405941 0.736264
250 K15 0.405172 0.702128
251 4TA 0.40458 0.739583
252 BTX 0.40458 0.806452
253 COD 0.40458 0.819149
254 6C6 0.40367 0.797753
255 GEK 0.403509 0.733333
256 A3T 0.401869 0.685393
257 J4G 0.401709 0.788889
258 K2K 0.401709 0.695652
259 AP0 0.401575 0.697917
260 DZD 0.401515 0.782609
261 K3K 0.4 0.655914
262 67D 0.4 0.89011
263 BS5 0.4 0.88172
264 V3L 0.4 0.744444
Similar Ligands (3D)
Ligand no: 1; Ligand: P5A; Similar ligands found: 7
No: Ligand Similarity coefficient
1 GNP 0.9069
2 FZT 0.9002
3 FZQ 0.8971
4 FZK 0.8890
5 3AT 0.8845
6 RUZ 0.8653
7 GDP 0.8634
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2J3M; Ligand: ATP; 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: 2j3m.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2J3M; Ligand: PRI; 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: 2j3m.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2J3M; Ligand: PRI; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2j3m.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2J3M; Ligand: ATP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2j3m.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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