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
Ligand no: 1; Ligand: P5A; Similar ligands found: 247
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 DSZ 0.642857 0.910112
10 NSS 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 LEU LMS 0.613861 0.880435
19 GSU 0.607843 0.931818
20 KAA 0.607843 0.988506
21 LMS 0.602273 0.896552
22 B1U 0.59434 0.822917
23 8PZ 0.584906 0.910112
24 YSA 0.579439 0.910112
25 SON 0.574468 0.777778
26 4YB 0.558559 0.911111
27 WSA 0.552632 0.920455
28 A 0.549451 0.741573
29 AMP 0.549451 0.741573
30 8Q2 0.547826 0.880435
31 649 0.53913 0.955056
32 CA0 0.536082 0.747253
33 A2D 0.531915 0.744444
34 ABM 0.531915 0.725275
35 45A 0.531915 0.725275
36 KG4 0.530612 0.747253
37 AT4 0.525773 0.758242
38 AOC 0.521277 0.666667
39 A12 0.520833 0.758242
40 BA3 0.520833 0.744444
41 AP2 0.520833 0.758242
42 AU1 0.520408 0.747253
43 ADX 0.520408 0.853933
44 8LE 0.519608 0.731183
45 5AL 0.519608 0.755556
46 ADP 0.515464 0.744444
47 AP5 0.515464 0.744444
48 B4P 0.515464 0.744444
49 SRA 0.510638 0.766667
50 AN2 0.510204 0.755556
51 ADP MG 0.510204 0.741573
52 GAP 0.509804 0.766667
53 SLU 0.508065 0.858696
54 M33 0.50505 0.736264
55 APC MG 0.504951 0.744444
56 XYA 0.5 0.681818
57 ATP 0.5 0.744444
58 5CD 0.5 0.651685
59 DAL AMP 0.5 0.736264
60 50T 0.5 0.717391
61 RAB 0.5 0.681818
62 ACP 0.5 0.747253
63 ADN 0.5 0.681818
64 HEJ 0.5 0.744444
65 9ZA 0.495327 0.741935
66 9ZD 0.495327 0.741935
67 SRP 0.495238 0.797753
68 8LH 0.495238 0.758242
69 ANP 0.495146 0.747253
70 AR6 0.49505 0.744444
71 APR 0.49505 0.744444
72 AQP 0.49505 0.744444
73 APC 0.49505 0.758242
74 5FA 0.49505 0.744444
75 PRX 0.49505 0.747253
76 3DH 0.494624 0.648352
77 4AD 0.490741 0.769231
78 A1R 0.490741 0.820225
79 A3R 0.490741 0.820225
80 ATP MG 0.490196 0.741573
81 ADP PO3 0.490196 0.741573
82 SAP 0.490196 0.769231
83 AD9 0.490196 0.728261
84 ADV 0.490196 0.758242
85 RBY 0.490196 0.758242
86 AGS 0.490196 0.769231
87 5N5 0.488636 0.681818
88 TXA 0.486486 0.73913
89 NB8 0.486486 0.771739
90 DLL 0.486239 0.755556
91 AHX 0.486239 0.791209
92 8LQ 0.485981 0.758242
93 ATF 0.485714 0.72043
94 5X8 0.485149 0.696629
95 A4D 0.483146 0.681818
96 3UK 0.481818 0.747253
97 8QN 0.481481 0.755556
98 OOB 0.481481 0.755556
99 TAT 0.480769 0.758242
100 ACQ 0.480769 0.747253
101 T99 0.480769 0.758242
102 DTA 0.478261 0.696629
103 PAJ 0.477064 0.726316
104 AMO 0.477064 0.777778
105 3OD 0.473214 0.747253
106 9K8 0.473214 0.73
107 MTA 0.473118 0.648352
108 00A 0.472727 0.723404
109 MAP 0.472222 0.731183
110 A22 0.472222 0.736264
111 ADP ALF 0.471698 0.694737
112 ALF ADP 0.471698 0.694737
113 H1Q 0.470588 0.733333
114 A3N 0.469388 0.659341
115 OAD 0.468468 0.747253
116 25A 0.46789 0.744444
117 EP4 0.467391 0.634409
118 ADP VO4 0.46729 0.736264
119 6YZ 0.46729 0.747253
120 VO4 ADP 0.46729 0.736264
121 9SN 0.464912 0.715789
122 GJV 0.464646 0.706522
123 B5V 0.464286 0.73913
124 LAD 0.464286 0.842697
125 WAQ 0.464286 0.820225
126 6RE 0.463918 0.695652
127 ADQ 0.463636 0.747253
128 HQG 0.462963 0.736264
129 M2T 0.462366 0.638298
130 LAQ 0.462185 0.804348
131 FA5 0.46087 0.777778
132 B5Y 0.46087 0.731183
133 YAP 0.46087 0.769231
134 ME8 0.460177 0.765957
135 PTJ 0.460177 0.715789
136 BIS 0.460177 0.741935
137 1ZZ 0.460177 0.765957
138 LPA AMP 0.458333 0.784946
139 ARG AMP 0.457627 0.776596
140 7MD 0.457627 0.844444
141 XAH 0.456897 0.844444
142 MYR AMP 0.45614 0.747368
143 ADP BMA 0.455357 0.728261
144 9X8 0.455357 0.75
145 NAX 0.454545 0.755319
146 NXX 0.454545 0.73913
147 DND 0.454545 0.73913
148 OZV 0.454545 0.744444
149 5SV 0.454545 0.752688
150 J7C 0.454545 0.703297
151 YLY 0.453846 0.817204
152 TYR AMP 0.452991 0.75
153 AMP DBH 0.452991 0.691489
154 TXE 0.45082 0.76087
155 7C5 0.449153 0.670213
156 B5M 0.448276 0.731183
157 4UU 0.445378 0.731183
158 DSH 0.444444 0.761364
159 NEC 0.444444 0.644444
160 25L 0.443478 0.736264
161 SAH 0.443396 0.719101
162 4UW 0.442623 0.708333
163 6V0 0.442623 0.734043
164 SFG 0.442308 0.704545
165 TAD 0.441667 0.763441
166 4UV 0.440678 0.731183
167 OMR 0.439024 0.757895
168 ZAS 0.438776 0.681319
169 A A 0.438596 0.725275
170 G3A 0.436975 0.715789
171 139 0.436508 0.774194
172 S4M 0.435644 0.723404
173 7MC 0.435484 0.826087
174 FYA 0.434783 0.775281
175 JB6 0.434783 0.8
176 YLP 0.434426 0.826087
177 48N 0.434426 0.734043
178 SA8 0.433962 0.688172
179 G5P 0.433333 0.715789
180 A4P 0.432 0.717172
181 MAO 0.431373 0.734043
182 UP5 0.430894 0.731183
183 NAI 0.430894 0.723404
184 TXD 0.430894 0.76087
185 A3G 0.43 0.727273
186 N5O 0.43 0.715909
187 SAI 0.429907 0.692308
188 DQV 0.429752 0.755556
189 GTA 0.429752 0.693878
190 IOT 0.428571 0.817204
191 3AM 0.428571 0.730337
192 TYM 0.427419 0.777778
193 AF3 ADP 3PG 0.427419 0.708333
194 SMM 0.427273 0.6875
195 S7M 0.427273 0.691489
196 AHZ 0.42623 0.71134
197 SAM 0.425926 0.691489
198 YLA 0.425197 0.826087
199 UPA 0.424 0.741935
200 4TC 0.424 0.734043
201 YLC 0.424 0.824176
202 YLB 0.424 0.826087
203 ATP A 0.423729 0.733333
204 ATP A A A 0.423729 0.733333
205 A7D 0.423077 0.727273
206 BT5 0.423077 0.797872
207 KOY 0.422764 0.692308
208 EEM 0.422018 0.65625
209 CNA 0.421875 0.758242
210 N5A 0.421569 0.693182
211 EO7 0.421569 0.857143
212 AR6 AR6 0.421488 0.725275
213 A5D 0.420561 0.696629
214 MHZ 0.419048 0.734043
215 F2R 0.418605 0.787234
216 2AM 0.418367 0.722222
217 A3P 0.417476 0.741573
218 A2P 0.417476 0.730337
219 A6D 0.417391 0.666667
220 NAD 0.415385 0.755556
221 AMP NAD 0.415385 0.736264
222 T5A 0.414062 0.75
223 594 0.413534 0.875
224 0UM 0.412281 0.736264
225 5AD 0.411111 0.602273
226 AYB 0.410853 0.817204
227 SXZ 0.410256 0.709677
228 GA7 0.409836 0.73913
229 AFH 0.409836 0.726316
230 A3S 0.409524 0.715909
231 A3D 0.409091 0.747253
232 7D5 0.408163 0.714286
233 NAJ PZO 0.406015 0.715789
234 OVE 0.405941 0.736264
235 K15 0.405172 0.702128
236 COD 0.40458 0.819149
237 4TA 0.40458 0.739583
238 BTX 0.40458 0.806452
239 6C6 0.40367 0.797753
240 GEK 0.403509 0.733333
241 A3T 0.401869 0.685393
242 J4G 0.401709 0.788889
243 AP0 0.401575 0.697917
244 DZD 0.401515 0.782609
245 67D 0.4 0.89011
246 V3L 0.4 0.744444
247 BS5 0.4 0.88172
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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