Receptor
PDB id Resolution Class Description Source Keywords
4HVC 2 Å EC: 6.1.1.17 CRYSTAL STRUCTURE OF HUMAN PROLYL-TRNA SYNTHETASE IN COMPLEX HALOFUGINONE AND ATP ANALOGUE HOMO SAPIENS LIGASE LIGASE-LIGASE INHIBITOR COMPLEX
Ref.: ATP-DIRECTED CAPTURE OF BIOACTIVE HERBAL-BASED MEDI HUMAN TRNA SYNTHETASE. NATURE V. 494 121 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ANP MG A:1601;
B:1601;
 Valid;
Valid;
 none;
none;
 submit data
526.471 n/a P(=O)...
HFG A:1602;
B:1602;
 Valid;
Valid;
 none;
none;
 submit data
414.681 C16 H17 Br Cl N3 O3 c1c2c...
ZN A:1604;
B:1604;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5VAD 2.36 Å EC: 6.1.1.17 CRYSTAL STRUCTURE OF HUMAN PROLYL-TRNA SYNTHETASE (PRS) IN C WITH INHIBITOR HOMO SAPIENS AMINOACYL-TRNA SYNTHETASE ATP DEPENDENT INHIBITOR LIGASE-INHIBITOR COMPLEX
Ref.: DISCOVERY OF A NOVEL PROLYL-TRNA SYNTHETASE INHIBIT ELUCIDATION OF ITS BINDING MODE TO THE ATP SITE IN WITH L-PROLINE. BIOCHEM. BIOPHYS. RES. V. 488 393 2017 COMMUN.
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5VAD Kd = 0.76 nM 91Y C21 H24 N4 O2 c1ccc2c(c1....
2 4HVC - HFG C16 H17 Br Cl N3 O3 c1c2c(cc(c....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5VAD Kd = 0.76 nM 91Y C21 H24 N4 O2 c1ccc2c(c1....
2 4HVC - HFG C16 H17 Br Cl N3 O3 c1c2c(cc(c....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5XIJ ic50 = 67 nM 873 C16 H21 N3 O3 c1ccc2c(c1....
2 5XIH ic50 = 68 nM 86U C16 H17 F2 N3 O2 c1c2c(cc(c....
3 5XIQ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
4 5XII ic50 = 72 nM 86X C16 H17 Cl F N3 O2 c1c2c(cc(c....
5 5XIK - 87C C16 H23 N3 O3 C1CCC2=C(C....
6 5XIG ic50 = 350 nM 87F C16 H19 N3 O2 c1ccc2c(c1....
7 4YDQ Kd ~ 300 nM HFG C16 H17 Br Cl N3 O3 c1c2c(cc(c....
8 4Q15 ic50 = 275 nM HFG C16 H17 Br Cl N3 O3 c1c2c(cc(c....
9 5IFU ic50 = 34 uM GBM C23 H28 Cl N3 O5 S COc1ccc(cc....
10 4WI1 ic50 = 5 uM 3O6 C18 H13 F5 N4 O Cn1c(c(c(n....
11 5VAD Kd = 0.76 nM 91Y C21 H24 N4 O2 c1ccc2c(c1....
12 4HVC - HFG C16 H17 Br Cl N3 O3 c1c2c(cc(c....
13 5XIO - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ANP MG; Similar ligands found: 352
No: Ligand ECFP6 Tc MDL keys Tc
1 ANP MG 1 1
2 ADP BEF 0.794872 0.957747
3 ADP MG 0.794872 0.957747
4 ATP MG 0.756098 0.957747
5 ADP PO3 0.756098 0.957747
6 BEF ADP 0.746988 0.931507
7 VO4 ADP 0.72093 0.932432
8 ALF ADP 0.72093 0.883117
9 AMP MG 0.717949 0.943662
10 AMP 0.683544 0.930556
11 A 0.683544 0.930556
12 A2D 0.679012 0.931507
13 GAP 0.678161 0.906667
14 ADP 0.674699 0.931507
15 ADP BMA 0.666667 0.906667
16 BA3 0.662651 0.931507
17 AU1 0.658824 0.958904
18 ABM 0.658537 0.905405
19 45A 0.658537 0.905405
20 APC MG 0.655172 0.931507
21 B4P 0.654762 0.931507
22 AP5 0.654762 0.931507
23 ATP A A A 0.649485 0.944444
24 ATP A 0.649485 0.944444
25 AN2 0.647059 0.945205
26 AT4 0.647059 0.894737
27 AP2 0.642857 0.894737
28 A12 0.642857 0.894737
29 DAL AMP 0.641304 0.918919
30 ANP 0.640449 0.958904
31 M33 0.639535 0.918919
32 SRA 0.634146 0.881579
33 HEJ 0.632184 0.931507
34 ATP 0.632184 0.931507
35 ACP 0.632184 0.906667
36 AR6 0.625 0.931507
37 PRX 0.625 0.881579
38 APR 0.625 0.931507
39 5FA 0.625 0.931507
40 APC 0.625 0.894737
41 AQP 0.625 0.931507
42 CA0 0.62069 0.906667
43 ADX 0.62069 0.839506
44 AD9 0.617977 0.906667
45 AGS 0.617977 0.883117
46 50T 0.613636 0.893333
47 KG4 0.613636 0.906667
48 MYR AMP 0.612245 0.829268
49 AR6 AR6 0.607843 0.931507
50 MAP 0.606383 0.933333
51 ACQ 0.604396 0.906667
52 TAT 0.604396 0.894737
53 T99 0.604396 0.894737
54 RBY 0.6 0.894737
55 ADV 0.6 0.894737
56 V2G 0.597826 0.884615
57 AHZ 0.596154 0.829268
58 ARG AMP 0.592233 0.819277
59 ATF 0.591398 0.894737
60 AMP DBH 0.588235 0.881579
61 6YZ 0.585106 0.906667
62 SRP 0.585106 0.894737
63 LMS 0.583333 0.839506
64 9X8 0.581633 0.883117
65 8LE 0.580645 0.883117
66 5AL 0.580645 0.918919
67 5AS 0.579545 0.790698
68 AF3 ADP 3PG 0.579439 0.85
69 ALF ADP 3PG 0.579439 0.85
70 HQG 0.578947 0.918919
71 NAD TDB 0.574074 0.931507
72 NAD IBO 0.574074 0.931507
73 SON 0.573034 0.894737
74 QA7 0.572917 0.883117
75 A22 0.572917 0.918919
76 JNT 0.571429 0.906667
77 8LH 0.568421 0.894737
78 5SV 0.56701 0.8375
79 9ZD 0.56701 0.896104
80 9ZA 0.56701 0.896104
81 OAD 0.565657 0.906667
82 ADQ 0.561224 0.906667
83 A3R 0.561224 0.871795
84 4AD 0.561224 0.907895
85 AMO 0.561224 0.894737
86 A1R 0.561224 0.871795
87 8LQ 0.556701 0.894737
88 AHX 0.555556 0.884615
89 DLL 0.555556 0.918919
90 3OD 0.554455 0.906667
91 NB8 0.554455 0.884615
92 AOC 0.551724 0.810811
93 ADN 0.551282 0.808219
94 XYA 0.551282 0.808219
95 RAB 0.551282 0.808219
96 OOB 0.55102 0.918919
97 25A 0.55102 0.931507
98 8QN 0.55102 0.918919
99 OZV 0.55102 0.931507
100 PO4 PO4 A A A A PO4 0.55 0.916667
101 LPA AMP 0.546296 0.829268
102 PAJ 0.545455 0.85
103 LAD 0.544554 0.85
104 WAQ 0.544554 0.871795
105 4TA 0.54386 0.819277
106 AMP NAD 0.54386 0.918919
107 NAD 0.54386 0.945205
108 NAJ PZO 0.543103 0.884615
109 3DH 0.541176 0.763158
110 00A 0.54 0.871795
111 1ZZ 0.539216 0.829268
112 FYA 0.539216 0.893333
113 BIS 0.539216 0.871795
114 TXA 0.539216 0.894737
115 ME8 0.539216 0.829268
116 KMQ 0.538462 0.894737
117 5N5 0.5375 0.783784
118 3UK 0.534653 0.906667
119 A3D 0.534483 0.932432
120 25L 0.533981 0.918919
121 AFH 0.53271 0.85
122 5CD 0.530864 0.794521
123 A4D 0.530864 0.783784
124 PR8 0.529412 0.839506
125 B5V 0.529412 0.894737
126 9SN 0.528846 0.860759
127 H1Q 0.526882 0.917808
128 G5A 0.526316 0.790698
129 NAJ PYZ 0.525 0.841463
130 NAQ 0.525 0.884615
131 JB6 0.524272 0.871795
132 PTJ 0.524272 0.860759
133 FA5 0.52381 0.894737
134 XAH 0.518868 0.851852
135 48N 0.518182 0.860759
136 YLP 0.518182 0.809524
137 NAE 0.516667 0.907895
138 Z5A 0.516393 0.833333
139 PAP 0.515789 0.917808
140 EP4 0.511905 0.74359
141 A5A 0.510204 0.819277
142 TSB 0.51 0.809524
143 B5M 0.509434 0.883117
144 B5Y 0.509434 0.883117
145 G3A 0.509259 0.860759
146 OMR 0.508929 0.819277
147 ZID 0.508197 0.932432
148 DTA 0.505882 0.776316
149 M2T 0.505882 0.746835
150 6RE 0.505618 0.75
151 SSA 0.50505 0.790698
152 7MD 0.504587 0.851852
153 G5P 0.504587 0.860759
154 YLB 0.504425 0.809524
155 YLC 0.504425 0.829268
156 A3P 0.5 0.930556
157 54H 0.5 0.8
158 TAD 0.5 0.85
159 NSS 0.5 0.811765
160 DQV 0.5 0.918919
161 DND 0.5 0.92
162 UP5 0.5 0.883117
163 52H 0.5 0.790698
164 4UV 0.5 0.883117
165 GTA 0.5 0.851852
166 MTA 0.5 0.763158
167 VMS 0.5 0.8
168 NAI 0.5 0.871795
169 TXE 0.495575 0.871795
170 NVA LMS 0.495146 0.784091
171 8X1 0.49505 0.764045
172 53H 0.49505 0.790698
173 5CA 0.49505 0.790698
174 J7C 0.494505 0.7375
175 A3N 0.494505 0.753247
176 7D5 0.494253 0.842105
177 139 0.491379 0.839506
178 L3W 0.491228 0.894737
179 4TC 0.491228 0.860759
180 AP0 0.491228 0.860759
181 GA7 0.490909 0.87013
182 4UU 0.490909 0.883117
183 LEU LMS 0.490385 0.761364
184 2A5 0.489583 0.857143
185 6MZ 0.48913 0.891892
186 7D3 0.48913 0.844156
187 S4M 0.48913 0.678161
188 AYB 0.487179 0.8
189 6V0 0.486726 0.860759
190 TXD 0.486726 0.871795
191 NAX 0.486726 0.839506
192 P5A 0.485714 0.755556
193 LSS 0.485437 0.772727
194 DSZ 0.485437 0.790698
195 ATR 0.484536 0.90411
196 NDE 0.484375 0.92
197 MAO 0.483871 0.771084
198 A2P 0.483871 0.916667
199 3AM 0.483146 0.890411
200 F2R 0.483051 0.809524
201 TYM 0.482456 0.894737
202 LAQ 0.482143 0.829268
203 9K8 0.481132 0.706522
204 YLA 0.478632 0.809524
205 7MC 0.478261 0.831325
206 UPA 0.478261 0.871795
207 ZAS 0.477778 0.826667
208 NDC 0.476923 0.884615
209 A4P 0.474138 0.790698
210 4UW 0.473684 0.85
211 GJV 0.473118 0.740741
212 GSU 0.471698 0.790698
213 KAA 0.471698 0.764045
214 IOT 0.470085 0.8
215 PPS 0.47 0.817073
216 5AD 0.469136 0.736111
217 7D4 0.46875 0.844156
218 8PZ 0.46789 0.790698
219 DSH 0.467391 0.716049
220 BTX 0.466667 0.809524
221 COD 0.466667 0.781609
222 NMN AMP PO4 0.466667 0.883117
223 T5A 0.466102 0.809524
224 ADJ 0.466102 0.819277
225 AV2 0.465347 0.855263
226 O02 0.464646 0.884615
227 5X8 0.463918 0.753247
228 YSA 0.463636 0.790698
229 B1U 0.463636 0.786517
230 BT5 0.46281 0.8
231 IMO 0.462366 0.890411
232 CNA 0.462185 0.92
233 SAM 0.46 0.702381
234 V3L 0.46 0.931507
235 80F 0.459016 0.809524
236 NWW 0.458824 0.726027
237 OVE 0.456522 0.844156
238 A2R 0.456311 0.918919
239 2AM 0.455556 0.878378
240 N01 0.455285 0.918919
241 ITT 0.453608 0.878378
242 MHZ 0.453608 0.709302
243 NAD BBN 0.452555 0.876543
244 A3G 0.451613 0.766234
245 NEC 0.451613 0.714286
246 6C6 0.45 0.846154
247 SFG 0.44898 0.74026
248 YLY 0.448 0.8
249 QXP 0.447619 0.755814
250 S7M 0.446602 0.702381
251 SMM 0.446602 0.697674
252 NAD CJ3 0.446043 0.845238
253 6IA 0.445545 0.804878
254 J4G 0.444444 0.883117
255 ENQ 0.444444 0.90411
256 CNV FAD 0.443662 0.764045
257 A7D 0.443299 0.766234
258 NO7 0.442308 0.87013
259 6AD 0.441176 0.85
260 SA8 0.44 0.698795
261 DZD 0.439024 0.85
262 N0B 0.4375 0.809524
263 71V 0.4375 0.848101
264 M24 0.436508 0.8625
265 SAI 0.435644 0.725
266 HFD 0.435644 0.883117
267 SAH 0.435644 0.734177
268 JSQ 0.435644 0.883117
269 QXG 0.435185 0.747126
270 NA7 0.435185 0.894737
271 4YB 0.434783 0.772727
272 DAT 0.434343 0.844156
273 CUU 0.434343 0.905405
274 GEK 0.433962 0.75
275 WSA 0.432203 0.8
276 649 0.432203 0.755556
277 EAD 0.430769 0.839506
278 FAD NBT 0.430556 0.76087
279 Y3J 0.430233 0.716216
280 0UM 0.429907 0.690476
281 7C5 0.429825 0.78481
282 COA FLC 0.429688 0.781609
283 A3S 0.428571 0.776316
284 K3K 0.428571 0.769231
285 FAD CNX 0.428571 0.701031
286 P1H 0.428571 0.819277
287 7D7 0.428571 0.733333
288 EEM 0.427184 0.702381
289 NAP 0.426357 0.932432
290 ARU 0.425926 0.804878
291 A5D 0.425743 0.776316
292 KY2 0.424528 0.702381
293 NWQ 0.423913 0.706667
294 2SA 0.423077 0.87013
295 TAP 0.423077 0.896104
296 DAL FAD PER 0.422819 0.758242
297 NDP DTT 0.422222 0.809524
298 GDP AF3 0.422018 0.807229
299 D4F 0.421875 0.829268
300 N5O 0.421053 0.730769
301 D5M 0.421053 0.842105
302 DA 0.421053 0.842105
303 K3E 0.421053 0.759494
304 AVV 0.420561 0.860759
305 A3T 0.42 0.786667
306 NA0 0.419847 0.92
307 NIA 0.419355 0.858974
308 NHD 0.419355 0.918919
309 V47 0.419048 0.773333
310 NAD NDT 0.418919 0.755319
311 R2V 0.418182 0.755814
312 3AT 0.417476 0.905405
313 DTP 0.417476 0.844156
314 AAM 0.416667 0.930556
315 8Q2 0.416667 0.764045
316 P33 FDA 0.416107 0.73913
317 P6G FDA 0.416107 0.764045
318 FDA 0.416058 0.781609
319 FAD NBA 0.415584 0.701031
320 38V 0.415385 0.829268
321 KOY 0.415254 0.792208
322 GDP BEF 0.415094 0.848101
323 AAT 0.413462 0.698795
324 DZ4 0.413462 0.87013
325 AMZ 0.413043 0.853333
326 N5A 0.412371 0.705128
327 PAX 0.412214 0.819277
328 FB0 0.411765 0.755556
329 GTP MG 0.411215 0.87013
330 APC G U 0.410853 0.825
331 PGS 0.41 0.848101
332 K15 0.409091 0.674419
333 A6D 0.409091 0.777778
334 0WD 0.408 0.860759
335 FAD T2C 0.407895 0.723404
336 6K6 0.407407 0.891892
337 BUA COA 0.405797 0.764045
338 KY8 0.405405 0.719512
339 K2K 0.405405 0.707317
340 AIR 0.404494 0.863014
341 QQX 0.404255 0.794872
342 KYB 0.40367 0.702381
343 NAJ 0.403226 0.918919
344 O05 0.401786 0.811765
345 SXZ 0.401786 0.702381
346 NFD 0.401575 0.896104
347 LQJ 0.4 0.905405
348 QQY 0.4 0.805195
349 7DD 0.4 0.917808
350 K2H 0.4 0.725
351 ACK 0.4 0.849315
352 62X 0.4 0.659091
Ligand no: 2; Ligand: HFG; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 HFG 1 1
2 87C 0.494382 0.808824
3 FQR 0.415842 0.774648
4 FQU 0.401961 0.857143
Similar Ligands (3D)
Ligand no: 1; Ligand: ANP MG; Similar ligands found: 1
No: Ligand Similarity coefficient
1 GNP 0.8566
Ligand no: 2; Ligand: HFG; Similar ligands found: 15
No: Ligand Similarity coefficient
1 873 0.9557
2 87F 0.9525
3 M0V 0.8907
4 EWT 0.8831
5 BAI 0.8824
6 OZR 0.8713
7 35K 0.8681
8 JHT 0.8655
9 4KN 0.8625
10 JQN 0.8621
11 HY7 0.8620
12 M85 0.8602
13 TUE 0.8597
14 IXF 0.8582
15 8Y4 0.8578
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VAD; Ligand: PRO; 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: 5vad.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5VAD; Ligand: PRO; 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: 5vad.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5VAD; Ligand: 91Y; 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: 5vad.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5VAD; Ligand: 91Y; 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: 5vad.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
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