Receptor
PDB id Resolution Class Description Source Keywords
3WDK 2.3 Å EC: 6.3.2.36 CRYSTAL STRUCTURE OF 4-PHOSPHOPANTOATE-BETA-ALANINE LIGASE C WITH REACTION INTERMEDIATE THERMOCOCCUS KODAKARENSIS LIGASE
Ref.: CRYSTAL STRUCTURE OF PHOSPHOPANTOTHENATE SYNTHETASE THERMOCOCCUS KODAKARENSIS PROTEINS V. 82 1924 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FLC A:302;
C:302;
D:302;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
189.1 C6 H5 O7 C(C(=...
PTJ A:301;
C:301;
D:301;
B:901;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
557.343 C16 H25 N5 O13 P2 CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3WDM 2 Å EC: 6.3.2.36 CRYSTAL STRUCTURE OF 4-PHOSPHOPANTOATE-BETA-ALANINE LIGASE F THERMOCOCCUS KODAKARENSIS THERMOCOCCUS KODAKARENSIS LIGASE
Ref.: CRYSTAL STRUCTURE OF PHOSPHOPANTOTHENATE SYNTHETASE THERMOCOCCUS KODAKARENSIS PROTEINS V. 82 1924 2014
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3WDM - ADN C10 H13 N5 O4 c1nc(c2c(n....
2 3WDK - PTJ C16 H25 N5 O13 P2 CC(C)(COP(....
3 4MB2 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3WDL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3WDM - ADN C10 H13 N5 O4 c1nc(c2c(n....
2 3WDK - PTJ C16 H25 N5 O13 P2 CC(C)(COP(....
3 4MB2 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3WDL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3WDM - ADN C10 H13 N5 O4 c1nc(c2c(n....
2 3WDK - PTJ C16 H25 N5 O13 P2 CC(C)(COP(....
3 4MB2 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3WDL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PTJ; Similar ligands found: 376
No: Ligand ECFP6 Tc MDL keys Tc
1 PTJ 1 1
2 PAJ 0.840909 0.961538
3 5AL 0.752809 0.934211
4 8QN 0.731183 0.934211
5 SRP 0.717391 0.886076
6 4AD 0.705263 0.875
7 CA0 0.704545 0.897436
8 AMO 0.6875 0.886076
9 ME8 0.676768 0.86747
10 AMP 0.670588 0.894737
11 A 0.670588 0.894737
12 LAD 0.666667 0.843373
13 A2D 0.666667 0.871795
14 ADP 0.662921 0.896104
15 TXA 0.66 0.910256
16 NB8 0.66 0.853659
17 BA3 0.651685 0.871795
18 M33 0.648352 0.884615
19 AP5 0.644444 0.871795
20 B4P 0.644444 0.871795
21 ATP 0.641304 0.896104
22 YAP 0.640777 0.875
23 FA5 0.640777 0.886076
24 AN2 0.637363 0.884615
25 PRX 0.634409 0.873418
26 AQP 0.634409 0.896104
27 5FA 0.634409 0.896104
28 ADX 0.630435 0.790698
29 DLL 0.63 0.909091
30 ABM 0.629214 0.871795
31 OOB 0.626263 0.909091
32 50T 0.623656 0.860759
33 ACP 0.623656 0.873418
34 AR6 0.617021 0.896104
35 APR 0.617021 0.896104
36 DAL AMP 0.616162 0.909091
37 YLP 0.614679 0.825581
38 ACQ 0.614583 0.873418
39 00A 0.613861 0.864198
40 1ZZ 0.61165 0.86747
41 SAP 0.610526 0.851852
42 AGS 0.610526 0.851852
43 AD9 0.610526 0.873418
44 25A 0.61 0.896104
45 3UK 0.607843 0.897436
46 TYM 0.603604 0.886076
47 ATF 0.602041 0.8625
48 PR8 0.601942 0.833333
49 WAQ 0.601942 0.864198
50 AMP MG 0.6 0.825
51 YLC 0.598214 0.845238
52 YLB 0.598214 0.847059
53 AHX 0.598039 0.831325
54 GAP 0.597938 0.873418
55 ANP 0.597938 0.873418
56 AP2 0.597826 0.8625
57 A12 0.597826 0.8625
58 COD 0.594828 0.860465
59 OAD 0.592233 0.922078
60 SRA 0.588889 0.85
61 9SN 0.584906 0.853659
62 A22 0.584158 0.884615
63 APC 0.583333 0.8625
64 YLA 0.582609 0.804598
65 TAT 0.581633 0.8625
66 3OD 0.580952 0.922078
67 AU1 0.578947 0.873418
68 5SV 0.578431 0.831325
69 AYB 0.577586 0.837209
70 A1R 0.572816 0.819277
71 ADQ 0.572816 0.873418
72 4UV 0.568807 0.875
73 SON 0.568421 0.910256
74 4UW 0.566372 0.865854
75 BIS 0.566038 0.841463
76 LAQ 0.5625 0.823529
77 ADP MG 0.5625 0.8375
78 ADV 0.561224 0.8625
79 RBY 0.561224 0.8625
80 25L 0.560748 0.884615
81 XAH 0.559633 0.802326
82 4UU 0.558559 0.875
83 48N 0.557522 0.876543
84 YLY 0.557377 0.837209
85 ADP BEF 0.556701 0.817073
86 BEF ADP 0.556701 0.817073
87 FYA 0.551402 0.8375
88 IOT 0.547009 0.816092
89 MYR AMP 0.546296 0.845238
90 ADP PO3 0.545455 0.87013
91 TYR AMP 0.545455 0.8625
92 52H 0.543689 0.827586
93 ATP MG 0.54 0.8375
94 OMR 0.534483 0.857143
95 N0B 0.531746 0.804598
96 AFH 0.530973 0.821429
97 AP0 0.529915 0.831325
98 NAI 0.525862 0.841463
99 6V0 0.525862 0.831325
100 TXD 0.525862 0.841463
101 ADP ALF 0.524272 0.807229
102 ALF ADP 0.524272 0.807229
103 53H 0.52381 0.827586
104 TSB 0.52381 0.784091
105 MAP 0.52381 0.851852
106 G3A 0.522124 0.853659
107 ARG AMP 0.521739 0.813953
108 TXE 0.521368 0.841463
109 ANP MG 0.519231 0.829268
110 ADP VO4 0.519231 0.860759
111 VO4 ADP 0.519231 0.860759
112 ADP BMA 0.518519 0.85
113 G5P 0.517544 0.853659
114 AOC 0.515789 0.759494
115 GTA 0.513043 0.845238
116 DND 0.512821 0.886076
117 NAX 0.512821 0.811765
118 NXX 0.512821 0.886076
119 BT5 0.512195 0.816092
120 XYA 0.511628 0.75641
121 RAB 0.511628 0.75641
122 ADN 0.511628 0.75641
123 5AS 0.510204 0.747253
124 A5A 0.509615 0.793103
125 JB6 0.509091 0.819277
126 LA8 ALF 3PG 0.508475 0.821429
127 ALF ADP 3PG 0.508475 0.821429
128 LPA AMP 0.504274 0.802326
129 AMP DBH 0.5 0.82716
130 A3P 0.5 0.894737
131 CNA 0.5 0.8625
132 TAD 0.5 0.821429
133 5N5 0.5 0.734177
134 54H 0.5 0.816092
135 VMS 0.5 0.816092
136 M24 0.496063 0.833333
137 A3D 0.496 0.897436
138 AF3 ADP 3PG 0.495798 0.821429
139 G5A 0.495146 0.747253
140 5X8 0.49505 0.75
141 7D5 0.494624 0.8125
142 5CD 0.494382 0.74359
143 ADJ 0.491803 0.793103
144 T5A 0.491803 0.804598
145 UPA 0.491667 0.841463
146 7MD 0.491379 0.823529
147 SSA 0.490566 0.747253
148 2A5 0.490196 0.82716
149 DCA 0.488189 0.872093
150 ETB 0.488189 0.882353
151 UP5 0.487395 0.851852
152 A A 0.486486 0.871795
153 LSS 0.486239 0.808989
154 NSS 0.486239 0.747253
155 ATR 0.485437 0.87013
156 PAP 0.485437 0.883117
157 A2P 0.484848 0.881579
158 AHZ 0.483051 0.823529
159 NVA LMS 0.481818 0.769231
160 5CA 0.481481 0.747253
161 0T1 0.48062 0.872093
162 COA 0.48062 0.872093
163 NAD 0.48 0.884615
164 139 0.479675 0.811765
165 7MC 0.479339 0.825581
166 4TC 0.479339 0.831325
167 EP4 0.478261 0.78481
168 A4D 0.477778 0.734177
169 LEU LMS 0.477477 0.808989
170 EAD 0.477273 0.833333
171 NAQ 0.476923 0.876543
172 V3L 0.47619 0.921053
173 A4P 0.47541 0.786517
174 7D3 0.474747 0.814815
175 6RE 0.474227 0.705882
176 NDE 0.474074 0.886076
177 FCX 0.473684 0.863636
178 FAM 0.473684 0.852273
179 3DH 0.473684 0.7375
180 DTA 0.473118 0.728395
181 M2T 0.473118 0.765432
182 DSZ 0.472727 0.766667
183 A2R 0.472222 0.909091
184 EEM 0.471698 0.72093
185 PPS 0.471698 0.790698
186 6AD 0.471698 0.843373
187 SA8 0.471154 0.738095
188 ITT 0.470588 0.846154
189 7D4 0.470588 0.814815
190 CAO 0.469697 0.842697
191 AMX 0.469697 0.882353
192 30N 0.469697 0.797872
193 COS 0.469697 0.852273
194 ATP A A A 0.469565 0.858974
195 NAE 0.469231 0.898734
196 3AM 0.46875 0.857143
197 ARU 0.468468 0.821429
198 BTX 0.468254 0.804598
199 MTA 0.468085 0.759494
200 2SA 0.46729 0.886076
201 SCO 0.466165 0.894118
202 CMX 0.466165 0.894118
203 AR6 AR6 0.466102 0.871795
204 SFG 0.466019 0.7375
205 IMO 0.464646 0.857143
206 P1H 0.463235 0.835294
207 MCD 0.463235 0.873563
208 SMM 0.462963 0.735632
209 ACO 0.462687 0.842697
210 NAD IBO 0.460317 0.898734
211 P5A 0.460177 0.715789
212 GSU 0.460177 0.766667
213 KAA 0.460177 0.723404
214 HAX 0.459259 0.852273
215 2MC 0.456522 0.815217
216 FB0 0.456522 0.811111
217 FYN 0.455882 0.872093
218 3KK 0.455882 0.852273
219 A3G 0.454545 0.740741
220 DZD 0.453125 0.821429
221 YSA 0.452991 0.747253
222 SAH 0.45283 0.731707
223 SAI 0.45283 0.722892
224 COK 0.452555 0.852273
225 OXK 0.452555 0.873563
226 CA6 0.452555 0.773196
227 SOP 0.452555 0.852273
228 A3T 0.451923 0.782051
229 ZID 0.451128 0.873418
230 MCA 0.45 0.863636
231 A3N 0.45 0.707317
232 COO 0.45 0.852273
233 J7C 0.45 0.714286
234 S7M 0.449541 0.701149
235 CMC 0.449275 0.873563
236 1VU 0.449275 0.842697
237 NMX 0.449275 0.806452
238 CO6 0.449275 0.852273
239 6IA 0.448598 0.865854
240 3AT 0.448598 0.871795
241 SAM 0.448598 0.72093
242 FNK 0.448276 0.831461
243 2CP 0.446809 0.863636
244 NAJ PZO 0.446154 0.809524
245 SCD 0.446043 0.894118
246 CAJ 0.446043 0.873563
247 S4M 0.445545 0.659341
248 GJV 0.445545 0.697674
249 1GZ 0.443662 0.842697
250 2AM 0.443299 0.846154
251 MLC 0.442857 0.873563
252 BCO 0.442857 0.852273
253 A1S 0.442857 0.852273
254 1HE 0.442857 0.833333
255 3HC 0.442857 0.862069
256 IVC 0.442857 0.862069
257 MAO 0.441176 0.747126
258 AMP NAD 0.440298 0.886076
259 DSH 0.44 0.674419
260 FDA 0.439716 0.818182
261 CAA 0.439716 0.862069
262 CO7 0.439716 0.852273
263 YE1 0.439716 0.862069
264 NA7 0.438596 0.8625
265 HXC 0.4375 0.833333
266 GRA 0.4375 0.873563
267 GEK 0.4375 0.72619
268 NJP 0.4375 0.875
269 MC4 0.43662 0.806452
270 SCA 0.43662 0.873563
271 NDC 0.435714 0.831325
272 WSA 0.435484 0.755556
273 ZAS 0.434343 0.710843
274 G A A A 0.434109 0.831325
275 0WD 0.434109 0.853659
276 0UM 0.433628 0.729412
277 COW 0.433566 0.842697
278 COF 0.433566 0.833333
279 HGG 0.433566 0.873563
280 2KQ 0.433566 0.853933
281 CA8 0.433566 0.773196
282 IRC 0.433566 0.862069
283 BYC 0.433566 0.852273
284 3CP 0.433566 0.873563
285 C2R 0.43299 0.858974
286 AMZ 0.43299 0.846154
287 A3S 0.432692 0.75
288 A7D 0.432692 0.719512
289 CO8 0.431507 0.833333
290 1CZ 0.431507 0.863636
291 4CA 0.430556 0.842697
292 FAQ 0.430556 0.852273
293 BCA 0.430556 0.842697
294 OVE 0.43 0.814815
295 A5D 0.429907 0.728395
296 62X 0.429825 0.735632
297 UCC 0.428571 0.833333
298 DCC 0.428571 0.833333
299 5F9 0.428571 0.833333
300 PGS 0.428571 0.797619
301 MYA 0.428571 0.833333
302 MFK 0.428571 0.833333
303 ST9 0.428571 0.833333
304 AV2 0.427273 0.825
305 71V 0.427184 0.819277
306 6FA 0.426573 0.825581
307 ODP 0.426357 0.843373
308 K15 0.426087 0.712644
309 6C6 0.425926 0.817073
310 NEC 0.425743 0.7125
311 TGC 0.424658 0.863636
312 DAT 0.424528 0.814815
313 4TA 0.423077 0.793103
314 WCA 0.422819 0.833333
315 NAJ PYZ 0.422222 0.811765
316 5AD 0.422222 0.710526
317 DTP 0.422018 0.814815
318 NDP 0.421875 0.853659
319 2NE 0.421769 0.833333
320 CIC 0.421769 0.873563
321 S0N 0.421769 0.873563
322 7C5 0.421488 0.802469
323 SFD 0.42069 0.72449
324 FAD 0.42069 0.835294
325 FAS 0.42069 0.835294
326 HDC 0.42 0.833333
327 F2N 0.419355 0.8
328 0FQ 0.418919 0.852273
329 4CO 0.418919 0.842697
330 62F 0.418919 0.823529
331 SXZ 0.418803 0.783133
332 TXP 0.418605 0.853659
333 NZQ 0.418605 0.843373
334 01A 0.416107 0.815217
335 0ET 0.416107 0.833333
336 P5F 0.415584 0.829545
337 MHZ 0.415094 0.688889
338 4YB 0.414634 0.75
339 YNC 0.414474 0.842697
340 DAK 0.414474 0.824176
341 CS8 0.413333 0.824176
342 1CV 0.413333 0.873563
343 6K6 0.412281 0.858974
344 AVV 0.412281 0.809524
345 CCQ 0.412162 0.815217
346 DA 0.411765 0.8125
347 8Z2 0.411765 0.824176
348 D5M 0.411765 0.8125
349 2VA 0.411215 0.807692
350 NPW 0.410853 0.823529
351 4KX 0.410596 0.824176
352 UOQ 0.410596 0.833333
353 NHW 0.410596 0.833333
354 NHM 0.410596 0.833333
355 NIA 0.41 0.764706
356 U A G G 0.409091 0.841463
357 MRS 0.407895 0.833333
358 MRR 0.407895 0.833333
359 HFQ 0.407895 0.833333
360 AAM 0.407767 0.894737
361 FAI 0.407767 0.846154
362 FAY 0.406667 0.823529
363 AAT 0.405405 0.659091
364 N6P 0.405172 0.844156
365 Y3J 0.404255 0.670886
366 RFL 0.403974 0.827586
367 GGZ 0.403509 0.747126
368 KB1 0.403361 0.689655
369 NA0 0.402878 0.910256
370 7D7 0.402174 0.6875
371 PO4 PO4 A A A A PO4 0.401709 0.833333
372 A6D 0.401709 0.674157
373 649 0.401575 0.715789
374 XNP 0.401515 0.811765
375 SO8 0.4 0.797468
376 VRT 0.4 0.756098
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3WDM; Ligand: ADN; Similar sites found: 21
This union binding pocket(no: 1) in the query (biounit: 3wdm.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3OFK SAH 0.01302 0.40913 1.85185
2 1UWK NAD 0.002837 0.41487 2.29885
3 1UWK URO 0.002837 0.41487 2.29885
4 3G2O SAM 0.003334 0.43297 2.68199
5 2VDV SAM 0.008792 0.42435 2.84553
6 1O97 FAD 0.009507 0.40152 3.44828
7 1O97 AMP 0.009507 0.40152 3.44828
8 5N53 8NB 0.03466 0.4109 3.58974
9 3LST SAH 0.02094 0.40594 3.83142
10 5HJM MTA 0.003955 0.42608 4.21456
11 3E3U NVC 0.01977 0.40716 4.56853
12 3BGD PM6 0.001357 0.40049 4.61538
13 2PT9 2MH 0.001824 0.41042 4.98084
14 1JQ3 AAT 0.00236 0.40502 4.98084
15 2I7C AAT 0.002908 0.40166 4.98084
16 1RL4 BL5 0.0312 0.41469 5.31915
17 1RL4 BRR 0.03815 0.40338 5.31915
18 4YAG NAI 0.003758 0.40733 5.36398
19 3DMH SAM 0.01063 0.40388 6.13027
20 5WSY 7UC 0.0436 0.4003 6.93642
21 1G55 SAH 0.0005437 0.46456 18.0077
Pocket No.: 2; Query (leader) PDB : 3WDM; Ligand: ADN; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3wdm.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3WDM; Ligand: ADN; Similar sites found: 7
This union binding pocket(no: 3) in the query (biounit: 3wdm.bio2) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2CBZ ATP 0.04541 0.4028 2.53165
2 4DMG SAM 0.02309 0.40842 4.21456
3 1EJ4 M7G 0.03659 0.4218 4.73684
4 4NSQ COA 0.01923 0.40233 5.26316
5 1RLZ NAD 0.001865 0.40111 5.74713
6 3GDH SAH 0.007749 0.40254 9.95851
7 2UZ1 TPP 0.007375 0.40079 9.96169
Pocket No.: 4; Query (leader) PDB : 3WDM; Ligand: ADN; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3wdm.bio2) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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