Receptor
PDB id Resolution Class Description Source Keywords
5TFZ 2.2 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF THE DIMETHYLSULFONIOPROPIONATE (DMSP) L COMPLEXED WITH NICKEL AND DIACRYLATE PELAGIBACTER UBIQUE (STRAIN HTCC1062) DMSP LYASE CUPIN NICKEL DEPENDENT METAL BINDING OXIDORED
Ref.: STRUCTURAL AND BIOCHEMICAL INSIGHTS INTO DIMETHYLSULFONIOPROPIONATE CLEAVAGE BY COFACTOR-BOU FROM THE PROLIFIC MARINE BACTERIUM PELAGIBACTER. BIOCHEMISTRY V. 56 2873 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
7BC B:205;
A:202;
 Valid;
Valid;
 none;
none;
 submit data
144.125 C6 H8 O4 C=CC(...
PEG B:202;
B:201;
B:203;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
106.12 C4 H10 O3 C(COC...
NI A:201;
B:204;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
58.693 Ni [Ni+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5TFZ 2.2 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF THE DIMETHYLSULFONIOPROPIONATE (DMSP) L COMPLEXED WITH NICKEL AND DIACRYLATE PELAGIBACTER UBIQUE (STRAIN HTCC1062) DMSP LYASE CUPIN NICKEL DEPENDENT METAL BINDING OXIDORED
Ref.: STRUCTURAL AND BIOCHEMICAL INSIGHTS INTO DIMETHYLSULFONIOPROPIONATE CLEAVAGE BY COFACTOR-BOU FROM THE PROLIFIC MARINE BACTERIUM PELAGIBACTER. BIOCHEMISTRY V. 56 2873 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 62 families.
1 5TFZ - 7BC C6 H8 O4 C=CC(=O)OC....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 5TFZ - 7BC C6 H8 O4 C=CC(=O)OC....
2 6A55 - DQY C5 H12 O2 S CS(C)CCC(=....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 5TFZ - 7BC C6 H8 O4 C=CC(=O)OC....
2 6A55 - DQY C5 H12 O2 S CS(C)CCC(=....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 7BC; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 7BC 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 7BC; Similar ligands found: 477
No: Ligand Similarity coefficient
1 650 0.9865
2 0VT 0.9641
3 URO 0.9598
4 AKG 0.9562
5 MUC 0.9513
6 GUA 0.9509
7 GLY GLY 0.9504
8 3OM 0.9489
9 OEG 0.9452
10 KQY 0.9449
11 PJL 0.9434
12 DGL 0.9433
13 OOG 0.9431
14 S2G 0.9416
15 GLU 0.9413
16 AG2 0.9408
17 LYS 0.9407
18 URP 0.9404
19 XIZ 0.9399
20 OCA 0.9398
21 TCA 0.9395
22 13P 0.9393
23 HCI 0.9390
24 011 0.9374
25 DIR 0.9372
26 3OL 0.9372
27 11C 0.9363
28 SHV 0.9362
29 2HG 0.9360
30 HIS 0.9359
31 OGA 0.9355
32 MEQ 0.9349
33 MHN 0.9342
34 3YP 0.9341
35 BHH 0.9339
36 KMH 0.9334
37 7OD 0.9333
38 HSO 0.9331
39 ACA 0.9330
40 R9M 0.9320
41 TIH 0.9318
42 HC4 0.9314
43 XUL 0.9308
44 2IT 0.9307
45 M1T 0.9304
46 HPN 0.9303
47 E4P 0.9302
48 5XA 0.9301
49 HL5 0.9298
50 AL0 0.9291
51 PO6 0.9289
52 Q9Z 0.9286
53 SIN 0.9283
54 FOM 0.9277
55 PGH 0.9276
56 OKG 0.9272
57 ENW 0.9271
58 64Z 0.9270
59 CPZ 0.9267
60 GGL 0.9267
61 ONL 0.9266
62 CYX 0.9266
63 PAC 0.9263
64 UN1 0.9259
65 MLT 0.9259
66 OTR 0.9254
67 P81 0.9253
68 HGA 0.9248
69 FK8 0.9247
70 6NA 0.9247
71 N6C 0.9246
72 8EW 0.9246
73 KDG 0.9242
74 AT3 0.9242
75 LTL 0.9240
76 DZA 0.9237
77 GLN 0.9235
78 AHN 0.9234
79 B40 0.9234
80 0L1 0.9232
81 4HP 0.9232
82 MSR 0.9231
83 G3P 0.9230
84 GP9 0.9229
85 6JN 0.9229
86 CCE 0.9228
87 CCD 0.9228
88 G3H 0.9228
89 ORN 0.9225
90 PML 0.9221
91 R20 0.9217
92 I1E 0.9217
93 ONH 0.9213
94 6XA 0.9209
95 DYT 0.9208
96 RB5 0.9205
97 KTA 0.9204
98 129 0.9203
99 PPY 0.9197
100 CXP 0.9196
101 SYM 0.9188
102 9GB 0.9186
103 IZC 0.9186
104 3HG 0.9185
105 GPJ 0.9184
106 LEU 0.9183
107 PHE 0.9182
108 ASP 0.9180
109 CFI 0.9180
110 DE5 0.9177
111 ASN 0.9177
112 5FX 0.9175
113 OCT 0.9172
114 J0Z 0.9172
115 ANN 0.9171
116 AHC 0.9170
117 8OZ 0.9170
118 9ON 0.9167
119 4LR 0.9162
120 IP8 0.9162
121 1BN 0.9158
122 9RW 0.9157
123 B3U 0.9151
124 RNS 0.9150
125 CCU 0.9148
126 PPT 0.9148
127 DHM 0.9147
128 HHI 0.9146
129 BNF 0.9146
130 4MV 0.9145
131 3S5 0.9144
132 49F 0.9144
133 ACH 0.9143
134 S2P 0.9142
135 XYL 0.9141
136 GPF 0.9139
137 PG0 0.9135
138 DHI 0.9132
139 3PG 0.9132
140 LMR 0.9130
141 SHI 0.9128
142 IWT 0.9126
143 7C3 0.9125
144 LNO 0.9125
145 4TB 0.9123
146 M45 0.9122
147 M6H 0.9121
148 RBL 0.9119
149 CHH 0.9119
150 NM2 0.9119
151 ROR 0.9115
152 RJY 0.9114
153 FUM 0.9110
154 PG3 0.9109
155 AE3 0.9108
156 DPN 0.9108
157 HPP 0.9105
158 2FM 0.9105
159 9J3 0.9105
160 DLY 0.9102
161 QDK 0.9102
162 QY9 0.9100
163 NTU 0.9097
164 EHM 0.9096
165 MPV 0.9095
166 NF3 0.9094
167 16D 0.9091
168 MHO 0.9090
169 VKC 0.9089
170 152 0.9088
171 SHO 0.9088
172 NSD 0.9086
173 AOS 0.9085
174 GRQ 0.9084
175 3HP 0.9084
176 L5V 0.9082
177 XLS 0.9082
178 HIC 0.9082
179 URQ 0.9082
180 1H1 0.9081
181 1GP 0.9081
182 DGN 0.9080
183 K6H 0.9080
184 NFA 0.9078
185 ALA ALA 0.9078
186 NYL 0.9077
187 1X4 0.9077
188 OAA 0.9076
189 GJZ 0.9074
190 9X6 0.9073
191 EOU 0.9071
192 S8V 0.9071
193 PSJ 0.9070
194 NM3 0.9070
195 BHU 0.9069
196 K6V 0.9068
197 4WL 0.9068
198 DAS 0.9066
199 GVA 0.9065
200 LYN 0.9064
201 H95 0.9058
202 HX4 0.9056
203 KPA 0.9054
204 HTX 0.9053
205 HFA 0.9053
206 OYA 0.9050
207 FBM 0.9047
208 SOR 0.9047
209 HX2 0.9045
210 4LW 0.9044
211 98J 0.9044
212 HDH 0.9044
213 3LR 0.9043
214 DAL DAL 0.9043
215 PHU 0.9042
216 PBA 0.9041
217 A5E 0.9040
218 RNT 0.9036
219 MET 0.9036
220 HQJ 0.9036
221 7UC 0.9034
222 R2P 0.9030
223 P7Y 0.9027
224 ARG 0.9027
225 TEO 0.9025
226 CLT 0.9022
227 PEP 0.9018
228 MED 0.9017
229 PPR 0.9011
230 TEG 0.9011
231 SEP 0.9006
232 HHH 0.9005
233 NLE 0.9004
234 264 0.9003
235 KMT 0.8998
236 A29 0.8997
237 MEV 0.8996
238 HE4 0.8995
239 TYR 0.8994
240 173 0.8993
241 SSC 0.8993
242 DAV 0.8990
243 IXW 0.8990
244 PH3 0.8990
245 J9N 0.8990
246 E79 0.8988
247 PRA 0.8987
248 MLZ 0.8985
249 SOL 0.8985
250 F4E 0.8985
251 LUQ 0.8983
252 5WZ 0.8982
253 6TZ 0.8981
254 ENV 0.8977
255 PKU 0.8975
256 PIM 0.8975
257 0V5 0.8975
258 JYD 0.8975
259 DLT 0.8970
260 MTL 0.8970
261 TZF 0.8969
262 SHF 0.8968
263 NMH 0.8967
264 SSB 0.8966
265 I38 0.8966
266 7VP 0.8964
267 CIR 0.8962
268 SD4 0.8960
269 NMG 0.8959
270 F90 0.8958
271 PGA 0.8956
272 TPA 0.8956
273 RTK 0.8955
274 S0W 0.8952
275 N9J 0.8952
276 YIE 0.8951
277 1SA 0.8949
278 LPK 0.8949
279 GCO 0.8948
280 OSE 0.8947
281 N4B 0.8947
282 NWH 0.8942
283 DQY 0.8941
284 HMS 0.8941
285 AOT 0.8940
286 BNL 0.8940
287 TYE 0.8939
288 PC 0.8937
289 GLY ALA 0.8936
290 GZ3 0.8935
291 DI6 0.8933
292 RB0 0.8933
293 FUD 0.8933
294 F9P 0.8930
295 ESX 0.8929
296 5XB 0.8928
297 OHJ 0.8927
298 HJH 0.8926
299 NCT 0.8925
300 DEZ 0.8923
301 6FZ 0.8923
302 SME 0.8919
303 XRG 0.8918
304 TAG 0.8917
305 2F6 0.8917
306 MF3 0.8913
307 GGB 0.8911
308 URS 0.8905
309 492 0.8905
310 GVM 0.8901
311 PIY 0.8901
312 SAF 0.8899
313 P58 0.8899
314 LNR 0.8898
315 LVD 0.8897
316 3BU 0.8896
317 BHL 0.8893
318 BHL BHL 0.8893
319 IAR 0.8891
320 3QO 0.8889
321 X1S 0.8888
322 8GL 0.8888
323 M3H 0.8887
324 DHY 0.8887
325 DXG 0.8886
326 HG3 0.8885
327 7WG 0.8885
328 CUW 0.8884
329 MAH 0.8884
330 HF2 0.8883
331 4LV 0.8881
332 HPV 0.8880
333 GLO 0.8879
334 KPC 0.8878
335 CS2 0.8872
336 1L5 0.8870
337 DAR 0.8870
338 YPN 0.8868
339 F98 0.8867
340 QUS 0.8867
341 ENO 0.8866
342 DXP 0.8864
343 ILO 0.8862
344 0OC 0.8858
345 3QM 0.8857
346 HL4 0.8857
347 B85 0.8857
348 5OY 0.8855
349 X1R 0.8855
350 LDP 0.8855
351 HBU 0.8854
352 PBN 0.8851
353 3SL 0.8848
354 SYC 0.8848
355 FBJ 0.8846
356 2RH 0.8843
357 AEG 0.8843
358 268 0.8843
359 8SZ 0.8843
360 4P5 0.8842
361 4VY 0.8842
362 3H2 0.8841
363 ITN 0.8838
364 069 0.8838
365 EGV 0.8838
366 K7M 0.8837
367 FHC 0.8835
368 PLU 0.8832
369 BPW 0.8832
370 2HC 0.8832
371 MSE 0.8832
372 PEL 0.8830
373 MES 0.8829
374 NSB 0.8828
375 XYH 0.8827
376 4ZA 0.8827
377 CFA 0.8822
378 M74 0.8822
379 HPL 0.8818
380 GWM 0.8817
381 XRX 0.8815
382 NNH 0.8815
383 TIU 0.8814
384 FIX 0.8813
385 RLG 0.8813
386 2UB 0.8812
387 XOG 0.8812
388 OC9 0.8812
389 SLZ 0.8812
390 LT1 0.8810
391 2CO 0.8809
392 2EH 0.8809
393 263 0.8807
394 0BP 0.8805
395 MSL 0.8802
396 O8Y 0.8801
397 MZT 0.8800
398 7MU 0.8798
399 4BF 0.8798
400 2JJ 0.8797
401 SPA 0.8797
402 SDD 0.8794
403 ISA 0.8792
404 Q06 0.8790
405 KNA 0.8790
406 GLY CYS 0.8790
407 6HN 0.8784
408 O45 0.8782
409 26P 0.8779
410 DER 0.8777
411 TZM 0.8775
412 0A9 0.8773
413 3PP 0.8769
414 DII 0.8768
415 S7A 0.8765
416 RUJ 0.8761
417 MT2 0.8760
418 2FT 0.8756
419 RAT 0.8755
420 1SH 0.8753
421 AFS 0.8752
422 LFC 0.8750
423 9SE 0.8748
424 GLR 0.8745
425 LX1 0.8744
426 EN1 0.8742
427 14W 0.8740
428 IVL 0.8738
429 Z70 0.8738
430 33S 0.8735
431 DTY 0.8732
432 RA7 0.8730
433 JX7 0.8730
434 9YT 0.8726
435 SPD 0.8724
436 M5E 0.8723
437 56D 0.8717
438 QFJ 0.8715
439 258 0.8712
440 K34 0.8705
441 QMP 0.8704
442 API 0.8702
443 ICB 0.8697
444 PFF 0.8692
445 FOC 0.8690
446 EDR 0.8682
447 1HS 0.8674
448 RP3 0.8673
449 4ZD 0.8671
450 REL 0.8670
451 J4K 0.8668
452 LL2 0.8667
453 HLP 0.8659
454 BL0 0.8653
455 2NP 0.8648
456 M44 0.8647
457 LY0 0.8646
458 LLH 0.8646
459 MPJ 0.8642
460 2D8 0.8642
461 4PN 0.8642
462 MLY 0.8640
463 SKJ 0.8639
464 TYC 0.8636
465 TB8 0.8635
466 YIV 0.8615
467 M3P 0.8606
468 58X 0.8595
469 HE2 0.8595
470 GOJ 0.8593
471 5LD 0.8592
472 PRO GLY 0.8588
473 EYV 0.8585
474 PHI 0.8570
475 KVP 0.8564
476 36E 0.8559
477 NFM 0.8538
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5TFZ; Ligand: 7BC; 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: 5tfz.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5TFZ; Ligand: 7BC; 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: 5tfz.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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