Receptor
PDB id Resolution Class Description Source Keywords
5JF6 1.7 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF TYPE 2 PDF FROM STREPTOCOCCUS AGALACTIA COMPLEX WITH INHIBITOR 6B (AB47) STREPTOCOCCUS AGALACTIAE PDF TYPE 2 NME N-TERMINAL METHIONINE EXCISION STREPTOCOCAGALACTIAE INHIBITOR 6B AB47 HYDROLASE
Ref.: A UNIQUE PEPTIDE DEFORMYLASE PLATFORM TO RATIONALLY AND CHALLENGE NOVEL ACTIVE COMPOUNDS. SCI REP V. 6 35429 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:310;
A:308;
A:306;
A:307;
A:304;
A:305;
A:309;
A:303;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
65.409 Zn [Zn+2...
ACT A:302;
 Invalid;
 none;
 submit data
59.044 C2 H3 O2 CC(=O...
BB4 A:301;
 Valid;
 none;
 Ki = 62 nM
269.095 C10 H9 Br N2 O2 c1cc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5JF2 2 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF TYPE 2 PDF FROM STREPTOCOCCUS AGALACTIA COMPLEX WITH INHIBITOR AT002 STREPTOCOCCUS AGALACTIAE PDF TYPE 2 NME N-TERMINAL METHIONINE EXCISION STREPTOCOCAGALACTIAE INHIBITOR AT002 HYDROLASE
Ref.: A UNIQUE PEPTIDE DEFORMYLASE PLATFORM TO RATIONALLY AND CHALLENGE NOVEL ACTIVE COMPOUNDS. SCI REP V. 6 35429 2016
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
2 5JEZ - MET ALA SER n/a n/a
3 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
4 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
5 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
6 5JF0 - MET ALA ARG n/a n/a
7 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
8 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
9 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
10 5JF8 Ki = 1428 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3SW8 Ki = 25910 nM 5LI C10 H10 Cl2 N2 O3 c1cc(c(c(c....
2 3SVJ Ki = 117 nM 4LI C27 H32 Cl N9 O2 S Cc1cccc(c1....
3 2AI7 ic50 = 0.4 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 2AIE ic50 = 2.2 uM SB9 C10 H14 N2 O2 Cc1cccc(n1....
5 2AIA ic50 = 3.9 uM SB8 C16 H15 N O4 c1ccc(cc1)....
6 6OW7 ic50 = 1 nM N9Y C20 H29 N5 O4 c1ccnc(c1)....
7 4EOX ic50 = 0.28 nM 0S5 C22 H29 N3 O5 c1ccc(cc1)....
8 6OW2 ic50 = 3 nM NB4 C22 H36 F N7 O4 Cc1nc(c(c(....
9 3STR Ki = 334 nM 3LI C28 H33 Cl N10 O4 S Cc1cccc(c1....
10 3G6N - MET ALA SER n/a n/a
11 2OKL - BB2 C19 H35 N3 O5 CCCCC[C@H]....
12 1LQY - BB2 C19 H35 N3 O5 CCCCC[C@H]....
13 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
14 5JEZ - MET ALA SER n/a n/a
15 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
16 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
17 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
18 5JF0 - MET ALA ARG n/a n/a
19 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
20 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
21 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
22 5JF8 Ki = 1428 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
50% Homology Family (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3SW8 Ki = 25910 nM 5LI C10 H10 Cl2 N2 O3 c1cc(c(c(c....
2 3SVJ Ki = 117 nM 4LI C27 H32 Cl N9 O2 S Cc1cccc(c1....
3 2AI7 ic50 = 0.4 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 2AIE ic50 = 2.2 uM SB9 C10 H14 N2 O2 Cc1cccc(n1....
5 2AIA ic50 = 3.9 uM SB8 C16 H15 N O4 c1ccc(cc1)....
6 6OW7 ic50 = 1 nM N9Y C20 H29 N5 O4 c1ccnc(c1)....
7 4EOX ic50 = 0.28 nM 0S5 C22 H29 N3 O5 c1ccc(cc1)....
8 6OW2 ic50 = 3 nM NB4 C22 H36 F N7 O4 Cc1nc(c(c(....
9 3STR Ki = 334 nM 3LI C28 H33 Cl N10 O4 S Cc1cccc(c1....
10 3G6N - MET ALA SER n/a n/a
11 2OKL - BB2 C19 H35 N3 O5 CCCCC[C@H]....
12 1Q1Y - BB2 C19 H35 N3 O5 CCCCC[C@H]....
13 1LQY - BB2 C19 H35 N3 O5 CCCCC[C@H]....
14 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
15 5JEZ - MET ALA SER n/a n/a
16 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
17 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
18 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
19 5JF0 - MET ALA ARG n/a n/a
20 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
21 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
22 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
23 5JF8 Ki = 1428 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: BB4; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 BB4 1 1
2 2SX 0.68 0.644444
Similar Ligands (3D)
Ligand no: 1; Ligand: BB4; Similar ligands found: 386
No: Ligand Similarity coefficient
1 MYI 0.9574
2 SRO 0.9558
3 IAC 0.9531
4 7ZC 0.9505
5 DTR 0.9469
6 NVU 0.9447
7 AC2 0.9425
8 IOP 0.9416
9 MQB 0.9411
10 ITW 0.9398
11 TRP 0.9389
12 TSR 0.9383
13 ET0 0.9360
14 3IL 0.9353
15 NPA 0.9343
16 HWH 0.9298
17 MNP 0.9280
18 96Z 0.9279
19 TQU 0.9274
20 1QP 0.9274
21 ASE 0.9273
22 IOS 0.9269
23 772 0.9263
24 ML1 0.9259
25 4Z9 0.9246
26 H7S 0.9243
27 C2Y 0.9243
28 2UD 0.9240
29 NLA 0.9235
30 M3Q 0.9223
31 8GK 0.9220
32 ZON 0.9212
33 3SU 0.9198
34 LTN 0.9195
35 28S 0.9192
36 ARP 0.9191
37 NIY 0.9190
38 3IB 0.9180
39 AMR 0.9173
40 EYY 0.9170
41 JHY 0.9156
42 EXG 0.9154
43 9BF 0.9154
44 RVE 0.9152
45 AOJ 0.9144
46 EV2 0.9134
47 N7I 0.9129
48 XEN 0.9127
49 TSS 0.9123
50 8XL 0.9121
51 QMS 0.9120
52 HLP 0.9117
53 8RK 0.9114
54 5JT 0.9113
55 14W 0.9111
56 TZM 0.9110
57 MMS 0.9108
58 61M 0.9104
59 39Z 0.9102
60 BC3 0.9098
61 C9E 0.9096
62 IWD 0.9093
63 108 0.9093
64 YTX 0.9090
65 9UL 0.9089
66 OMD 0.9089
67 NWD 0.9085
68 0FR 0.9082
69 DTE 0.9082
70 APS 0.9078
71 BQ2 0.9078
72 FWD 0.9077
73 CWD 0.9067
74 SBK 0.9067
75 GA2 0.9066
76 2LY 0.9063
77 S7D 0.9062
78 2O6 0.9060
79 EYM 0.9058
80 ETV 0.9057
81 92P 0.9055
82 DHY 0.9053
83 R4E 0.9046
84 I2E 0.9042
85 0LH 0.9038
86 NFZ 0.9034
87 5WN 0.9033
88 XI7 0.9029
89 KYN 0.9029
90 4KL 0.9025
91 BZM 0.9024
92 3EB 0.9023
93 6DP 0.9021
94 PW1 0.9018
95 SYE 0.9016
96 M5H 0.9015
97 5OF 0.9014
98 TXW 0.9007
99 C4E 0.9007
100 6HP 0.9006
101 BWD 0.9002
102 9F8 0.9002
103 4OG 0.9000
104 EYA 0.8998
105 3C4 0.8994
106 OA1 0.8994
107 NAL 0.8985
108 NIP 0.8982
109 F52 0.8982
110 LL1 0.8979
111 790 0.8978
112 7MX 0.8972
113 DNC 0.8972
114 8G6 0.8970
115 CTE 0.8969
116 CDY 0.8968
117 CX4 0.8968
118 57O 0.8967
119 W8G 0.8967
120 78U 0.8964
121 3AK 0.8962
122 B0K 0.8956
123 G1P 0.8954
124 ONZ 0.8953
125 67Y 0.8952
126 MD6 0.8951
127 6J9 0.8950
128 DAH 0.8948
129 JXW 0.8948
130 BK9 0.8947
131 X2M 0.8946
132 H4B 0.8945
133 GNG 0.8944
134 CIY 0.8943
135 G6P 0.8943
136 EOL 0.8942
137 XFE 0.8939
138 DHC 0.8938
139 EV3 0.8936
140 Q5M 0.8934
141 H35 0.8932
142 B41 0.8932
143 S7G 0.8930
144 5O5 0.8929
145 RK4 0.8929
146 0JD 0.8929
147 AZY 0.8928
148 EXL 0.8924
149 KWB 0.8924
150 B5A 0.8923
151 JY2 0.8922
152 4B0 0.8919
153 3N4 0.8919
154 ZIQ 0.8919
155 YIH 0.8916
156 EYV 0.8912
157 6C9 0.8910
158 6FG 0.8907
159 6HO 0.8906
160 CC5 0.8906
161 9FE 0.8902
162 5V7 0.8900
163 CSN 0.8899
164 LSQ 0.8898
165 9E3 0.8898
166 3L1 0.8895
167 C0W 0.8894
168 HA5 0.8894
169 JGY 0.8891
170 FXH 0.8891
171 CFA 0.8890
172 VJJ 0.8889
173 M6Z 0.8887
174 531 0.8886
175 LLT 0.8884
176 KF5 0.8882
177 JYW 0.8879
178 536 0.8878
179 0GA 0.8877
180 5AD 0.8873
181 OW7 0.8872
182 EGR 0.8871
183 KED 0.8871
184 J4K 0.8870
185 EYJ 0.8868
186 IBM 0.8866
187 ALN 0.8865
188 30G 0.8865
189 MDR 0.8864
190 LLG 0.8863
191 PE2 0.8863
192 OX2 0.8861
193 C9M 0.8861
194 AEH 0.8860
195 2FD 0.8860
196 ML2 0.8860
197 5MD 0.8859
198 JXK 0.8858
199 QBM 0.8857
200 5WU 0.8856
201 2KU 0.8854
202 JXQ 0.8854
203 I59 0.8850
204 R9G 0.8850
205 0OP 0.8849
206 QH3 0.8848
207 JYK 0.8847
208 A4V 0.8846
209 0XR 0.8844
210 YF3 0.8843
211 XQI 0.8841
212 L21 0.8840
213 1U7 0.8840
214 H7Y 0.8838
215 M02 0.8837
216 6XC 0.8836
217 HJB 0.8832
218 HQ9 0.8831
219 HA6 0.8829
220 FT6 0.8828
221 535 0.8827
222 8Y7 0.8825
223 ZEZ 0.8824
224 6C5 0.8821
225 BG6 0.8821
226 GO8 0.8820
227 7FF 0.8818
228 3D8 0.8816
229 15A 0.8815
230 QTS 0.8815
231 QUB 0.8815
232 EY7 0.8814
233 34L 0.8814
234 1Q4 0.8813
235 RDV 0.8811
236 S3C 0.8811
237 5F1 0.8810
238 4AV 0.8808
239 ZME 0.8806
240 X0T 0.8804
241 FPL 0.8803
242 0OO 0.8802
243 VXX 0.8799
244 657 0.8798
245 MJW 0.8798
246 YO5 0.8797
247 JAA 0.8796
248 H2B 0.8796
249 MS0 0.8795
250 M4E 0.8794
251 2DL 0.8793
252 JF1 0.8790
253 0H5 0.8789
254 GNR 0.8789
255 IM4 0.8787
256 ALE 0.8784
257 HBI 0.8783
258 4BX 0.8780
259 F95 0.8779
260 SQV 0.8778
261 RE4 0.8777
262 7VY 0.8777
263 ZIP 0.8774
264 LTT 0.8773
265 4AB 0.8773
266 FNA 0.8772
267 THM 0.8772
268 LI7 0.8770
269 5TO 0.8770
270 DEW 0.8769
271 CCV 0.8769
272 FWB 0.8767
273 3GC 0.8766
274 2K8 0.8762
275 D8Q 0.8762
276 HWD 0.8761
277 4VT 0.8761
278 BZQ 0.8757
279 R8Y 0.8754
280 6J5 0.8753
281 S8D 0.8752
282 6Q3 0.8750
283 PLP 0.8745
284 HPT 0.8743
285 3D1 0.8743
286 ISJ 0.8743
287 3Y7 0.8743
288 S8G 0.8742
289 EUH 0.8736
290 MXD 0.8736
291 3AD 0.8735
292 N1Y 0.8735
293 JXT 0.8730
294 K68 0.8727
295 4XY 0.8726
296 GOE 0.8726
297 3W1 0.8724
298 64E 0.8722
299 CR1 0.8721
300 HVE 0.8721
301 8U3 0.8719
302 96U 0.8719
303 TR7 0.8718
304 MP5 0.8716
305 4R1 0.8715
306 H4E 0.8711
307 1HR 0.8711
308 YOF 0.8711
309 E7R 0.8708
310 DE7 0.8707
311 3XH 0.8706
312 4ME 0.8706
313 11X 0.8703
314 GUS 0.8695
315 FUZ 0.8693
316 ISC 0.8693
317 T6Z 0.8691
318 3HP 0.8688
319 3TC 0.8685
320 9KH 0.8684
321 64F 0.8684
322 S24 0.8680
323 TWB 0.8677
324 3B4 0.8677
325 BGP 0.8673
326 LDC 0.8670
327 55D 0.8668
328 TOH 0.8667
329 GZ2 0.8666
330 MPP 0.8666
331 AX8 0.8665
332 JYT 0.8664
333 NQH 0.8656
334 LP8 0.8654
335 ZYC 0.8653
336 NBV 0.8652
337 RZH 0.8651
338 NPL 0.8649
339 4VS 0.8648
340 CL9 0.8648
341 54X 0.8647
342 IAG 0.8647
343 ENO 0.8644
344 1AE 0.8643
345 S3P 0.8643
346 774 0.8641
347 BDI 0.8641
348 ABF 0.8637
349 RUG 0.8635
350 BHS 0.8634
351 YIE 0.8634
352 TLG 0.8633
353 JTF 0.8633
354 GMP 0.8631
355 GRX 0.8630
356 D80 0.8630
357 54F 0.8627
358 NFM 0.8626
359 ID2 0.8626
360 PXP 0.8623
361 M9N 0.8621
362 GFP 0.8618
363 6VD 0.8609
364 LIP 0.8609
365 FSU 0.8606
366 3R6 0.8603
367 HJ7 0.8603
368 NBG 0.8601
369 PRZ 0.8600
370 XRX 0.8588
371 ZYW 0.8586
372 KYA 0.8586
373 7AP 0.8582
374 XQK 0.8581
375 TMC 0.8580
376 0DN 0.8577
377 NQ7 0.8574
378 SAF 0.8569
379 I4D 0.8566
380 AED 0.8560
381 78P 0.8559
382 8VN 0.8558
383 PTB 0.8543
384 5BT 0.8542
385 QTV 0.8534
386 B61 0.8530
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5JF2; Ligand: SF7; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 5jf2.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1G27 BB1 38.0952
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