Receptor
PDB id Resolution Class Description Source Keywords
2ai7 2 Å EC: 3.5.1.88 S.PNEUMONIAE POLYPEPTIDE DEFORMYLASE COMPLEXED WITH SB- 485345 STREPTOCOCCUS PNEUMONIAE HYDROLASE
Ref.: STRUCTURAL VARIATION AND INHIBITOR BINDING IN POLYPEPTIDE DEFORMYLASE FROM FOUR DIFFERENT BACTERIAL SPECIES PROTEIN SCI. V. 12 349 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NI A:301;
 Part of Protein;
 none;
 submit data
58.693 Ni [Ni+2...
SB7 A:300;
 Valid;
 none;
 ic50 = 0.4 uM
181.232 C10 H15 N O2 c1ccc...
SO4 A:3001;
 Invalid;
 none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4EOX 1.78 Å EC: 3.5.1.88 X-RAY STRUCTURE OF POLYPEPTIDE DEFORMYLASE BOUND TO A ACYLPR INHIBITOR STREPTOCOCCUS PNEUMONIAE ALPHA-BETA PEPTIDE DEFORMYLASE METAL ION BINDING HYDROLASEHYDROLASE INHIBITOR COMPLEX
Ref.: ACYLPROLINAMIDES: A NEW CLASS OF PEPTIDE DEFORMYLAS INHIBITORS WITH IN VIVO ANTIBACTERIAL ACTIVITY. BIOORG.MED.CHEM.LETT. V. 22 4028 2012
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 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....
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: SB7; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 SB7 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: SB7; Similar ligands found: 436
No: Ligand Similarity coefficient
1 KPV 0.9650
2 SB9 0.9636
3 OJD 0.9512
4 3GZ 0.9432
5 CLT 0.9425
6 1PS 0.9375
7 LVD 0.9361
8 JFM 0.9346
9 PPY 0.9316
10 5PV 0.9303
11 DPN 0.9271
12 11X 0.9258
13 HAR 0.9253
14 NMM 0.9252
15 BZQ 0.9212
16 4TB 0.9203
17 S0B 0.9193
18 XI7 0.9190
19 ARG 0.9188
20 PHE 0.9186
21 JX7 0.9186
22 GGB 0.9184
23 5TO 0.9182
24 PUE 0.9179
25 NK5 0.9177
26 TPM 0.9177
27 6MW 0.9174
28 XRS 0.9172
29 4YZ 0.9154
30 PBN 0.9147
31 4JK 0.9146
32 AOY 0.9145
33 Z70 0.9137
34 0OM 0.9131
35 LL2 0.9130
36 6HN 0.9129
37 4FP 0.9123
38 3VQ 0.9121
39 0V7 0.9116
40 PBA 0.9115
41 LPB 0.9113
42 6C8 0.9111
43 3IP 0.9109
44 CIR 0.9107
45 PCS 0.9106
46 3QO 0.9106
47 IJ1 0.9103
48 3H2 0.9103
49 0QA 0.9102
50 22F 0.9100
51 VUR 0.9098
52 ILO 0.9096
53 ZE7 0.9095
54 TZP 0.9095
55 D53 0.9094
56 API 0.9089
57 IAR 0.9088
58 LZ5 0.9084
59 EN1 0.9083
60 0A9 0.9080
61 AHN 0.9079
62 DAR 0.9078
63 JKK 0.9078
64 4ZD 0.9078
65 GNW 0.9077
66 EYV 0.9070
67 HX8 0.9070
68 848 0.9067
69 BSA 0.9061
70 LPA 0.9059
71 6C4 0.9058
72 T03 0.9056
73 JMG 0.9055
74 I2E 0.9055
75 0V8 0.9054
76 WT2 0.9053
77 HPP 0.9047
78 ENV 0.9046
79 IPO 0.9040
80 37E 0.9036
81 M6H 0.9035
82 G14 0.9034
83 6C9 0.9034
84 D4G 0.9031
85 MES 0.9030
86 DHC 0.9027
87 8YH 0.9023
88 N9J 0.9022
89 6J5 0.9021
90 NOT 0.9017
91 N9M 0.9016
92 M3P 0.9009
93 KDG 0.9003
94 26P 0.9002
95 ALY 0.9001
96 HFA 0.9000
97 TRP 0.9000
98 PML 0.8997
99 JF5 0.8996
100 HL6 0.8994
101 N2Y 0.8992
102 FHV 0.8989
103 HC4 0.8988
104 2NP 0.8988
105 BZM 0.8987
106 HRG 0.8983
107 PQV 0.8983
108 27K 0.8983
109 GVA 0.8983
110 8CC 0.8981
111 2MR 0.8976
112 6C5 0.8976
113 DHH 0.8973
114 NPI 0.8973
115 FZ3 0.8972
116 A51 0.8972
117 3YP 0.8969
118 EXY 0.8969
119 SX2 0.8964
120 KYN 0.8963
121 3KJ 0.8963
122 P93 0.8958
123 EGV 0.8956
124 NNH 0.8955
125 KLE 0.8955
126 Q06 0.8955
127 LVP 0.8952
128 OOG 0.8950
129 DKA 0.8950
130 IJ4 0.8949
131 EYJ 0.8948
132 6FG 0.8945
133 5C1 0.8944
134 RP3 0.8944
135 8CV 0.8943
136 9VQ 0.8940
137 TYR 0.8940
138 0NX 0.8940
139 XRX 0.8939
140 0XR 0.8934
141 ZZU 0.8929
142 HCI 0.8926
143 B41 0.8926
144 GRQ 0.8923
145 5KJ 0.8921
146 DA2 0.8920
147 QME 0.8918
148 GB5 0.8915
149 PRO GLY 0.8914
150 5LD 0.8912
151 Q04 0.8910
152 TMG 0.8908
153 EEK 0.8902
154 492 0.8902
155 D3G 0.8901
156 MF3 0.8900
157 ZEA 0.8899
158 5E5 0.8899
159 RA7 0.8899
160 TEG 0.8899
161 ENW 0.8896
162 7O4 0.8896
163 68B 0.8895
164 DAH 0.8893
165 TB8 0.8893
166 3CX 0.8893
167 ZEZ 0.8892
168 0OO 0.8892
169 GHQ 0.8892
170 A7Q 0.8890
171 TCA 0.8889
172 M5P 0.8889
173 ENO 0.8888
174 D2G 0.8887
175 2M7 0.8884
176 NFA 0.8884
177 BQ2 0.8883
178 ABH 0.8882
179 KAP 0.8882
180 GO8 0.8881
181 J9Y 0.8880
182 MLY 0.8879
183 2E6 0.8879
184 MFY 0.8876
185 2FX 0.8875
186 M3L 0.8874
187 NFZ 0.8874
188 TR7 0.8873
189 ODK 0.8870
190 H35 0.8865
191 BP7 0.8863
192 HSA 0.8862
193 MJW 0.8859
194 TOH 0.8859
195 0OP 0.8859
196 6N4 0.8858
197 1L5 0.8858
198 4AU 0.8857
199 JM2 0.8856
200 E8U 0.8856
201 HNM 0.8856
202 RDV 0.8855
203 4BX 0.8855
204 5B2 0.8852
205 F63 0.8852
206 A8K 0.8851
207 JOV 0.8850
208 0ON 0.8850
209 WA2 0.8847
210 P81 0.8846
211 9J6 0.8843
212 3S9 0.8841
213 YIP 0.8840
214 2E4 0.8840
215 HLP 0.8839
216 1YO 0.8838
217 KPA 0.8837
218 2FM 0.8836
219 795 0.8836
220 0K7 0.8833
221 VIO 0.8833
222 R9J 0.8827
223 HXY 0.8824
224 YIE 0.8823
225 HF2 0.8822
226 IC9 0.8821
227 EQA 0.8821
228 4FF 0.8820
229 92G 0.8820
230 GT4 0.8819
231 PLP 0.8814
232 DZA 0.8812
233 2E5 0.8810
234 3D3 0.8809
235 47V 0.8809
236 YF3 0.8808
237 NAL 0.8808
238 MLZ 0.8807
239 6XA 0.8805
240 TZM 0.8804
241 GLR 0.8804
242 EVF 0.8802
243 5F8 0.8801
244 FER 0.8801
245 LR2 0.8800
246 X48 0.8798
247 RGP 0.8798
248 S0A 0.8796
249 5DL 0.8795
250 BVS 0.8795
251 F90 0.8795
252 AX4 0.8795
253 GO2 0.8793
254 D1G 0.8789
255 6L6 0.8789
256 S8G 0.8787
257 QJA 0.8787
258 RE4 0.8786
259 4Z1 0.8785
260 C53 0.8782
261 2J5 0.8782
262 YE6 0.8781
263 MP5 0.8781
264 S7D 0.8775
265 S0F 0.8775
266 E3X 0.8774
267 6Q3 0.8774
268 D8Q 0.8774
269 54F 0.8773
270 S7A 0.8773
271 9BF 0.8770
272 O45 0.8770
273 D9Z 0.8770
274 PZX 0.8770
275 7VY 0.8768
276 E9S 0.8768
277 3IB 0.8768
278 TYC 0.8767
279 2UB 0.8767
280 GXG 0.8767
281 2JJ 0.8761
282 9JT 0.8760
283 GLY GLY GLY 0.8759
284 11C 0.8756
285 64Z 0.8754
286 HPL 0.8754
287 P58 0.8754
288 U13 0.8753
289 GZ2 0.8753
290 PLR 0.8753
291 L06 0.8748
292 2JX 0.8748
293 CBE 0.8746
294 1X4 0.8743
295 5FL 0.8742
296 MD6 0.8742
297 EMU 0.8742
298 C82 0.8741
299 DTR 0.8736
300 QIV 0.8733
301 HL4 0.8732
302 PO6 0.8731
303 3IL 0.8730
304 58X 0.8729
305 MMJ 0.8728
306 FCD 0.8728
307 1KJ 0.8726
308 1HR 0.8724
309 4KJ 0.8723
310 ZZA 0.8721
311 PHQ DAL 0.8720
312 AHL 0.8720
313 7OD 0.8715
314 B5A 0.8714
315 SOJ 0.8714
316 4LV 0.8713
317 XCG 0.8713
318 PPT 0.8710
319 QH3 0.8710
320 CXP 0.8707
321 9PL 0.8706
322 AHC 0.8702
323 MMS 0.8700
324 3XH 0.8700
325 KLS 0.8697
326 A18 0.8697
327 YOF 0.8697
328 JVD 0.8697
329 PHQ ALA 0.8696
330 2P3 0.8695
331 6ZX 0.8695
332 6FR 0.8695
333 1N5 0.8695
334 36M 0.8695
335 5LI 0.8693
336 5WN 0.8693
337 3VW 0.8691
338 4LW 0.8690
339 4XF 0.8690
340 EQW 0.8689
341 5VU 0.8688
342 YZM 0.8687
343 1XS 0.8686
344 TOM 0.8682
345 MJ5 0.8679
346 HSX 0.8678
347 IYR 0.8678
348 531 0.8675
349 4DI 0.8673
350 F98 0.8673
351 28B 0.8672
352 A9B 0.8672
353 Q4G 0.8670
354 S0W 0.8668
355 5OY 0.8667
356 GNR 0.8666
357 M5B 0.8664
358 Y3L 0.8662
359 KNA 0.8661
360 NRG 0.8661
361 C4E 0.8661
362 A6Z 0.8660
363 DXG 0.8658
364 ZIP 0.8657
365 0LO 0.8655
366 PRA 0.8655
367 3VX 0.8653
368 L1T 0.8653
369 RK4 0.8652
370 A5P 0.8652
371 DTB 0.8650
372 DMA 0.8650
373 GJG 0.8649
374 GB4 0.8649
375 LSQ 0.8647
376 OA1 0.8645
377 IVL 0.8645
378 S1D 0.8644
379 4GU 0.8637
380 0SY 0.8637
381 TX4 0.8635
382 FSA 0.8635
383 STV 0.8634
384 EXR 0.8631
385 GGG 0.8629
386 DED 0.8625
387 BPW 0.8625
388 C9M 0.8623
389 TH4 0.8623
390 5WK 0.8622
391 HJD 0.8621
392 4G2 0.8617
393 LUQ 0.8617
394 CTE 0.8613
395 HHV 0.8609
396 F06 0.8608
397 5O5 0.8607
398 YIH 0.8607
399 J4K 0.8605
400 N4B 0.8603
401 5NR 0.8603
402 7KE 0.8594
403 WCU 0.8593
404 28A 0.8592
405 PNP 0.8592
406 9B3 0.8591
407 ITW 0.8589
408 2D2 0.8589
409 S7V 0.8588
410 VBC 0.8585
411 AOT 0.8585
412 5H6 0.8584
413 N91 0.8581
414 8D6 0.8577
415 JSX 0.8576
416 K48 0.8571
417 B1J 0.8571
418 DBS 0.8567
419 DER 0.8566
420 FZM 0.8564
421 Q86 0.8563
422 P80 0.8563
423 RKV 0.8562
424 1AJ 0.8561
425 536 0.8556
426 PLP PMP 0.8547
427 LJ3 0.8545
428 JGB 0.8545
429 4Z3 0.8545
430 X6W 0.8544
431 D1Y 0.8533
432 PIQ 0.8530
433 F18 0.8523
434 AUV 0.8517
435 BZS 0.8514
436 HJ1 0.8508
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4EOX; Ligand: 0S5; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 4eox.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 1G27 BB1 38.6905
2 1G27 BB1 38.6905
3 1G27 BB1 38.6905
4 1RL4 BRR 49.4681
5 1RL4 BRR 49.4681
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