Receptor
PDB id Resolution Class Description Source Keywords
4xew 2.47 Å EC: 2.6.1.62 CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE (BI MYCOBACTERIUM TUBERCULOSIS, COMPLEXED WITH A HTS LEAD COMPO MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCH37RV) INHIBITOR COMPLEX TRANSAMINASE PLP TRANSFERASE-TRANSFERASE COMPLEX
Ref.: FRAGMENT-BASED EXPLORATION OF BINDING SITE FLEXIBIL MYCOBACTERIUM TUBERCULOSIS BIOA. J.MED.CHEM. V. 58 5208 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
40N A:502;
B:502;
 Valid;
Valid;
 none;
none;
 ic50 = 0.44 uM
283.254 C16 H10 F N O3 c1ccc...
PLP B:501;
A:501;
 Invalid;
Invalid;
 none;
none;
 submit data
247.142 C8 H10 N O6 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KGS 2.1 Å EC: 2.6.1.62 CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE (BI MYCOBACTERIUM TUBERCULOSIS, COMPLEXED WITH AN INHIBITOR OPTF ROM HTS LEAD: 5-[4-(1,3-BENZODIOXOL-5-YLCARBONYL)PIPERAZIN3- DIHYDROINDEN-1-ONE MYCOBACTERIUM BOVIS (STRAIN ATCC BAA-9AF2122/97) TRANSAMINASE PLP TRANSFERASE TRANSFERASE-INHIBITOR COMPLETRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: STRUCTURE-BASED OPTIMIZATION OF PYRIDOXAL 5'-PHOSPHATE-DEPENDENT TRANSAMINASE ENZYME (BIOA) I THAT TARGET BIOTIN BIOSYNTHESIS IN MYCOBACTERIUM TUBERCULOSIS. J. MED. CHEM. V. 60 5507 2017
Members (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4WYC Kd = 15 uM 3VS C10 H9 N3 O c1cc(ccc1C....
2 4CXR - 2BG C8 H8 N2 S c1ccc2c(c1....
3 3TFU - PL8 C16 H22 N3 O7 P Cc1c(c(c(c....
4 4MQR - 2B9 C14 H15 N4 O6 P CC1=C(/C(=....
5 4MQP - 2B1 C15 H15 N4 O5 P S Cc1c(c(c(c....
6 4XJO Kd = 132 nM 41O C20 H17 Cl N2 O2 c1cc(cc(c1....
7 5KGS Kd = 74 nM 6SR C21 H20 N2 O4 c1cc2c(cc1....
8 4W1W ic50 = 0.195 uM 3G8 C18 H17 N O3 S CCN(CC)c1c....
9 4WYG Kd = 6.8 uM 3W1 C11 H12 Cl N3 c1cc(ccc1C....
10 4MQQ - 2B6 C16 H15 N4 O6 P S Cc1c(c(c(c....
11 4XEW ic50 = 0.44 uM 40N C16 H10 F N O3 c1ccc(c(c1....
12 4W1V ic50 = 0.659 uM 3GS C16 H14 F N O5 S COC(=O)c1c....
13 4XJP Kd = 108 nM 41N C20 H20 N2 O4 CC(=O)c1cc....
14 4WYF Kd = 21.7 uM 3VX C11 H9 N O2 CC(=O)Nc1c....
15 4WYA Kd = 6.9 uM 3VQ C10 H8 N2 O S c1ccnc(c1)....
16 4W1X - 3G9 C19 H19 Cl N2 O2 CC(=O)c1cc....
17 5KGT - 6SQ C20 H20 Cl N O2 CC(=O)c1cc....
18 4WYE Kd = 41.8 uM 3VW C12 H15 N O c1ccc(cc1)....
19 4CXQ - KAP C9 H17 N O3 C[C@@H](C(....
20 4WYD Kd = 11.7 uM 3VR C12 H15 N3 CNCc1ccc(c....
21 3LV2 - SFG C15 H23 N7 O5 c1nc(c2c(n....
22 5TE2 - 7B9 C16 H22 N3 O7 P Cc1c(c(c(c....
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4WYC Kd = 15 uM 3VS C10 H9 N3 O c1cc(ccc1C....
2 4CXR - 2BG C8 H8 N2 S c1ccc2c(c1....
3 3TFU - PL8 C16 H22 N3 O7 P Cc1c(c(c(c....
4 4MQR - 2B9 C14 H15 N4 O6 P CC1=C(/C(=....
5 4MQP - 2B1 C15 H15 N4 O5 P S Cc1c(c(c(c....
6 4XJO Kd = 132 nM 41O C20 H17 Cl N2 O2 c1cc(cc(c1....
7 5KGS Kd = 74 nM 6SR C21 H20 N2 O4 c1cc2c(cc1....
8 4W1W ic50 = 0.195 uM 3G8 C18 H17 N O3 S CCN(CC)c1c....
9 4WYG Kd = 6.8 uM 3W1 C11 H12 Cl N3 c1cc(ccc1C....
10 4MQQ - 2B6 C16 H15 N4 O6 P S Cc1c(c(c(c....
11 4XEW ic50 = 0.44 uM 40N C16 H10 F N O3 c1ccc(c(c1....
12 4W1V ic50 = 0.659 uM 3GS C16 H14 F N O5 S COC(=O)c1c....
13 4XJP Kd = 108 nM 41N C20 H20 N2 O4 CC(=O)c1cc....
14 4WYF Kd = 21.7 uM 3VX C11 H9 N O2 CC(=O)Nc1c....
15 4WYA Kd = 6.9 uM 3VQ C10 H8 N2 O S c1ccnc(c1)....
16 4W1X - 3G9 C19 H19 Cl N2 O2 CC(=O)c1cc....
17 5KGT - 6SQ C20 H20 Cl N O2 CC(=O)c1cc....
18 4WYE Kd = 41.8 uM 3VW C12 H15 N O c1ccc(cc1)....
19 4CXQ - KAP C9 H17 N O3 C[C@@H](C(....
20 4WYD Kd = 11.7 uM 3VR C12 H15 N3 CNCc1ccc(c....
21 3LV2 - SFG C15 H23 N7 O5 c1nc(c2c(n....
22 5TE2 - 7B9 C16 H22 N3 O7 P Cc1c(c(c(c....
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4WYC Kd = 15 uM 3VS C10 H9 N3 O c1cc(ccc1C....
2 4CXR - 2BG C8 H8 N2 S c1ccc2c(c1....
3 3TFU - PL8 C16 H22 N3 O7 P Cc1c(c(c(c....
4 4W1W ic50 = 0.195 uM 3G8 C18 H17 N O3 S CCN(CC)c1c....
5 4WYG Kd = 6.8 uM 3W1 C11 H12 Cl N3 c1cc(ccc1C....
6 4MQQ - 2B6 C16 H15 N4 O6 P S Cc1c(c(c(c....
7 4XEW ic50 = 0.44 uM 40N C16 H10 F N O3 c1ccc(c(c1....
8 4W1V ic50 = 0.659 uM 3GS C16 H14 F N O5 S COC(=O)c1c....
9 4XJP Kd = 108 nM 41N C20 H20 N2 O4 CC(=O)c1cc....
10 4WYF Kd = 21.7 uM 3VX C11 H9 N O2 CC(=O)Nc1c....
11 4WYA Kd = 6.9 uM 3VQ C10 H8 N2 O S c1ccnc(c1)....
12 4W1X - 3G9 C19 H19 Cl N2 O2 CC(=O)c1cc....
13 5KGT - 6SQ C20 H20 Cl N O2 CC(=O)c1cc....
14 4WYE Kd = 41.8 uM 3VW C12 H15 N O c1ccc(cc1)....
15 4CXQ - KAP C9 H17 N O3 C[C@@H](C(....
16 4WYD Kd = 11.7 uM 3VR C12 H15 N3 CNCc1ccc(c....
17 3LV2 - SFG C15 H23 N7 O5 c1nc(c2c(n....
18 5TE2 - 7B9 C16 H22 N3 O7 P Cc1c(c(c(c....
19 1MLZ - TZA PLP n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 40N; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 40N 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 40N; Similar ligands found: 378
No: Ligand Similarity coefficient
1 NIF 0.9470
2 3WL 0.9456
3 1V3 0.9449
4 CUE 0.9449
5 SNJ 0.9420
6 6JM 0.9400
7 LIG 0.9378
8 DX2 0.9378
9 FSE 0.9342
10 738 0.9335
11 Q8G 0.9328
12 DFV 0.9316
13 1V4 0.9313
14 Q8D 0.9306
15 6QT 0.9291
16 QUE 0.9278
17 22M 0.9275
18 205 0.9269
19 DX8 0.9267
20 LU2 0.9257
21 6JO 0.9243
22 AGI 0.9236
23 CU8 0.9230
24 6XC 0.9220
25 DDC 0.9211
26 NAR 0.9205
27 HWB 0.9195
28 NKI 0.9194
29 F40 0.9191
30 1HP 0.9189
31 BRY 0.9188
32 MYU 0.9173
33 801 0.9170
34 121 0.9170
35 RGK 0.9167
36 HUL 0.9163
37 WLH 0.9162
38 3XL 0.9160
39 KMP 0.9160
40 FL8 0.9156
41 NVS 0.9153
42 II4 0.9148
43 EQU 0.9146
44 57D 0.9145
45 3JC 0.9144
46 124 0.9143
47 AJ4 0.9143
48 MI2 0.9141
49 20D 0.9139
50 QS4 0.9138
51 BMZ 0.9132
52 CR4 0.9132
53 122 0.9132
54 9CE 0.9128
55 0MB 0.9127
56 DFL 0.9125
57 RF2 0.9112
58 2GE 0.9108
59 MYC 0.9101
60 DEH 0.9100
61 LI7 0.9099
62 BBP 0.9096
63 Q0K 0.9093
64 EST 0.9093
65 AJ6 0.9090
66 2XY 0.9089
67 IXM 0.9083
68 D25 0.9082
69 KXN 0.9081
70 PIQ 0.9080
71 1V8 0.9076
72 J84 0.9075
73 338 0.9074
74 120 0.9073
75 47X 0.9070
76 0DF 0.9069
77 7EH 0.9067
78 IDZ 0.9063
79 SO7 0.9063
80 DH2 0.9059
81 SAK 0.9056
82 J3Z 0.9054
83 DX7 0.9050
84 J8G 0.9043
85 AX1 0.9038
86 272 0.9034
87 E6Q 0.9033
88 97K 0.9032
89 39R 0.9031
90 K4T 0.9026
91 DQH 0.9025
92 D64 0.9024
93 3F4 0.9018
94 A73 0.9017
95 FX5 0.9017
96 SDN 0.9016
97 802 0.9015
98 6DQ 0.9010
99 1V1 0.9010
100 2OX 0.9007
101 196 0.9006
102 GEN 0.9005
103 1Q4 0.9005
104 XZ1 0.9002
105 6B5 0.9002
106 5NN 0.9001
107 MRI 0.9001
108 SZ5 0.9000
109 EI1 0.8999
110 CDJ 0.8999
111 3DE 0.8997
112 6DE 0.8996
113 M3W 0.8996
114 CC6 0.8993
115 CWE 0.8993
116 W8L 0.8992
117 7M5 0.8991
118 AP6 0.8991
119 658 0.8989
120 4L2 0.8988
121 7L4 0.8988
122 27F 0.8988
123 6VW 0.8988
124 WG8 0.8986
125 X8I 0.8984
126 E9L 0.8984
127 DTQ 0.8983
128 5ZM 0.8982
129 4AJ 0.8982
130 4RV 0.8981
131 08C 0.8981
132 7ZO 0.8981
133 21E 0.8979
134 H2W 0.8978
135 25F 0.8977
136 ECS 0.8977
137 Q7U 0.8976
138 43G 0.8975
139 LWS 0.8975
140 F4U 0.8972
141 ESM 0.8970
142 4UE 0.8968
143 DNF SER 0.8967
144 SER DNF 0.8967
145 SNB 0.8958
146 Q11 0.8957
147 O9Q 0.8954
148 789 0.8954
149 O9Z 0.8954
150 X2L 0.8952
151 9XZ 0.8951
152 O9T 0.8951
153 4NR 0.8950
154 A63 0.8949
155 A05 0.8945
156 BHF 0.8943
157 AO 0.8943
158 7M2 0.8942
159 7VF 0.8939
160 YE7 0.8937
161 4QX 0.8936
162 AUE 0.8935
163 YZ9 0.8935
164 ZAR 0.8934
165 OTA 0.8933
166 ESR 0.8930
167 TGW 0.8930
168 6BK 0.8929
169 VT3 0.8926
170 0UL 0.8926
171 MKN 0.8924
172 P4L 0.8922
173 7G2 0.8914
174 LVY 0.8914
175 108 0.8912
176 9YD 0.8911
177 517 0.8908
178 HH6 0.8905
179 IQW 0.8903
180 7LU 0.8902
181 EES 0.8900
182 WDW 0.8893
183 JV5 0.8890
184 E92 0.8876
185 H50 0.8875
186 D26 0.8872
187 HMO 0.8871
188 Q12 0.8869
189 3C3 0.8867
190 1UZ 0.8867
191 0NJ 0.8866
192 IRH 0.8862
193 DBE 0.8862
194 RSV 0.8861
195 Q92 0.8859
196 7FC 0.8857
197 5DE 0.8855
198 SU9 0.8855
199 GJG 0.8854
200 AUG 0.8852
201 TVC 0.8852
202 5OR 0.8848
203 15Q 0.8848
204 3GX 0.8842
205 17M 0.8839
206 5KN 0.8839
207 TFX 0.8838
208 7EL 0.8837
209 G2V 0.8836
210 FNT 0.8833
211 23M 0.8833
212 3QI 0.8832
213 2QU 0.8832
214 824 0.8830
215 4CN 0.8825
216 EF2 0.8825
217 62D 0.8824
218 AXX 0.8824
219 LC1 0.8823
220 69W 0.8822
221 9ME 0.8821
222 A9B 0.8821
223 AOM 0.8819
224 1V0 0.8818
225 T21 0.8817
226 OSY 0.8817
227 5WW 0.8816
228 3RH 0.8815
229 22T 0.8814
230 ESZ 0.8814
231 AQN 0.8812
232 334 0.8811
233 E98 0.8810
234 3Q1 0.8808
235 FCW 0.8807
236 521 0.8807
237 2JX 0.8803
238 J8D 0.8803
239 7M9 0.8802
240 J3B 0.8802
241 4P9 0.8800
242 91F 0.8800
243 BIT 0.8799
244 KOM 0.8798
245 5EZ 0.8797
246 4B8 0.8794
247 K8W 0.8793
248 BXZ 0.8792
249 51Y 0.8790
250 OUA 0.8789
251 3MI 0.8787
252 2QV 0.8787
253 BL4 0.8787
254 0SX 0.8786
255 Y70 0.8785
256 AV7 0.8785
257 135 0.8781
258 3G5 0.8777
259 FZB 0.8776
260 KP2 0.8774
261 KU1 0.8774
262 1UT 0.8772
263 6FX 0.8771
264 1UR 0.8771
265 OUG 0.8768
266 6JP 0.8768
267 F36 0.8765
268 LZ4 0.8765
269 WST 0.8763
270 MT6 0.8760
271 NFG 0.8757
272 JVB 0.8756
273 H0V 0.8753
274 T5J 0.8753
275 I0D 0.8751
276 68C 0.8751
277 3Q2 0.8751
278 MQS 0.8750
279 6XR 0.8747
280 5E2 0.8746
281 ZTW 0.8745
282 0OK 0.8743
283 B7H 0.8742
284 L6Y 0.8741
285 GUS 0.8741
286 52F 0.8736
287 4YE 0.8735
288 U14 0.8733
289 I0G 0.8733
290 5XM 0.8730
291 KW7 0.8730
292 IYX 0.8727
293 WCU 0.8727
294 SJR 0.8725
295 A64 0.8724
296 3WK 0.8721
297 0DJ 0.8718
298 IRG 0.8718
299 35K 0.8716
300 OPA 0.8716
301 Q4G 0.8716
302 555 0.8715
303 80R 0.8715
304 XYP XYP 0.8713
305 BL7 0.8711
306 MQR 0.8710
307 R18 0.8700
308 LJ5 0.8700
309 L1T 0.8697
310 1FE 0.8696
311 90G 0.8695
312 5VU 0.8695
313 DN8 0.8692
314 4ZF 0.8692
315 4HG 0.8690
316 6EL 0.8688
317 PFT 0.8685
318 797 0.8684
319 SGW 0.8684
320 20N 0.8682
321 4R0 0.8678
322 C4E 0.8677
323 7DE 0.8675
324 FT6 0.8673
325 AVX 0.8671
326 5WK 0.8669
327 7FZ 0.8665
328 XEV 0.8663
329 5B2 0.8663
330 RFZ 0.8662
331 ESL 0.8660
332 S0J 0.8654
333 BJ4 0.8651
334 DXK 0.8650
335 NAL 0.8647
336 BL6 0.8646
337 AJ1 0.8644
338 IPJ 0.8642
339 4YF 0.8642
340 AD6 0.8638
341 E8Z 0.8637
342 7FU 0.8637
343 A6W 0.8637
344 4KN 0.8632
345 U3P 0.8628
346 UN9 0.8628
347 XYS XYS 0.8625
348 6AN 0.8624
349 3D9 0.8623
350 U12 0.8622
351 T34 0.8620
352 ERJ 0.8616
353 4K9 0.8614
354 6WL 0.8613
355 8M5 0.8613
356 ALH 0.8611
357 47V 0.8610
358 8WB 0.8606
359 4UM 0.8593
360 2V4 0.8588
361 5ET 0.8581
362 YE6 0.8580
363 5C1 0.8579
364 C3P 0.8576
365 O53 0.8576
366 1CE 0.8576
367 M16 0.8574
368 TEF 0.8566
369 JTK 0.8566
370 041 0.8557
371 NPX 0.8557
372 U4J 0.8556
373 6H2 0.8552
374 K6N 0.8530
375 AJ8 0.8530
376 5P3 0.8530
377 NU3 0.8527
378 AOI 0.8520
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KGS; Ligand: 6SR; Similar sites found with APoc: 9
This union binding pocket(no: 1) in the query (biounit: 5kgs.bio1) has 44 residues
No: Leader PDB Ligand Sequence Similarity
1 4ZSY RW2 24.9453
2 4ZM4 PLP 27.1335
3 4ZM4 PLP 27.1335
4 4UOX PLP 35.2298
5 4UOX PLP 35.2298
6 4UOX PUT 35.2298
7 4ADC PLP 35.7143
8 3A8U PLP 47.216
9 3A8U PLP 47.216
Pocket No.: 2; Query (leader) PDB : 5KGS; Ligand: 6SR; Similar sites found with APoc: 8
This union binding pocket(no: 2) in the query (biounit: 5kgs.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
1 4ZSY RW2 24.9453
2 4ZM4 PLP 27.1335
3 4ZM4 PLP 27.1335
4 4UOX PLP 35.2298
5 4UOX PLP 35.2298
6 4UOX PUT 35.2298
7 3A8U PLP 47.216
8 3A8U PLP 47.216
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