Receptor
PDB id Resolution Class Description Source Keywords
3K14 1.7 Å EC: 4.6.1.12 CO-CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPH SYNTHASE FROM BURKHOLDERIA PSEUDOMALLEI WITH FOL FRAGMENT 53 -METHYL-5,6-DIHYDROIMIDAZO[2,1-B][1,3]THIAZOLE-2-CARBOXYLA BURKHOLDERIA PSEUDOMALLEI NIAID SSGCID SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTDISEASE FRAGMENT CRYSTALLOGRAPHY FRAGMENT-BASED DRUG-DESIFRAGMENTS OF LIFE ISOPRENE BIOSYNTHESIS LYASE METAL-BIND
Ref.: LEVERAGING STRUCTURE DETERMINATION WITH FRAGMENT SC FOR INFECTIOUS DISEASE DRUG TARGETS: MECP SYNTHASE BURKHOLDERIA PSEUDOMALLEI. J STRUCT FUNCT GENOMICS V. 12 63 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
535 A:164;
B:164;
C:164;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
210.253 C9 H10 N2 O2 S CCOC(...
ACT C:165;
 Invalid;
 none;
 submit data
59.044 C2 H3 O2 CC(=O...
CL A:165;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
K A:166;
 Invalid;
 none;
 submit data
39.098 K [K+]
ZN A:163;
B:163;
C:163;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3JVH 1.69 Å EC: 4.6.1.12 CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSP SYNTHASE FROM BURKHOLDERIA PSEUDOMALLEI WITH FOL FRAGMENT 8 BURKHOLDERIA PSEUDOMALLEI NIAID SSGCID SEATTLE DTRUCTURAL GENOMICS CENTER FOR INFECTDISEASE FRAGMENT CRYSTALLOGRAPHY FRAGMENTS OF LIFE ZINC-FRAGMENT ISOPRENE BIOSYNTHESIS LYASE METAL-BINDING STRUGENOMICS SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS
Ref.: LEVERAGING STRUCTURE DETERMINATION WITH FRAGMENT SC FOR INFECTIOUS DISEASE DRUG TARGETS: MECP SYNTHASE BURKHOLDERIA PSEUDOMALLEI. J STRUCT FUNCT GENOMICS V. 12 63 2011
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 3IEW - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
2 3QHD - CTN C9 H13 N3 O5 C1=CN(C(=O....
3 3K2X - I5A C9 H12 I N3 O4 C1=CN(C(=O....
4 3F0G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
5 3IKE - CYT C4 H5 N3 O C1=C(NC(=O....
6 3IEQ - C C9 H14 N3 O8 P C1=CN(C(=O....
7 3IKF - 717 C6 H6 N2 O S c1csc2n1cc....
8 3JVH - HHV C10 H11 N5 O c1cc(cnc1)....
9 3P10 - CTN C9 H13 N3 O5 C1=CN(C(=O....
10 3MBM - CYT C4 H5 N3 O C1=C(NC(=O....
11 3P0Z - CTN C9 H13 N3 O5 C1=CN(C(=O....
12 3K14 - 535 C9 H10 N2 O2 S CCOC(=O)c1....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1T0A - FPP C15 H28 O7 P2 CC(=CCC/C(....
2 4C8G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
3 4C8E - C5P C9 H14 N3 O8 P C1=CN(C(=O....
4 3ERN Kd = 18.91 mM CAR C9 H14 N3 O8 P C1=CN(C(=O....
5 2GZL Kd = 15 uM 2AA C23 H31 N5 O13 P2 S CN(C)c1ccc....
6 3ELC Kd = 2.02 mM F01 C9 H12 F N3 O5 C1=C(C(=NC....
7 1JY8 - CDI C5 H12 O9 P2 C[C@@]1([C....
8 1GX1 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
9 1U3L - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
10 1H47 - GPP C10 H20 O7 P2 CC(=CCC/C(....
11 1H48 - CDI C5 H12 O9 P2 C[C@@]1([C....
12 2AMT Kd = 36 uM 1AA C18 H24 N4 O13 P2 c1ccc(c(c1....
13 3IKE - CYT C4 H5 N3 O C1=C(NC(=O....
14 3IEQ - C C9 H14 N3 O8 P C1=CN(C(=O....
15 3IKF - 717 C6 H6 N2 O S c1csc2n1cc....
16 3JVH - HHV C10 H11 N5 O c1cc(cnc1)....
17 3P10 - CTN C9 H13 N3 O5 C1=CN(C(=O....
18 3MBM - CYT C4 H5 N3 O C1=C(NC(=O....
19 3P0Z - CTN C9 H13 N3 O5 C1=CN(C(=O....
20 3K14 - 535 C9 H10 N2 O2 S CCOC(=O)c1....
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1T0A - FPP C15 H28 O7 P2 CC(=CCC/C(....
2 4C8I - CIT C6 H8 O7 C(C(=O)O)C....
3 4C8G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
4 4C8E - C5P C9 H14 N3 O8 P C1=CN(C(=O....
5 3ERN Kd = 18.91 mM CAR C9 H14 N3 O8 P C1=CN(C(=O....
6 2GZL Kd = 15 uM 2AA C23 H31 N5 O13 P2 S CN(C)c1ccc....
7 3ELC Kd = 2.02 mM F01 C9 H12 F N3 O5 C1=C(C(=NC....
8 1JY8 - CDI C5 H12 O9 P2 C[C@@]1([C....
9 1GX1 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
10 1U3L - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
11 1H47 - GPP C10 H20 O7 P2 CC(=CCC/C(....
12 1H48 - CDI C5 H12 O9 P2 C[C@@]1([C....
13 2AMT Kd = 36 uM 1AA C18 H24 N4 O13 P2 c1ccc(c(c1....
14 3IEW - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
15 3QHD - CTN C9 H13 N3 O5 C1=CN(C(=O....
16 3K2X - I5A C9 H12 I N3 O4 C1=CN(C(=O....
17 3F0G - C5P C9 H14 N3 O8 P C1=CN(C(=O....
18 3IKE - CYT C4 H5 N3 O C1=C(NC(=O....
19 3IEQ - C C9 H14 N3 O8 P C1=CN(C(=O....
20 3IKF - 717 C6 H6 N2 O S c1csc2n1cc....
21 3JVH - HHV C10 H11 N5 O c1cc(cnc1)....
22 3P10 - CTN C9 H13 N3 O5 C1=CN(C(=O....
23 3MBM - CYT C4 H5 N3 O C1=C(NC(=O....
24 3P0Z - CTN C9 H13 N3 O5 C1=CN(C(=O....
25 3K14 - 535 C9 H10 N2 O2 S CCOC(=O)c1....
26 1IV4 - C5P C9 H14 N3 O8 P C1=CN(C(=O....
27 2PMP - C5P C9 H14 N3 O8 P C1=CN(C(=O....
28 2UZH - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 535; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 535 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 535; Similar ligands found: 430
No: Ligand Similarity coefficient
1 KMY 0.9429
2 MAJ 0.9354
3 36M 0.9342
4 7MX 0.9335
5 CFA 0.9328
6 NFM 0.9324
7 BQ2 0.9317
8 EYV 0.9310
9 EYJ 0.9299
10 3TC 0.9270
11 I2E 0.9259
12 1QP 0.9245
13 ODO 0.9237
14 RPN 0.9223
15 I3E 0.9220
16 EYY 0.9209
17 IAC 0.9199
18 LNR 0.9195
19 4I8 0.9195
20 H4E 0.9175
21 6VD 0.9161
22 SYE 0.9151
23 6NI 0.9147
24 7ME 0.9146
25 MQB 0.9139
26 MS9 0.9138
27 AAN 0.9131
28 SKF 0.9131
29 EVF 0.9130
30 S24 0.9130
31 6NT 0.9119
32 61M 0.9117
33 ZON 0.9115
34 P9E 0.9112
35 YPN 0.9107
36 3NY 0.9100
37 5NI 0.9096
38 DEW 0.9096
39 1A7 0.9096
40 F4E 0.9089
41 327 0.9088
42 8XL 0.9085
43 ARP 0.9077
44 2ZM 0.9072
45 NLA 0.9069
46 HC4 0.9069
47 D2G 0.9066
48 TSR 0.9066
49 JDN 0.9055
50 QMS 0.9053
51 CC5 0.9052
52 4AV 0.9047
53 MS0 0.9046
54 657 0.9041
55 1F1 0.9039
56 4NS 0.9035
57 IOS 0.9034
58 36E 0.9030
59 D1G 0.9029
60 M4S 0.9027
61 NVU 0.9027
62 0HN 0.9025
63 ITW 0.9020
64 2O6 0.9019
65 CSN 0.9015
66 TRP 0.9015
67 EUE 0.9014
68 ESX 0.9010
69 AHC 0.9010
70 EN1 0.9009
71 7AP 0.9009
72 DTY 0.9007
73 TYR 0.9007
74 N4E 0.9006
75 EUH 0.9006
76 2O8 0.9004
77 9UL 0.9003
78 1OS 0.8999
79 15N 0.8996
80 HHH 0.8994
81 SRO 0.8993
82 9R5 0.8990
83 EYM 0.8989
84 THA 0.8988
85 SNO 0.8988
86 8ZE 0.8987
87 4NZ 0.8985
88 GO8 0.8980
89 PQZ 0.8980
90 27K 0.8979
91 9VQ 0.8979
92 CWJ 0.8976
93 6KT 0.8972
94 OTR 0.8972
95 PNP 0.8971
96 M3Q 0.8971
97 SBK 0.8969
98 ESP 0.8969
99 MNP 0.8968
100 YOF 0.8967
101 MP5 0.8967
102 0HO 0.8966
103 3N1 0.8965
104 23J 0.8964
105 AMR 0.8962
106 6DP 0.8961
107 BZ2 0.8960
108 DAH 0.8960
109 HA5 0.8959
110 4WL 0.8958
111 4NP 0.8957
112 AM4 0.8956
113 ABI 0.8954
114 EYA 0.8954
115 JB8 0.8951
116 FUD 0.8949
117 PPN 0.8949
118 JAW 0.8946
119 BIO 0.8944
120 DVQ 0.8943
121 F52 0.8942
122 ICB 0.8941
123 DHC 0.8939
124 RNO 0.8939
125 52C 0.8937
126 5DS 0.8932
127 DX3 0.8931
128 NK5 0.8929
129 3EB 0.8929
130 49O 0.8928
131 D3G 0.8927
132 9BF 0.8927
133 MD6 0.8920
134 S7G 0.8911
135 MR1 0.8908
136 PHE 0.8907
137 5WN 0.8906
138 Y4L 0.8901
139 4RU 0.8901
140 BZJ 0.8899
141 EV2 0.8899
142 97T 0.8899
143 C2Y 0.8898
144 AA 0.8895
145 4CM 0.8894
146 PLR 0.8893
147 DHY 0.8893
148 H2B 0.8892
149 HBI 0.8892
150 DTR 0.8889
151 8Y7 0.8883
152 K82 0.8881
153 PH3 0.8879
154 SQV 0.8879
155 OCZ 0.8878
156 ROI 0.8876
157 259 0.8876
158 K97 0.8875
159 EV3 0.8874
160 XI7 0.8874
161 TB8 0.8874
162 IQ5 0.8873
163 ANF 0.8869
164 J9Q 0.8869
165 2K8 0.8869
166 HNM 0.8868
167 MPU 0.8866
168 2LY 0.8865
169 PJW 0.8859
170 4SX 0.8858
171 XQI 0.8857
172 HLP 0.8855
173 PNZ 0.8855
174 IYR 0.8852
175 9FL 0.8851
176 YF3 0.8848
177 27B 0.8848
178 N2M 0.8847
179 0A1 0.8841
180 0J4 0.8841
181 FA0 0.8840
182 LR5 0.8839
183 SAN 0.8838
184 NQH 0.8837
185 6ZX 0.8837
186 4ZA 0.8834
187 5O6 0.8834
188 F1A 0.8832
189 TYE 0.8832
190 3Y7 0.8830
191 IOP 0.8828
192 4P5 0.8828
193 BB4 0.8827
194 5GT 0.8826
195 VNL 0.8823
196 HPP 0.8822
197 AES 0.8822
198 CLU 0.8821
199 6HP 0.8817
200 ETV 0.8817
201 4J8 0.8815
202 7CT 0.8813
203 EKZ 0.8811
204 3IB 0.8811
205 YIE 0.8810
206 FBS 0.8808
207 8GK 0.8807
208 ONR 0.8807
209 FBF 0.8805
210 0F9 0.8804
211 G6P 0.8803
212 BPY 0.8802
213 OW7 0.8802
214 3AE 0.8802
215 KBZ 0.8800
216 PBN 0.8800
217 3R4 0.8799
218 GNR 0.8799
219 NAG 0.8798
220 7PJ 0.8796
221 C9E 0.8795
222 EXD 0.8794
223 J6W 0.8792
224 AAS 0.8790
225 ZEC 0.8790
226 AMS 0.8790
227 86L 0.8789
228 ESI 0.8789
229 T1N 0.8788
230 PMP 0.8787
231 0NX 0.8785
232 4BY 0.8784
233 DHB 0.8783
234 GF1 0.8783
235 HSX 0.8781
236 PXP 0.8780
237 42J 0.8780
238 X0V 0.8780
239 PLP 0.8780
240 AEG 0.8778
241 TSU 0.8777
242 428 0.8774
243 3VX 0.8773
244 LZ2 0.8771
245 54Z 0.8770
246 S7J 0.8770
247 4NB 0.8767
248 2HO 0.8766
249 4M0 0.8766
250 2BG 0.8765
251 NPX 0.8765
252 RA7 0.8763
253 BPW 0.8761
254 4ZD 0.8759
255 PLP PMP 0.8755
256 4HP 0.8755
257 1WC 0.8755
258 HQJ 0.8754
259 SN4 0.8752
260 OQC 0.8752
261 5AD 0.8751
262 2F6 0.8750
263 C8O 0.8750
264 HQD 0.8750
265 5OO 0.8749
266 0J5 0.8749
267 X0U 0.8749
268 9LI 0.8747
269 4NM 0.8744
270 5CU 0.8743
271 ANN 0.8743
272 5O5 0.8743
273 X04 0.8743
274 N2I 0.8743
275 TAG 0.8742
276 VD9 0.8740
277 BZ3 0.8739
278 DOB 0.8738
279 5GU 0.8738
280 4JC 0.8737
281 PO6 0.8736
282 ZEZ 0.8735
283 TZF 0.8733
284 PFL 0.8732
285 LQ2 0.8730
286 YIH 0.8730
287 IFP 0.8729
288 NPS 0.8729
289 BHA 0.8727
290 5XC 0.8727
291 5LA 0.8726
292 AC2 0.8726
293 R9Y 0.8724
294 3CR 0.8724
295 BP7 0.8723
296 FER 0.8723
297 INO 0.8723
298 MPK 0.8722
299 363 0.8720
300 AMH 0.8719
301 AN3 0.8718
302 F69 0.8716
303 GO2 0.8710
304 AZM 0.8709
305 4TB 0.8707
306 LDP 0.8706
307 DUR 0.8702
308 PH2 0.8702
309 H35 0.8701
310 MXD 0.8701
311 8WO 0.8700
312 JTH 0.8699
313 EY7 0.8698
314 FK8 0.8698
315 HX4 0.8696
316 46P 0.8695
317 R7T 0.8693
318 848 0.8693
319 92K 0.8692
320 QQQ 0.8691
321 173 0.8690
322 Z25 0.8689
323 YZ9 0.8686
324 6HO 0.8686
325 68A 0.8686
326 5OF 0.8685
327 6TZ 0.8685
328 F4K 0.8685
329 7O4 0.8685
330 4KL 0.8683
331 KTJ 0.8683
332 ENO 0.8681
333 R20 0.8679
334 KJU 0.8679
335 E3D 0.8677
336 SG2 0.8677
337 G1P 0.8675
338 X48 0.8674
339 3C4 0.8673
340 KYA 0.8672
341 NYL 0.8672
342 TT4 0.8672
343 14N 0.8671
344 LAO 0.8671
345 0OL 0.8671
346 YI6 0.8669
347 NGA 0.8669
348 4NC 0.8666
349 AH9 0.8666
350 DJN 0.8666
351 DCZ 0.8666
352 1M2 0.8663
353 5QY 0.8662
354 PAB 0.8661
355 4AA 0.8658
356 22L 0.8656
357 XK0 0.8656
358 BNF 0.8655
359 PHB 0.8653
360 X11 0.8653
361 4ME 0.8651
362 RBJ 0.8651
363 N9J 0.8649
364 HHT 0.8649
365 GLP 0.8648
366 1Z6 0.8646
367 KTW 0.8646
368 KGK 0.8642
369 E4P 0.8642
370 STT 0.8641
371 TGX 0.8640
372 QBS 0.8640
373 XCG 0.8635
374 P72 0.8635
375 A2G 0.8633
376 UFV 0.8633
377 54E 0.8632
378 NDG 0.8632
379 HF2 0.8631
380 5NS 0.8630
381 PPY 0.8629
382 PD2 0.8628
383 KP2 0.8628
384 YZM 0.8625
385 5LD 0.8619
386 AEF 0.8619
387 4MA 0.8616
388 OA3 0.8613
389 X6P 0.8610
390 5F8 0.8609
391 N7I 0.8609
392 H4B 0.8607
393 PRZ 0.8606
394 B1J 0.8606
395 GDE 0.8606
396 258 0.8605
397 PBZ 0.8605
398 CKA 0.8604
399 NPO 0.8603
400 K5W 0.8602
401 U7E 0.8601
402 1Y6 0.8598
403 URC 0.8597
404 SW7 0.8597
405 IWT 0.8594
406 BZE 0.8592
407 4I5 0.8591
408 W81 0.8590
409 AC6 0.8585
410 7WR 0.8584
411 UNJ 0.8583
412 JND 0.8575
413 Q24 0.8575
414 ICO 0.8574
415 39U 0.8574
416 27L 0.8573
417 T9G 0.8567
418 DBS 0.8565
419 L5V 0.8562
420 5FL 0.8554
421 LVD 0.8553
422 5NU 0.8551
423 MZM 0.8550
424 SVD 0.8546
425 BVA 0.8542
426 8MO 0.8537
427 3IP 0.8537
428 1PS 0.8520
429 E1K 0.8516
430 HBO 0.8515
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3JVH; Ligand: HHV; 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: 3jvh.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3JVH; Ligand: HHV; 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: 3jvh.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3JVH; Ligand: HHV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3jvh.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback