Receptor
PDB id Resolution Class Description Source Keywords
4UMB 2.17 Å EC: 2.5.1.54 STRUCTURAL ANALYSIS OF SUBSTRATE-MIMICKING INHIBITORS IN COMPLEX WITH NEISSERIA MENINGITIDIS 3-DEOXY-D-ARABINO- H EPTULOSONATE 7-PHOSPHATE SYNTHASE - THE IMPORTANCE OF AC COMMODATING THE ACTIVE SITE WATER NEISSERIA MENINGITIDIS TRANSFERASE DAH7PS DAHPS AROMATIC AMINO ACIDS SHIKIMATE OXOCARBENIUM ION MENINGITIS
Ref.: STRUCTURAL ANALYSIS OF SUBSTRATE-MIMICKING INHIBITO COMPLEX WITH NEISSERIA MENINGITIDIS 3-DEOXY-D-ARABI HEPTULOSONATE 7-PHOSPHATE SYNTHASE - THE IMPORTANCE ACCOMMODATING THE ACTIVE SITE WATER. BIOORG.CHEM. V. 57 242 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
0V5 B:1351;
C:1351;
A:1353;
D:1351;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 Ki = 99 uM
170.058 C3 H7 O6 P C[C@H...
PO4 D:1352;
B:1352;
A:1352;
C:1352;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
94.971 O4 P [O-]P...
MN D:1350;
A:1351;
C:1350;
B:1350;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4UMA 1.76 Å EC: 2.5.1.54 STRUCTURAL ANALYSIS OF SUBSTRATE-MIMICKING INHIBITORS IN COMPLEX WITH NEISSERIA MENINGITIDIS 3 DEOXY D ARABINO H EPTULOSONATE 7 PHOSPHATE SYNTHASE THE IMPORTANCE OF AC COMMODATING THE ACTIVE SITE WATER NEISSERIA MENINGITIDIS TRANSFERASE DAH7PS DAHPS AROMATIC AMINO ACIDS SHIKIMATE OXOCARBENIUM ION ENZYME INHIBITORS MENINGITIS
Ref.: STRUCTURAL ANALYSIS OF SUBSTRATE-MIMICKING INHIBITO COMPLEX WITH NEISSERIA MENINGITIDIS 3-DEOXY-D-ARABI HEPTULOSONATE 7-PHOSPHATE SYNTHASE - THE IMPORTANCE ACCOMMODATING THE ACTIVE SITE WATER. BIOORG.CHEM. V. 57 242 2014
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4UMB Ki = 99 uM 0V5 C3 H7 O6 P C[C@H](C(=....
2 4UMC Ki = 360 uM PEQ C3 H7 O6 P C[C@@H](C(....
3 4HSO Kd = 22 uM TYR C9 H11 N O3 c1cc(ccc1C....
4 4UCG - PEP C3 H5 O6 P C=C(C(=O)O....
5 5DCE - TRP C11 H12 N2 O2 c1ccc2c(c1....
6 4UC5 - PHE C9 H11 N O2 c1ccc(cc1)....
7 4HSN - PEP C3 H5 O6 P C=C(C(=O)O....
8 4UMA Ki = 3.9 uM GZ3 C4 H7 O5 P C/C(=CP(=O....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4UMB Ki = 99 uM 0V5 C3 H7 O6 P C[C@H](C(=....
2 4UMC Ki = 360 uM PEQ C3 H7 O6 P C[C@@H](C(....
3 4HSO Kd = 22 uM TYR C9 H11 N O3 c1cc(ccc1C....
4 4UCG - PEP C3 H5 O6 P C=C(C(=O)O....
5 5DCE - TRP C11 H12 N2 O2 c1ccc2c(c1....
6 4UC5 - PHE C9 H11 N O2 c1ccc(cc1)....
7 4HSN - PEP C3 H5 O6 P C=C(C(=O)O....
8 4UMA Ki = 3.9 uM GZ3 C4 H7 O5 P C/C(=CP(=O....
9 1N8F - PEP C3 H5 O6 P C=C(C(=O)O....
10 1GG1 - PGA C2 H5 O6 P C(C(=O)O)O....
11 5CKS Kd = 3.1 uM 52L C7 H14 N O10 P C([C@H]([C....
50% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4UMB Ki = 99 uM 0V5 C3 H7 O6 P C[C@H](C(=....
2 4UMC Ki = 360 uM PEQ C3 H7 O6 P C[C@@H](C(....
3 4HSO Kd = 22 uM TYR C9 H11 N O3 c1cc(ccc1C....
4 4UCG - PEP C3 H5 O6 P C=C(C(=O)O....
5 5DCE - TRP C11 H12 N2 O2 c1ccc2c(c1....
6 4UC5 - PHE C9 H11 N O2 c1ccc(cc1)....
7 4HSN - PEP C3 H5 O6 P C=C(C(=O)O....
8 4UMA Ki = 3.9 uM GZ3 C4 H7 O5 P C/C(=CP(=O....
9 1OAB - PEP C3 H5 O6 P C=C(C(=O)O....
10 1OFO - PGA C2 H5 O6 P C(C(=O)O)O....
11 1OF6 - DTY C9 H11 N O3 c1cc(ccc1C....
12 1OF8 - G3P C3 H9 O6 P C([C@H](CO....
13 1OFA - PEP C3 H5 O6 P C=C(C(=O)O....
14 1HFB - PEP C3 H5 O6 P C=C(C(=O)O....
15 1N8F - PEP C3 H5 O6 P C=C(C(=O)O....
16 1GG1 - PGA C2 H5 O6 P C(C(=O)O)O....
17 5CKS Kd = 3.1 uM 52L C7 H14 N O10 P C([C@H]([C....
18 6AGM - TYR C9 H11 N O3 c1cc(ccc1C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 0V5; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 PEQ 1 1
2 0V5 1 1
3 TPO 0.5 0.727273
4 PEZ 0.5 0.833333
5 2PG 0.482759 0.705882
6 XSP 0.466667 0.923077
7 3PG 0.40625 0.727273
8 DG2 0.4 0.75
Similar Ligands (3D)
Ligand no: 1; Ligand: 0V5; Similar ligands found: 574
No: Ligand Similarity coefficient
1 PEP 1.0000
2 GZ3 0.9881
3 SPV 0.9840
4 R67 0.9817
5 3SL 0.9737
6 PPR 0.9661
7 PGA 0.9629
8 FB2 0.9572
9 LEU 0.9517
10 ASP 0.9513
11 AKG 0.9513
12 PMB 0.9494
13 LMR 0.9491
14 OAA 0.9472
15 ASN 0.9470
16 ACH 0.9458
17 COI 0.9456
18 PAH 0.9454
19 LLQ 0.9450
20 DS0 0.9437
21 HG3 0.9436
22 IOM 0.9427
23 DYA 0.9418
24 JYD 0.9411
25 CMS 0.9406
26 2RH 0.9396
27 KVP 0.9392
28 X1S 0.9385
29 CIZ 0.9384
30 TEO 0.9381
31 G2H 0.9380
32 40E 0.9373
33 AL0 0.9372
34 1SA 0.9372
35 GP9 0.9354
36 152 0.9348
37 HL5 0.9342
38 TSU 0.9336
39 A09 0.9333
40 GLN 0.9328
41 MLT 0.9325
42 ITN 0.9322
43 GLU 0.9319
44 8K2 0.9315
45 2PN 0.9294
46 SAN 0.9294
47 3PP 0.9294
48 1GP 0.9290
49 DGL 0.9290
50 DGN 0.9289
51 4J8 0.9283
52 1SH 0.9283
53 AAS 0.9279
54 FBS 0.9275
55 G3P 0.9268
56 PGH 0.9266
57 G3H 0.9263
58 13P 0.9260
59 LTL 0.9260
60 HBU 0.9252
61 CRN 0.9251
62 FCR 0.9247
63 173 0.9239
64 1DV 0.9233
65 1DQ 0.9227
66 BAM 0.9219
67 GVM 0.9217
68 GUA 0.9217
69 98J 0.9212
70 BEN 0.9211
71 PBC 0.9211
72 POP 0.9211
73 CYX 0.9209
74 BEZ 0.9203
75 PPV 0.9200
76 FCN 0.9199
77 CCD 0.9193
78 NCA 0.9189
79 CFI 0.9188
80 6M4 0.9188
81 PSE 0.9187
82 HX2 0.9187
83 DAS 0.9186
84 SRT 0.9184
85 PZA 0.9182
86 QMP 0.9180
87 IP8 0.9180
88 SIN 0.9175
89 TLA 0.9175
90 2CO 0.9174
91 UNU 0.9172
92 MDN 0.9170
93 HIO 0.9170
94 SEP 0.9169
95 NIO 0.9168
96 PHB 0.9165
97 A20 0.9164
98 FB1 0.9163
99 6PC 0.9163
100 6JN 0.9160
101 FUM 0.9159
102 2AS 0.9158
103 TAR 0.9157
104 FBV 0.9154
105 ICF 0.9153
106 NBZ 0.9151
107 MAE 0.9147
108 X0V 0.9143
109 ILE 0.9137
110 3LR 0.9137
111 KMH 0.9136
112 AHB 0.9134
113 PLU 0.9133
114 NPO 0.9130
115 3HB 0.9129
116 DAL DAL 0.9128
117 GAB 0.9127
118 PC 0.9127
119 NTN 0.9126
120 ISZ 0.9124
121 2IT 0.9119
122 GGL 0.9119
123 BE2 0.9118
124 2HG 0.9115
125 51R 0.9112
126 HZP 0.9111
127 ONL 0.9110
128 P22 0.9109
129 SD4 0.9105
130 4LR 0.9105
131 OPE 0.9102
132 NM2 0.9101
133 NM3 0.9101
134 PIS 0.9101
135 AMS 0.9100
136 3NT 0.9099
137 RHU 0.9097
138 IFP 0.9096
139 SAL 0.9095
140 SKG 0.9091
141 URP 0.9090
142 BHO 0.9090
143 SYM 0.9088
144 PAB 0.9085
145 LNO 0.9081
146 MLE 0.9079
147 VGL 0.9079
148 ES6 0.9078
149 KVV 0.9077
150 93K 0.9075
151 TB6 0.9073
152 ZGL 0.9072
153 SS2 0.9072
154 INO 0.9071
155 ORN 0.9071
156 YCP 0.9070
157 AT3 0.9070
158 OSE 0.9069
159 PBZ 0.9063
160 DHB 0.9062
161 S0H 0.9060
162 NMG 0.9058
163 9ON 0.9057
164 S2G 0.9057
165 FBW 0.9056
166 SPA 0.9055
167 7N0 0.9054
168 DBX 0.9053
169 Z82 0.9053
170 GPJ 0.9050
171 GPF 0.9050
172 IHG 0.9048
173 AC6 0.9047
174 MYJ 0.9046
175 H95 0.9042
176 XCZ 0.9039
177 4MV 0.9038
178 VAL 0.9038
179 URQ 0.9036
180 HPS 0.9035
181 UGC 0.9032
182 PMF 0.9032
183 8EW 0.9029
184 QY9 0.9029
185 MET 0.9028
186 GJZ 0.9027
187 JKE 0.9026
188 TZC 0.9024
189 DQY 0.9019
190 1Y6 0.9019
191 RMN 0.9018
192 NLE 0.9017
193 NIZ 0.9017
194 XLS 0.9015
195 DAB 0.9015
196 RNT 0.9014
197 OVV 0.9014
198 4NC 0.9013
199 60P 0.9011
200 23J 0.9010
201 NXA 0.9010
202 SMN 0.9006
203 QSC 0.9005
204 SS1 0.9004
205 ODV 0.9004
206 PZI 0.9003
207 BNS 0.9001
208 9RW 0.9001
209 4MA 0.9000
210 3YP 0.8999
211 HSE 0.8999
212 XYL 0.8995
213 RB5 0.8995
214 TIU 0.8995
215 HIS 0.8989
216 HBD 0.8989
217 RBL 0.8987
218 4SX 0.8986
219 ROR 0.8986
220 3U4 0.8985
221 FEH 0.8984
222 SC2 0.8983
223 GAG 0.8983
224 HYP 0.8982
225 7VD 0.8982
226 SMV 0.8981
227 P72 0.8975
228 7BC 0.8975
229 GG6 0.8974
230 NVA 0.8974
231 IZC 0.8973
232 3OC 0.8969
233 9YL 0.8969
234 SYC 0.8969
235 FQI 0.8968
236 JBN 0.8967
237 53C 0.8967
238 4CS 0.8967
239 7WG 0.8967
240 IXW 0.8967
241 HMS 0.8964
242 OEM 0.8964
243 2PC 0.8963
244 VNJ 0.8962
245 9X6 0.8961
246 EKZ 0.8961
247 DCO 0.8961
248 HDA 0.8961
249 129 0.8960
250 8OZ 0.8957
251 CCE 0.8952
252 2HO 0.8951
253 PAE 0.8949
254 K5W 0.8948
255 SHF 0.8948
256 E4P 0.8947
257 MED 0.8946
258 KIV 0.8943
259 I4B 0.8941
260 MTL 0.8940
261 PAC 0.8940
262 9X7 0.8939
263 4FH 0.8937
264 GLY ALA 0.8937
265 K34 0.8935
266 1P3 0.8932
267 GRO 0.8929
268 F9P 0.8928
269 PYC 0.8927
270 TFB 0.8926
271 OGA 0.8925
272 8GL 0.8925
273 MUC 0.8924
274 EDR 0.8923
275 B85 0.8923
276 FAN 0.8923
277 TP5 0.8922
278 MNN 0.8921
279 HSM 0.8921
280 FBT 0.8918
281 CP 0.8917
282 PRO 0.8913
283 UY7 0.8912
284 LYS 0.8909
285 7A8 0.8908
286 QDK 0.8907
287 RSO 0.8907
288 SHA 0.8906
289 SOL 0.8906
290 DYT 0.8906
291 M58 0.8906
292 OK7 0.8904
293 DOB 0.8903
294 RNS 0.8901
295 MPD 0.8901
296 HPV 0.8901
297 FSG 0.8900
298 URS 0.8898
299 TPA 0.8897
300 PG3 0.8895
301 DCL 0.8894
302 PHU 0.8893
303 UYA 0.8891
304 RAT 0.8888
305 3BZ 0.8888
306 273 0.8887
307 I1E 0.8884
308 LY0 0.8884
309 1DJ 0.8883
310 SW7 0.8883
311 CXF 0.8881
312 SOR 0.8878
313 TIH 0.8876
314 GLY GLY 0.8876
315 IT2 0.8875
316 14J 0.8874
317 PCT 0.8873
318 GLO 0.8869
319 ZBT 0.8868
320 TZL 0.8868
321 XUL 0.8867
322 3V4 0.8865
323 2D8 0.8865
324 5CU 0.8864
325 THR 0.8864
326 3AB 0.8862
327 FOA 0.8862
328 CDV 0.8860
329 OTR 0.8859
330 MXN 0.8859
331 5AC 0.8859
332 FA0 0.8859
333 3BU 0.8858
334 69O 0.8857
335 EHM 0.8856
336 C5A 0.8854
337 HYA 0.8854
338 HBA 0.8854
339 GYE 0.8852
340 K7M 0.8851
341 BAE 0.8850
342 SVD 0.8850
343 IP0 0.8848
344 SJ5 0.8841
345 3SK 0.8841
346 AC0 0.8840
347 J9T 0.8840
348 THE 0.8839
349 FBM 0.8839
350 MRZ 0.8835
351 ASC 0.8834
352 4P5 0.8833
353 RTK 0.8833
354 XBT 0.8832
355 SAT 0.8827
356 BZ3 0.8827
357 0OC 0.8826
358 54D 0.8825
359 C21 0.8825
360 FLA 0.8824
361 R9S 0.8823
362 HCI 0.8821
363 DHS 0.8818
364 3FH 0.8816
365 T2C 0.8815
366 FK8 0.8815
367 RIP 0.8815
368 AC5 0.8813
369 JZ7 0.8813
370 HCS 0.8813
371 HSO 0.8812
372 DMV 0.8809
373 XXG 0.8807
374 PCA 0.8805
375 FA1 0.8805
376 069 0.8805
377 JZ5 0.8804
378 XRG 0.8803
379 BZX 0.8802
380 9TZ 0.8801
381 TZE 0.8800
382 4HP 0.8799
383 GBD 0.8798
384 FUC 0.8798
385 VAH 0.8797
386 4VP 0.8797
387 HDH 0.8796
388 1WD 0.8796
389 KMT 0.8794
390 9YT 0.8794
391 XM0 0.8792
392 OHP 0.8792
393 3S5 0.8790
394 4SV 0.8790
395 FP1 0.8788
396 LPK 0.8786
397 XX2 0.8782
398 4M0 0.8782
399 MRY 0.8781
400 RUJ 0.8781
401 8EZ 0.8780
402 MZT 0.8777
403 APG 0.8775
404 I38 0.8775
405 OXQ 0.8775
406 PEL 0.8775
407 N8P 0.8773
408 MEQ 0.8772
409 IQ0 0.8771
410 2LP 0.8768
411 1DU 0.8767
412 LNR 0.8767
413 GLY CYS 0.8767
414 2AL 0.8767
415 PRS 0.8767
416 NK2 0.8766
417 271 0.8764
418 GCO 0.8764
419 GBN 0.8764
420 1LN 0.8764
421 LEA 0.8763
422 3HA 0.8763
423 AHN 0.8763
424 M6W 0.8761
425 HTX 0.8760
426 HY1 0.8760
427 6NA 0.8758
428 41K 0.8758
429 M3H 0.8758
430 23W 0.8757
431 KOJ 0.8756
432 PEA 0.8755
433 5XB 0.8754
434 MNM 0.8753
435 DBH 0.8753
436 GTK 0.8751
437 K6H 0.8747
438 8GC 0.8747
439 WCE 0.8747
440 EDG 0.8746
441 3HP 0.8744
442 ORO 0.8744
443 DOR 0.8740
444 URF 0.8739
445 261 0.8738
446 T9G 0.8735
447 KBB 0.8733
448 ABU 0.8732
449 HBX 0.8730
450 3M0 0.8728
451 A13 0.8720
452 JLZ 0.8719
453 HF2 0.8718
454 NMJ 0.8717
455 7WV 0.8716
456 LER 0.8710
457 PPY 0.8710
458 PAF 0.8708
459 FBJ 0.8703
460 51F 0.8702
461 2CK 0.8700
462 HY3 0.8699
463 5OB 0.8698
464 PYD 0.8693
465 826 0.8693
466 CXP 0.8691
467 EYK 0.8690
468 PKU 0.8687
469 DE5 0.8687
470 34D 0.8687
471 PHE 0.8684
472 NNO 0.8684
473 KPL 0.8684
474 M4T 0.8683
475 SNE 0.8681
476 HFA 0.8681
477 BE7 0.8681
478 M4S 0.8679
479 N4B 0.8678
480 1X4 0.8676
481 MSE 0.8675
482 O7U 0.8675
483 4ZA 0.8674
484 MJ2 0.8674
485 2FY 0.8674
486 SIF 0.8674
487 4PN 0.8674
488 NCT 0.8672
489 TH7 0.8670
490 4FA 0.8668
491 RM1 0.8668
492 CSS 0.8665
493 4JC 0.8664
494 LDP 0.8663
495 AMC 0.8662
496 4A3 0.8661
497 WBU 0.8660
498 NK 0.8660
499 AEF 0.8659
500 DHK 0.8658
501 HMU 0.8655
502 RBJ 0.8655
503 FHB 0.8654
504 449 0.8654
505 ABN 0.8651
506 SKM 0.8650
507 IDM 0.8648
508 BDF 0.8647
509 SYN 0.8645
510 BMA 0.8644
511 FUL 0.8644
512 G4D 0.8642
513 9TY 0.8640
514 3F0 0.8639
515 FYU 0.8637
516 KTA 0.8636
517 4NG 0.8635
518 6CS 0.8635
519 M45 0.8634
520 BP9 0.8633
521 MAK 0.8632
522 HPA 0.8630
523 174 0.8626
524 PSJ 0.8624
525 HMH 0.8622
526 HHA 0.8622
527 CS2 0.8621
528 D1X 0.8621
529 FPY 0.8621
530 GZL 0.8621
531 23B 0.8619
532 PIM 0.8619
533 IFL 0.8617
534 LRH 0.8615
535 ABE 0.8615
536 4XR 0.8614
537 PBE 0.8613
538 7HP 0.8611
539 5HN 0.8610
540 GLL 0.8609
541 TYE 0.8608
542 24B 0.8605
543 DMJ 0.8605
544 8H8 0.8603
545 4SD 0.8602
546 FRU 0.8600
547 WOT 0.8600
548 282 0.8598
549 NOJ 0.8597
550 45L 0.8596
551 RJY 0.8595
552 JFJ 0.8595
553 LDU 0.8592
554 Q88 0.8592
555 4WL 0.8590
556 ALO 0.8590
557 ADE 0.8590
558 XAN 0.8586
559 6OT 0.8584
560 R2B 0.8584
561 5NI 0.8583
562 Q02 0.8582
563 IFM 0.8578
564 FPI 0.8574
565 4JL 0.8571
566 SSN 0.8568
567 GUN 0.8565
568 265 0.8562
569 2KT 0.8562
570 PBA 0.8561
571 1SP 0.8556
572 3AL 0.8540
573 GIF 0.8540
574 6M9 0.8530
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4UMA; Ligand: GZ3; Similar sites found with APoc: 8
This union binding pocket(no: 1) in the query (biounit: 4uma.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4C1K PEP 24.8092
2 4C1K PEP 24.8092
3 4C1K PEP 24.8092
4 4C1K PEP 24.8092
5 4C1K PEP 24.8092
6 4C1K PEP 24.8092
7 3TFC PEP 27.3504
8 3TFC PEP 27.3504
Pocket No.: 2; Query (leader) PDB : 4UMA; Ligand: GZ3; Similar sites found with APoc: 8
This union binding pocket(no: 2) in the query (biounit: 4uma.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4C1K PEP 24.8092
2 4C1K PEP 24.8092
3 4C1K PEP 24.8092
4 4C1K PEP 24.8092
5 4C1K PEP 24.8092
6 4C1K PEP 24.8092
7 3TFC PEP 27.3504
8 3TFC PEP 27.3504
Pocket No.: 3; Query (leader) PDB : 4UMA; Ligand: GZ3; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 4uma.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4C1K PEP 24.8092
2 4C1K PEP 24.8092
3 4C1K PEP 24.8092
4 4C1K PEP 24.8092
5 4C1K PEP 24.8092
6 4C1K PEP 24.8092
7 3TFC PEP 27.3504
8 3TFC PEP 27.3504
Pocket No.: 4; Query (leader) PDB : 4UMA; Ligand: GZ3; Similar sites found with APoc: 8
This union binding pocket(no: 4) in the query (biounit: 4uma.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4C1K PEP 24.8092
2 4C1K PEP 24.8092
3 4C1K PEP 24.8092
4 4C1K PEP 24.8092
5 4C1K PEP 24.8092
6 4C1K PEP 24.8092
7 3TFC PEP 27.3504
8 3TFC PEP 27.3504
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