Receptor
PDB id Resolution Class Description Source Keywords
5ZHW 2.18 Å EC: 3.4.16.4 VANYB IN COMPLEX WITH D-ALANINE-D-ALANINE ENTEROCOCCUS FAECALIS V583 VANCOMYCIN RESISTANCE PEPTIDASE METALLOPEPTIDASE FAMILY M1HYDROLASE
Ref.: STRUCTURAL BASIS FOR THE SUBSTRATE RECOGNITION OF PEPTIDOGLYCAN PENTAPEPTIDES BY ENTEROCOCCUS FAECALI INT. J. BIOL. MACROMOL. V. 119 335 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PG4 A:305;
B:305;
 Invalid;
Invalid;
 none;
none;
 submit data
194.226 C8 H18 O5 C(COC...
GOL B:304;
A:304;
 Invalid;
Invalid;
 none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
DAL DAL A:302;
B:302;
 Valid;
Valid;
 none;
none;
 submit data
160.173 n/a O=C([...
CU B:301;
A:301;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
63.546 Cu [Cu+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5ZHW 2.18 Å EC: 3.4.16.4 VANYB IN COMPLEX WITH D-ALANINE-D-ALANINE ENTEROCOCCUS FAECALIS V583 VANCOMYCIN RESISTANCE PEPTIDASE METALLOPEPTIDASE FAMILY M1HYDROLASE
Ref.: STRUCTURAL BASIS FOR THE SUBSTRATE RECOGNITION OF PEPTIDOGLYCAN PENTAPEPTIDES BY ENTEROCOCCUS FAECALI INT. J. BIOL. MACROMOL. V. 119 335 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 5ZHW - DAL DAL n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 5ZHW - DAL DAL n/a n/a
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 5ZHW - DAL DAL n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DAL DAL; Similar ligands found: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 DAL DAL 1 1
2 ALA ALA ALA 0.766667 0.923077
3 ALA ALA ALA ALA ALA ALA ALA 0.741935 0.923077
4 ALA ALA 0.548387 1
5 ALA THR ALA ALA 0.536585 0.774194
6 ALA ALA ALA ALA SER ALA ALA 0.511111 0.648649
7 ALA ALA ALA ALA ALA 0.461538 0.846154
8 ALA ALA ALA ALA 0.461538 0.846154
9 C0O DAL DAL 0.454545 0.727273
10 MET VAL GLY GLY VAL VAL ILE ALA 0.447368 0.827586
11 ALA DGL 0.425 0.71875
12 ASP GLN ILE ILE 0.416667 0.774194
13 MET ALA ALA 0.413043 0.631579
Similar Ligands (3D)
Ligand no: 1; Ligand: DAL DAL; Similar ligands found: 538
No: Ligand Similarity coefficient
1 GLU 0.9679
2 AKG 0.9615
3 DGL 0.9613
4 OGA 0.9593
5 3LR 0.9502
6 2HG 0.9472
7 5XB 0.9471
8 GLN 0.9469
9 TAR 0.9466
10 AL0 0.9426
11 173 0.9418
12 I38 0.9415
13 9ON 0.9406
14 DGN 0.9402
15 SMN 0.9381
16 LY0 0.9378
17 2AS 0.9375
18 SYM 0.9364
19 2IT 0.9360
20 LMR 0.9360
21 HHH 0.9355
22 GUA 0.9352
23 PEP 0.9344
24 ZGL 0.9335
25 8OZ 0.9334
26 GRO 0.9333
27 KDG 0.9328
28 S2G 0.9324
29 ONL 0.9314
30 PAC 0.9307
31 FOC 0.9302
32 DHY 0.9298
33 2D8 0.9296
34 LYN 0.9295
35 JYD 0.9281
36 RAT 0.9280
37 HL5 0.9277
38 3PG 0.9270
39 SRT 0.9270
40 LEU 0.9264
41 HPV 0.9254
42 PPY 0.9253
43 9RW 0.9251
44 ASP 0.9247
45 NCT 0.9246
46 PHE 0.9243
47 HIS 0.9240
48 TYL 0.9232
49 ISZ 0.9229
50 GGL 0.9224
51 DIR 0.9223
52 BHO 0.9222
53 ORN 0.9221
54 2FT 0.9216
55 9YT 0.9213
56 MED 0.9213
57 LFC 0.9211
58 GVG 0.9208
59 MLT 0.9204
60 BHU 0.9203
61 UN1 0.9190
62 4WK 0.9187
63 TLA 0.9187
64 ASN 0.9183
65 SAF 0.9180
66 41K 0.9179
67 AHB 0.9178
68 FK8 0.9173
69 MET 0.9170
70 K6H 0.9169
71 SEP 0.9166
72 SD4 0.9164
73 MHO 0.9163
74 ILE 0.9159
75 0L1 0.9156
76 QY9 0.9153
77 BNL 0.9149
78 FA3 0.9144
79 DHI 0.9142
80 GLY GLY 0.9138
81 9SE 0.9136
82 UGC 0.9133
83 DPN 0.9132
84 TZL 0.9131
85 1DJ 0.9129
86 HF2 0.9129
87 0V5 0.9128
88 ACH 0.9126
89 3SL 0.9125
90 HCI 0.9125
91 CCE 0.9124
92 DZA 0.9119
93 PGA 0.9119
94 8GL 0.9117
95 OEG 0.9117
96 GCO 0.9111
97 CS2 0.9111
98 MNN 0.9110
99 9J3 0.9105
100 FA1 0.9103
101 4HP 0.9102
102 MXN 0.9098
103 152 0.9097
104 G3P 0.9097
105 OOG 0.9095
106 7OD 0.9092
107 OKG 0.9090
108 GJZ 0.9087
109 GZ3 0.9086
110 I1E 0.9085
111 SOR 0.9085
112 I4B 0.9083
113 0VT 0.9081
114 AC6 0.9081
115 KMH 0.9078
116 C5A 0.9077
117 COI 0.9077
118 9RH 0.9075
119 PPR 0.9072
120 PZI 0.9071
121 CFI 0.9071
122 MPJ 0.9070
123 DLY 0.9066
124 SPV 0.9066
125 F9P 0.9065
126 MCO 0.9065
127 OSE 0.9065
128 PSJ 0.9064
129 LYS 0.9063
130 PMF 0.9063
131 AOT 0.9063
132 HDH 0.9062
133 LUQ 0.9060
134 2PG 0.9059
135 HG3 0.9059
136 R2P 0.9059
137 RUJ 0.9055
138 REL 0.9052
139 AFS 0.9052
140 OAA 0.9052
141 XUL 0.9052
142 FEH 0.9052
143 GLO 0.9051
144 A3M 0.9047
145 MTL 0.9043
146 7BC 0.9043
147 MZT 0.9041
148 3HG 0.9041
149 M6W 0.9038
150 PHU 0.9038
151 49F 0.9037
152 8EW 0.9036
153 4P5 0.9035
154 46P 0.9033
155 7C3 0.9031
156 CMS 0.9031
157 N6C 0.9030
158 IXW 0.9030
159 DAS 0.9029
160 4ZA 0.9029
161 TPA 0.9027
162 3YP 0.9026
163 SDD 0.9025
164 S2P 0.9025
165 0OC 0.9025
166 FBJ 0.9022
167 HGA 0.9018
168 PO6 0.9017
169 449 0.9016
170 KMT 0.9015
171 DHS 0.9014
172 TSU 0.9014
173 APG 0.9013
174 THE 0.9013
175 PIM 0.9007
176 4WL 0.9007
177 JF6 0.9005
178 SHV 0.9005
179 RMN 0.9004
180 MSE 0.9000
181 IP8 0.8996
182 AEG 0.8996
183 QMP 0.8994
184 GTK 0.8992
185 PEQ 0.8992
186 PBA 0.8991
187 URS 0.8990
188 SME 0.8989
189 GOJ 0.8988
190 HL4 0.8988
191 1XA 0.8988
192 TAG 0.8987
193 3HP 0.8987
194 MUC 0.8987
195 PBZ 0.8986
196 2AL 0.8984
197 E4P 0.8981
198 DE5 0.8981
199 KVP 0.8980
200 GLR 0.8979
201 6NT 0.8979
202 HY1 0.8977
203 B3U 0.8976
204 LNR 0.8975
205 XYH 0.8972
206 FBM 0.8972
207 TEO 0.8972
208 DYT 0.8971
209 HNK 0.8971
210 CPZ 0.8970
211 FIX 0.8969
212 NLE 0.8968
213 SNU 0.8968
214 TIH 0.8967
215 MSR 0.8967
216 KTA 0.8965
217 3AL 0.8961
218 QUS 0.8960
219 3BU 0.8960
220 MES 0.8960
221 ASC 0.8958
222 GBN 0.8957
223 EHM 0.8953
224 DQA 0.8951
225 2BX 0.8951
226 URP 0.8948
227 Q03 0.8946
228 3NY 0.8945
229 RUY 0.8945
230 S8V 0.8943
231 HNL 0.8942
232 CXP 0.8941
233 CHH 0.8941
234 SKM 0.8941
235 HPS 0.8937
236 SER THR 0.8936
237 069 0.8934
238 61M 0.8932
239 AT3 0.8931
240 1SA 0.8931
241 SKJ 0.8929
242 EKZ 0.8929
243 NM3 0.8928
244 2CO 0.8927
245 13P 0.8926
246 N4B 0.8925
247 XIZ 0.8925
248 IZC 0.8924
249 J9Q 0.8923
250 L5V 0.8922
251 IWT 0.8921
252 AOS 0.8920
253 NIZ 0.8920
254 A9P 0.8918
255 HFA 0.8918
256 MLE 0.8918
257 0HN 0.8917
258 XLS 0.8915
259 R20 0.8915
260 HQJ 0.8914
261 3A9 0.8913
262 A09 0.8913
263 J0Z 0.8913
264 XRG 0.8912
265 SYC 0.8911
266 RNT 0.8910
267 3C4 0.8910
268 7N0 0.8909
269 LLQ 0.8908
270 2ZM 0.8908
271 P58 0.8908
272 RJY 0.8906
273 GP9 0.8905
274 IOM 0.8905
275 FUD 0.8904
276 1GP 0.8902
277 FCR 0.8902
278 TYR 0.8901
279 NFA 0.8901
280 HSO 0.8901
281 5FX 0.8900
282 3QM 0.8900
283 M4T 0.8899
284 CIZ 0.8899
285 BNF 0.8898
286 HYA 0.8897
287 7WG 0.8896
288 23J 0.8895
289 3MF 0.8895
290 4LV 0.8894
291 MSL 0.8894
292 ROR 0.8892
293 54D 0.8892
294 G3H 0.8891
295 X1S 0.8891
296 TT4 0.8889
297 7VP 0.8888
298 SOL 0.8887
299 HNH 0.8887
300 3MV 0.8886
301 2EH 0.8886
302 GGB 0.8885
303 MEQ 0.8885
304 XYL 0.8884
305 DXG 0.8884
306 RB5 0.8883
307 RB0 0.8883
308 HIC 0.8882
309 GPF 0.8882
310 GLY ALA 0.8881
311 SHI 0.8879
312 7A8 0.8879
313 KOJ 0.8878
314 B40 0.8877
315 98J 0.8876
316 B85 0.8876
317 CXF 0.8876
318 AG2 0.8875
319 4PN 0.8875
320 6NA 0.8874
321 1F1 0.8873
322 5NI 0.8873
323 OK7 0.8872
324 AHN 0.8870
325 HTX 0.8868
326 HBD 0.8867
327 ZBT 0.8866
328 HMS 0.8865
329 TYE 0.8865
330 PAH 0.8862
331 PC 0.8862
332 FF3 0.8861
333 271 0.8861
334 PGH 0.8860
335 URO 0.8860
336 5WZ 0.8860
337 HDL 0.8858
338 2RH 0.8858
339 MPV 0.8857
340 SPA 0.8856
341 RNS 0.8854
342 DHK 0.8854
343 1BN 0.8854
344 Q02 0.8853
345 4FA 0.8852
346 NLP 0.8851
347 4FH 0.8850
348 SS2 0.8849
349 K34 0.8847
350 X0V 0.8844
351 K6V 0.8842
352 RSO 0.8840
353 PEA 0.8838
354 4LR 0.8837
355 52C 0.8836
356 36Y 0.8836
357 51R 0.8835
358 CCD 0.8834
359 ABI 0.8832
360 129 0.8831
361 8SZ 0.8831
362 GPJ 0.8830
363 6TZ 0.8830
364 J9N 0.8829
365 6NI 0.8829
366 GVM 0.8824
367 PH3 0.8821
368 M3H 0.8820
369 3AB 0.8820
370 YRL 0.8818
371 SIN 0.8818
372 3CR 0.8818
373 LPK 0.8817
374 PG0 0.8816
375 LTL 0.8815
376 PJL 0.8814
377 1DV 0.8813
378 L99 0.8813
379 AEF 0.8813
380 M6H 0.8812
381 LNO 0.8810
382 MD0 0.8810
383 ITN 0.8810
384 3OC 0.8810
385 ICB 0.8810
386 PRA 0.8810
387 M1Z 0.8809
388 LDP 0.8808
389 1L5 0.8808
390 RBL 0.8806
391 PLU 0.8806
392 269 0.8805
393 XIY 0.8804
394 Q9Z 0.8803
395 NF3 0.8803
396 HX4 0.8803
397 BEN 0.8802
398 PBC 0.8800
399 OTR 0.8798
400 XCZ 0.8797
401 ORO 0.8796
402 JRB 0.8796
403 4TB 0.8795
404 258 0.8793
405 ALE 0.8790
406 QBS 0.8788
407 GZQ 0.8786
408 TZE 0.8786
409 1CO 0.8783
410 HDA 0.8783
411 IHG 0.8779
412 HPP 0.8779
413 JLZ 0.8779
414 PKU 0.8778
415 4VY 0.8778
416 OHP 0.8777
417 XBT 0.8775
418 3S5 0.8773
419 268 0.8773
420 SHA 0.8773
421 8U3 0.8773
422 M45 0.8769
423 NM2 0.8768
424 J9T 0.8768
425 ICF 0.8768
426 PIY 0.8767
427 EDR 0.8767
428 ISD 0.8766
429 TPO 0.8765
430 BAM 0.8764
431 DAR 0.8759
432 1SH 0.8759
433 ACA 0.8756
434 SOE 0.8756
435 BHH 0.8753
436 K7M 0.8753
437 A29 0.8752
438 45L 0.8751
439 263 0.8747
440 4LW 0.8745
441 791 0.8743
442 53C 0.8743
443 NMG 0.8743
444 PRO GLY 0.8743
445 R9M 0.8742
446 DTY 0.8742
447 CEE 0.8742
448 P7Y 0.8741
449 MAH 0.8739
450 40E 0.8737
451 CIT 0.8736
452 NYL 0.8735
453 FOM 0.8730
454 XSP 0.8727
455 DOR 0.8727
456 NCA 0.8726
457 RTK 0.8724
458 FUM 0.8722
459 4SX 0.8721
460 DLT 0.8719
461 NSB 0.8711
462 GWM 0.8711
463 PZA 0.8710
464 SR1 0.8710
465 AX3 0.8709
466 HYP 0.8709
467 JDN 0.8705
468 A13 0.8703
469 40F 0.8699
470 2F6 0.8699
471 Q07 0.8696
472 QDK 0.8696
473 ICT 0.8695
474 BNS 0.8694
475 56D 0.8694
476 F4E 0.8692
477 KVV 0.8690
478 CTV 0.8690
479 PCS 0.8686
480 SHF 0.8686
481 SC2 0.8680
482 FBW 0.8678
483 EN1 0.8678
484 AVI 0.8676
485 AHC 0.8675
486 M5E 0.8674
487 R67 0.8674
488 92K 0.8672
489 CLT 0.8669
490 FSG 0.8668
491 AS3 0.8668
492 TIU 0.8667
493 DS0 0.8667
494 R9S 0.8660
495 PBN 0.8656
496 XX3 0.8656
497 AFR 0.8651
498 NOJ 0.8650
499 FQI 0.8643
500 ENV 0.8642
501 D1X 0.8640
502 97T 0.8639
503 N9J 0.8638
504 GCU 0.8634
505 ZXD 0.8628
506 8K2 0.8624
507 B09 0.8624
508 NXA 0.8622
509 Q06 0.8619
510 FLC 0.8616
511 WCE 0.8615
512 G2H 0.8615
513 S24 0.8613
514 7MU 0.8613
515 EOL 0.8613
516 PAF 0.8613
517 QSC 0.8613
518 1X4 0.8612
519 EOU 0.8609
520 4MV 0.8604
521 FRU 0.8602
522 0BP 0.8599
523 DER 0.8597
524 PPT 0.8597
525 3V4 0.8591
526 M44 0.8585
527 XDK 0.8584
528 JZ7 0.8583
529 DII 0.8578
530 JZA 0.8575
531 2HU 0.8574
532 PFF 0.8568
533 PSE 0.8566
534 DMJ 0.8554
535 GLC 0.8553
536 8GC 0.8542
537 34D 0.8523
538 XQI 0.8522
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5ZHW; Ligand: DAL DAL; Similar sites found with APoc: 7
This union binding pocket(no: 1) in the query (biounit: 5zhw.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 4MUQ 2D8 41.6667
2 4MUQ LY0 41.6667
3 4MUS LY0 44.5498
4 4MUS 2D8 44.5498
5 4MUS LY0 44.5498
6 4MUS 2D8 44.5498
7 4OX5 DAL 45.4545
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