Receptor
PDB id Resolution Class Description Source Keywords
4Q6O 1.41 Å NON-ENZYME: OTHER STRUCTURAL ANALYSIS OF THE MDAP-BOUND FORM OF HELICOBACTER P CSD4, A D,L-CARBOXYPEPTIDASE HELICOBACTER PYLORI M14 METALLOPEPTIDASE DL-CARBOXYPEPTIDASE PEPTIDOGLYCAN CHYDROLASE
Ref.: STRUCTURAL BASIS FOR THE RECOGNITION OF MURAMYLTRIP HELICOBACTER PYLORI CSD4, A D,L-CARBOXYPEPTIDASE CO THE HELICAL CELL SHAPE ACTA CRYSTALLOGR.,SECT.D V. 70 2800 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
API A:504;
Valid;
none;
submit data
190.197 C7 H14 N2 O4 C(C[C...
GOL A:508;
A:506;
A:507;
A:505;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
CA A:501;
A:502;
A:503;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5D2R 1.9 Å NON-ENZYME: OTHER INHIBITOR BOUND CELL SHAPE DETERMINANT PROTEIN CSD4 FROM HEL PYLORI HELICOBACTER PYLORI MIXED ALPHA BETA SANDWICH CARBOXYPEPTIDASE M14 HYDROLASE-INHIBITOR COMPLEX
Ref.: A BACTERIAL CELL SHAPE-DETERMINING INHIBITOR. ACS CHEM.BIOL. V. 11 981 2016
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 4WCK - API C7 H14 N2 O4 C(C[C@H](C....
2 4WCL - API C7 H14 N2 O4 C(C[C@H](C....
3 4Q6Q - API C7 H14 N2 O4 C(C[C@H](C....
4 4Q6O - API C7 H14 N2 O4 C(C[C@H](C....
5 5D2R Ki = 1.5 uM 56W C14 H25 N2 O9 P CC(=O)N[C@....
6 4WCM - API C7 H14 N2 O4 C(C[C@H](C....
7 4WCN - 3KS C17 H28 N4 O9 C[C@@H](C(....
8 4Q6N - MHI C15 H26 N4 O8 C[C@@H](C(....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 4WCK - API C7 H14 N2 O4 C(C[C@H](C....
2 4WCL - API C7 H14 N2 O4 C(C[C@H](C....
3 4Q6Q - API C7 H14 N2 O4 C(C[C@H](C....
4 4Q6O - API C7 H14 N2 O4 C(C[C@H](C....
5 5D2R Ki = 1.5 uM 56W C14 H25 N2 O9 P CC(=O)N[C@....
6 4WCM - API C7 H14 N2 O4 C(C[C@H](C....
7 4WCN - 3KS C17 H28 N4 O9 C[C@@H](C(....
8 4Q6N - MHI C15 H26 N4 O8 C[C@@H](C(....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 4WCK - API C7 H14 N2 O4 C(C[C@H](C....
2 4WCL - API C7 H14 N2 O4 C(C[C@H](C....
3 4Q6Q - API C7 H14 N2 O4 C(C[C@H](C....
4 4Q6O - API C7 H14 N2 O4 C(C[C@H](C....
5 5D2R Ki = 1.5 uM 56W C14 H25 N2 O9 P CC(=O)N[C@....
6 4WCM - API C7 H14 N2 O4 C(C[C@H](C....
7 4WCN - 3KS C17 H28 N4 O9 C[C@@H](C(....
8 4Q6N - MHI C15 H26 N4 O8 C[C@@H](C(....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: API; Similar ligands found: 59
No: Ligand ECFP6 Tc MDL keys Tc
1 API 1 1
2 6CL 0.655172 0.961538
3 ORN 0.653846 0.785714
4 NLE 0.62963 0.724138
5 DLY 0.607143 0.758621
6 11C 0.607143 0.923077
7 UN1 0.607143 0.923077
8 DHH 0.586207 0.821429
9 LYS 0.586207 0.733333
10 5OY 0.566667 0.631579
11 ONH 0.566667 0.638889
12 NPI 0.566667 0.888889
13 2JJ 0.566667 0.631579
14 DAB 0.56 0.7
15 HSE 0.56 0.677419
16 26P 0.548387 0.827586
17 HCS 0.538462 0.689655
18 NVA 0.538462 0.714286
19 CIR 0.53125 0.685714
20 DAR 0.515152 0.611111
21 ARG 0.515152 0.611111
22 2NP 0.515152 0.75
23 MLZ 0.515152 0.611111
24 EXY 0.5 0.611111
25 2RA 0.5 0.612903
26 DGN 0.5 0.793103
27 ABA 0.5 0.666667
28 GLN 0.5 0.793103
29 DGL 0.5 0.884615
30 SER 0.5 0.633333
31 DSN 0.5 0.633333
32 DBB 0.5 0.666667
33 GLU 0.5 0.884615
34 GGL 0.5 0.884615
35 C2N 0.48 0.642857
36 DCY 0.48 0.62069
37 CYS 0.48 0.62069
38 HRG 0.472222 0.611111
39 ILO 0.472222 0.611111
40 ALY 0.472222 0.685714
41 ONL 0.466667 0.733333
42 ASP 0.461538 0.75
43 ASN 0.461538 0.65625
44 DAS 0.461538 0.75
45 NOT 0.459459 0.611111
46 2FM 0.454545 0.625
47 MED 0.451613 0.606061
48 MET 0.451613 0.606061
49 4JK 0.447368 0.621622
50 WT2 0.435897 0.727273
51 AS2 0.428571 0.740741
52 LEU 0.428571 0.62069
53 HGA 0.424242 0.648649
54 9YT 0.424242 0.638889
55 REZ 0.414634 0.757576
56 2YH 0.414634 0.705882
57 MEQ 0.411765 0.69697
58 5CT 0.404762 0.638889
59 MF3 0.4 0.606061
Similar Ligands (3D)
Ligand no: 1; Ligand: API; Similar ligands found: 343
No: Ligand Similarity coefficient
1 H35 1.0000
2 6HN 0.9609
3 NNH 0.9570
4 Z70 0.9541
5 GGB 0.9459
6 XRX 0.9407
7 DA3 0.9405
8 MLY 0.9400
9 ZZU 0.9363
10 DXG 0.9338
11 DER 0.9333
12 9J6 0.9330
13 ENO 0.9324
14 SZ7 0.9318
15 IAR 0.9308
16 NMM 0.9287
17 FB6 0.9279
18 F98 0.9266
19 JX7 0.9265
20 TEG 0.9249
21 GLR 0.9237
22 ABH 0.9236
23 GVA 0.9228
24 11X 0.9223
25 RGP 0.9212
26 KYN 0.9212
27 E8U 0.9205
28 4ZD 0.9205
29 M3L 0.9190
30 HAR 0.9179
31 XOG 0.9179
32 J9Y 0.9177
33 L06 0.9169
34 37E 0.9154
35 4DI 0.9153
36 XRS 0.9151
37 O45 0.9146
38 TYR 0.9137
39 ENW 0.9134
40 M3P 0.9128
41 JMG 0.9126
42 NFZ 0.9119
43 9GB 0.9117
44 VUR 0.9114
45 XI7 0.9112
46 3KJ 0.9102
47 OOG 0.9102
48 GB5 0.9093
49 SB7 0.9089
50 DA2 0.9087
51 EGV 0.9086
52 KDG 0.9082
53 KPV 0.9078
54 EN1 0.9071
55 DTY 0.9067
56 5KJ 0.9065
57 LPB 0.9063
58 4TB 0.9063
59 AHL 0.9063
60 LPA 0.9054
61 7OD 0.9048
62 FOM 0.9041
63 3YP 0.9032
64 DIR 0.9023
65 KLS 0.9019
66 KPA 0.9019
67 SB9 0.9016
68 5TO 0.9013
69 PML 0.9010
70 1PS 0.9009
71 PPY 0.9009
72 DAH 0.9007
73 TZP 0.9005
74 FHV 0.9004
75 A51 0.9002
76 E79 0.8997
77 TYC 0.8996
78 A5P 0.8993
79 IVL 0.8991
80 5PV 0.8983
81 MMS 0.8979
82 YIP 0.8977
83 HLP 0.8976
84 DXP 0.8975
85 HF2 0.8970
86 1YO 0.8970
87 KPC 0.8968
88 PHE 0.8968
89 L22 0.8968
90 M6H 0.8967
91 SOJ 0.8963
92 E4P 0.8957
93 1N5 0.8956
94 LUQ 0.8952
95 CLT 0.8952
96 AOY 0.8950
97 6C4 0.8948
98 BSA 0.8943
99 S2C 0.8941
100 DPN 0.8939
101 GRQ 0.8939
102 LL2 0.8936
103 ENG 0.8935
104 GNW 0.8933
105 6J5 0.8932
106 E9S 0.8927
107 OJD 0.8925
108 3CX 0.8925
109 YOF 0.8923
110 MES 0.8922
111 011 0.8920
112 JF5 0.8918
113 EQW 0.8918
114 DHM 0.8917
115 IJ6 0.8917
116 PFF 0.8914
117 4FP 0.8910
118 4Z0 0.8907
119 QFJ 0.8907
120 S0A 0.8905
121 KNA 0.8903
122 6C9 0.8902
123 DEZ 0.8899
124 6MW 0.8898
125 DLT 0.8896
126 KLE 0.8893
127 G14 0.8892
128 FHC 0.8890
129 VAL VAL 0.8889
130 3QO 0.8887
131 ENV 0.8885
132 R9J 0.8883
133 6FG 0.8883
134 TOH 0.8880
135 IPO 0.8879
136 58X 0.8878
137 OCA 0.8875
138 6C8 0.8872
139 JFM 0.8867
140 NFA 0.8866
141 6C5 0.8865
142 5AB 0.8865
143 FXY 0.8864
144 T03 0.8864
145 0XR 0.8860
146 IYR 0.8859
147 JOV 0.8853
148 RLG 0.8853
149 8SZ 0.8852
150 BZQ 0.8852
151 5LD 0.8849
152 7XA 0.8847
153 LVD 0.8842
154 536 0.8841
155 AHN 0.8839
156 TMG 0.8836
157 TRP 0.8836
158 N9J 0.8836
159 4TP 0.8835
160 4LW 0.8834
161 56D 0.8833
162 P58 0.8832
163 PRO GLY 0.8832
164 1HS 0.8832
165 TZM 0.8831
166 0ON 0.8828
167 PBA 0.8826
168 3CR 0.8825
169 0A9 0.8824
170 848 0.8824
171 RP3 0.8823
172 TCA 0.8822
173 D53 0.8821
174 MJW 0.8821
175 3XH 0.8818
176 JZA 0.8817
177 2OR 0.8817
178 HFA 0.8817
179 Q04 0.8815
180 PHQ DAL 0.8814
181 P93 0.8813
182 PBN 0.8812
183 650 0.8811
184 3IP 0.8809
185 0L1 0.8809
186 1X4 0.8808
187 RED 0.8806
188 N2Y 0.8804
189 KAP 0.8803
190 EIP 0.8803
191 2D8 0.8800
192 MVH 0.8799
193 TB8 0.8797
194 RQD 0.8796
195 RES 0.8796
196 LGT 0.8795
197 PAU 0.8792
198 Q9Z 0.8791
199 5RP 0.8790
200 DNN 0.8789
201 531 0.8787
202 P81 0.8783
203 8AC 0.8782
204 3H2 0.8781
205 HIC 0.8779
206 3PG 0.8778
207 TPM 0.8771
208 G3M 0.8770
209 DKA 0.8769
210 0NX 0.8764
211 DTR 0.8762
212 I2E 0.8761
213 EQA 0.8758
214 LY0 0.8757
215 S7V 0.8757
216 1VK 0.8755
217 2M7 0.8755
218 HL4 0.8753
219 M74 0.8752
220 64Z 0.8750
221 DDK 0.8750
222 LYN 0.8750
223 7R4 0.8749
224 S7D 0.8749
225 4BF 0.8746
226 4Z1 0.8744
227 HPP 0.8742
228 HX8 0.8742
229 RP5 0.8739
230 2O8 0.8738
231 GGG 0.8737
232 K7M 0.8736
233 R5P 0.8736
234 B3U 0.8735
235 HC4 0.8733
236 ABF 0.8732
237 A18 0.8732
238 HSA 0.8727
239 HSX 0.8727
240 CS2 0.8725
241 Y4L 0.8724
242 GZ2 0.8723
243 3VW 0.8721
244 JPQ 0.8721
245 YIE 0.8720
246 BVS 0.8720
247 LZ5 0.8720
248 2FX 0.8718
249 GB4 0.8717
250 CXP 0.8716
251 HCI 0.8716
252 R10 0.8715
253 C82 0.8713
254 EYJ 0.8706
255 7C3 0.8704
256 7BC 0.8702
257 A7Q 0.8702
258 E0O 0.8700
259 4LV 0.8698
260 XIZ 0.8696
261 GLY GLY GLY 0.8696
262 N9M 0.8693
263 ODK 0.8693
264 RDV 0.8692
265 X48 0.8691
266 2LT 0.8686
267 XDK 0.8685
268 M45 0.8683
269 FZM 0.8682
270 NRG 0.8679
271 P80 0.8679
272 8CV 0.8678
273 DDW 0.8678
274 R2P 0.8677
275 TYE 0.8677
276 ISA 0.8676
277 9B3 0.8676
278 68B 0.8671
279 S0W 0.8671
280 4CF 0.8671
281 ERZ 0.8670
282 MUK 0.8670
283 LSQ 0.8669
284 DHC 0.8665
285 6L6 0.8665
286 HPV 0.8661
287 0OO 0.8655
288 QME 0.8654
289 AHC 0.8653
290 6HO 0.8652
291 HXY 0.8651
292 PC 0.8650
293 92G 0.8646
294 3VQ 0.8645
295 IC9 0.8645
296 1OS 0.8644
297 1L5 0.8639
298 PPT 0.8637
299 IPE 0.8637
300 S7A 0.8635
301 JGB 0.8633
302 DX5 0.8633
303 PMV 0.8633
304 CCD 0.8627
305 J4K 0.8626
306 HL6 0.8626
307 F06 0.8625
308 PH3 0.8624
309 SPD 0.8623
310 PUE 0.8614
311 AT3 0.8611
312 QH3 0.8605
313 FUD 0.8602
314 PO6 0.8602
315 M5E 0.8598
316 492 0.8592
317 BRH 0.8588
318 ZGL 0.8586
319 DI6 0.8585
320 1A5 0.8585
321 AG2 0.8584
322 47V 0.8581
323 P7Y 0.8581
324 YZM 0.8579
325 4LR 0.8579
326 NSB 0.8576
327 5SP 0.8573
328 IP8 0.8563
329 4XF 0.8561
330 3QM 0.8561
331 2D2 0.8561
332 6Q3 0.8559
333 SOR 0.8557
334 HNK 0.8555
335 DTE 0.8555
336 TU0 0.8543
337 PLP 0.8541
338 ZZA 0.8539
339 B41 0.8538
340 833 0.8528
341 G3P 0.8524
342 AKG 0.8521
343 LR2 0.8519
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5D2R; Ligand: 56W; 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: 5d2r.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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