Receptor
PDB id Resolution Class Description Source Keywords
6M7I 1.7 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF KPC-2 WITH COMPOUND 3 KLEBSIELLA PNEUMONIAE CARBAPENEMASE TETRAZOLE INHIBITOR COMPLEX HYDROLASE HYDINHIBITOR COMPLEX
Ref.: ACTIVE-SITE DRUGGABILITY OF CARBAPENEMASES AND BROAD-SPECTRUM INHIBITOR DISCOVERY. ACS INFECT DIS. V. 5 1013 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
J84 A:303;
A:301;
A:304;
A:302;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 Ki = 386 uM
296.115 C10 H7 Cl2 N7 c1cc(...
GOL A:305;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6D19 1.45 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF KPC-2 COMPLEXED WITH COMPOUND 9 KLEBSIELLA PNEUMONIAE BETA-LACTAMASE CARBAPENEMASE PHOSPHONATE INHIBITOR HYDROHYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: HETEROARYL PHOSPHONATES AS NONCOVALENT INHIBITORS O SERINE- AND METALLOCARBAPENEMASES. J.MED.CHEM. V. 62 8480 2019
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 48 families.
1 6XJ8 Kd = 220 uM 8YF C12 H19 N3 O5 S [H]/N=C/NC....
2 6MEY Ki = 479 uM O5E C15 H14 N6 O c1ccc(cc1)....
3 6D15 Ki = 32.9 uM TWB C12 H13 O5 P Cc1cc2c(cc....
4 6D18 Ki = 1.4 uM GTV C12 H13 O5 P Cc1cc(c2c(....
5 6D17 Ki = 15.3 uM VKE C11 H9 O7 P c1c2c(cc3c....
6 6XD7 - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
7 6V1J - QNA C10 H9 B F O5 [B-]1([C@@....
8 6M7I Ki = 386 uM J84 C10 H7 Cl2 N7 c1cc(c(cc1....
9 5UJ3 - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
10 6D16 Ki = 8.4 uM FUJ C11 H11 O6 P COc1ccc2c(....
11 6D19 Ki = 0.246 uM YKG C11 H10 Br O5 P Cc1cc2c(c(....
12 6MLL Ki = 239 uM N1G C17 H13 N7 O c1ccc(cc1)....
13 5UJ4 - SFR C12 H17 N O6 S C[C@H]([C@....
14 6MNP - 1CE C12 H12 N6 O S C1CCc2c(c3....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 41 families.
1 6XJ8 Kd = 220 uM 8YF C12 H19 N3 O5 S [H]/N=C/NC....
2 6MEY Ki = 479 uM O5E C15 H14 N6 O c1ccc(cc1)....
3 6D15 Ki = 32.9 uM TWB C12 H13 O5 P Cc1cc2c(cc....
4 6D18 Ki = 1.4 uM GTV C12 H13 O5 P Cc1cc(c2c(....
5 6D17 Ki = 15.3 uM VKE C11 H9 O7 P c1c2c(cc3c....
6 6XD7 - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
7 6V1J - QNA C10 H9 B F O5 [B-]1([C@@....
8 6M7I Ki = 386 uM J84 C10 H7 Cl2 N7 c1cc(c(cc1....
9 5UJ3 - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
10 6D16 Ki = 8.4 uM FUJ C11 H11 O6 P COc1ccc2c(....
11 6D19 Ki = 0.246 uM YKG C11 H10 Br O5 P Cc1cc2c(c(....
12 6MLL Ki = 239 uM N1G C17 H13 N7 O c1ccc(cc1)....
13 5UJ4 - SFR C12 H17 N O6 S C[C@H]([C@....
14 6MNP - 1CE C12 H12 N6 O S C1CCc2c(c3....
50% Homology Family (57)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 5EOE - CIT C6 H8 O7 C(C(=O)O)C....
2 5EOO - CIT C6 H8 O7 C(C(=O)O)C....
3 6XJ8 Kd = 220 uM 8YF C12 H19 N3 O5 S [H]/N=C/NC....
4 6MEY Ki = 479 uM O5E C15 H14 N6 O c1ccc(cc1)....
5 6D15 Ki = 32.9 uM TWB C12 H13 O5 P Cc1cc2c(cc....
6 6D18 Ki = 1.4 uM GTV C12 H13 O5 P Cc1cc(c2c(....
7 6D17 Ki = 15.3 uM VKE C11 H9 O7 P c1c2c(cc3c....
8 6XD7 - ZZ7 C16 H21 N3 O5 S CC1([C@@H]....
9 6V1J - QNA C10 H9 B F O5 [B-]1([C@@....
10 6M7I Ki = 386 uM J84 C10 H7 Cl2 N7 c1cc(c(cc1....
11 5UJ3 - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
12 6D16 Ki = 8.4 uM FUJ C11 H11 O6 P COc1ccc2c(....
13 6D19 Ki = 0.246 uM YKG C11 H10 Br O5 P Cc1cc2c(c(....
14 6MLL Ki = 239 uM N1G C17 H13 N7 O c1ccc(cc1)....
15 5UJ4 - SFR C12 H17 N O6 S C[C@H]([C@....
16 6MNP - 1CE C12 H12 N6 O S C1CCc2c(c3....
17 3BFF - FPM C12 H15 N O5 S C[C@H]([C@....
18 6B68 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
19 6B6F - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
20 6B69 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
21 6B6A - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
22 4QB8 - 1TE C16 H21 N3 O4 S2 C[C@@H]1[C....
23 6B6C - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
24 6B6D - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
25 3NY4 - SMX C18 H18 N6 O5 S2 Cn1c(nnn1)....
26 6B6E - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
27 6CYU - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
28 5TWE - CAZ C17 H19 N5 O7 S2 CC(C)(C(=O....
29 4XXR - JSC C22 H17 N2 O6 Ru S CC1([C@@H]....
30 6MIA - 1CE C12 H12 N6 O S C1CCc2c(c3....
31 3G31 Ki = 1.3 mM GF1 C12 H15 N O4 C[C@@H](C(....
32 3G34 Ki = 1.1 mM 1CE C12 H12 N6 O S C1CCc2c(c3....
33 3HLW - CE3 C16 H17 N5 O7 S2 CC(=O)OCC1....
34 3G30 Ki = 3.1 mM G30 C11 H9 F2 N O3 c1cc(c(cc1....
35 6CYQ - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
36 3HVF - PNK C16 H20 N2 O5 S CC1([C@@H]....
37 3G32 Ki = 0.194 mM 3G3 C11 H9 N5 O2 c1ccc2c(c1....
38 3G2Z Ki = 4.4 mM GZ2 C7 H9 N5 O C1CC(=CC(=....
39 6BU3 Ki = 0.28 uM 3GK C16 H10 F3 N7 O c1cc(cc(c1....
40 3G35 Ki = 0.021 mM F13 C14 H10 F N5 O c1cc(cc(c1....
41 5FQJ - 6NT C6 H4 N4 O2 c1cc2c(cc1....
42 6TY6 - 6NT C6 H4 N4 O2 c1cc2c(cc1....
43 5FQK Kd = 15.8 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
44 5NE2 Ki = 84 pM DGL C5 H9 N O4 C(CC(=O)O)....
45 6QW7 - DSN C3 H7 N O3 C([C@H](C(....
46 2ZD8 - MER C17 H27 N3 O5 S C[C@@H]1[C....
47 1VM1 - TAZ C10 H12 N4 O5 S C[C@@]1([C....
48 3MKE - CZ6 C16 H25 B N4 O6 S B1(O[C@H](....
49 4FH2 - 0RN C8 H11 N O5 S CC1([C@@H]....
50 3SOI - CIT C6 H8 O7 C(C(=O)O)C....
51 2Y91 - 98J C5 H8 O4 C(CO)C(=O)....
52 1PZP Ki = 480 uM FTA C16 H13 N7 c1ccc(cc1)....
53 1PZO Ki = 460 uM CBT C15 H13 Cl2 N5 c1cc(ccc1C....
54 1NY0 - NBF C14 H16 B N O4 B(CNC(=O)c....
55 1NXY - SM2 C14 H14 B N O5 S B([C@H](c1....
56 3P98 - CIT C6 H8 O7 C(C(=O)O)C....
57 1W7F - ICT C6 H8 O7 C([C@@H]([....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: J84; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 J84 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: J84; Similar ligands found: 301
No: Ligand Similarity coefficient
1 KW7 0.9560
2 F4U 0.9431
3 EF2 0.9426
4 6EL 0.9377
5 90M 0.9301
6 D25 0.9265
7 6WR 0.9256
8 47X 0.9244
9 5DE 0.9232
10 6DE 0.9215
11 9FG 0.9212
12 4DE 0.9211
13 5C1 0.9203
14 0OK 0.9202
15 EES 0.9178
16 YE6 0.9175
17 205 0.9174
18 121 0.9171
19 801 0.9171
20 789 0.9168
21 A9B 0.9165
22 7EH 0.9164
23 H75 0.9163
24 NVS 0.9160
25 JOB 0.9159
26 AJ6 0.9151
27 LZJ 0.9150
28 HMO 0.9142
29 FCW 0.9138
30 1HP 0.9120
31 TGW 0.9116
32 Y70 0.9113
33 LVY 0.9113
34 9JT 0.9112
35 22M 0.9111
36 3DE 0.9110
37 CR4 0.9105
38 122 0.9105
39 BMZ 0.9105
40 GEN 0.9102
41 0UL 0.9102
42 SJR 0.9102
43 4FC 0.9102
44 SNV 0.9098
45 D26 0.9090
46 Q0K 0.9083
47 124 0.9077
48 40N 0.9075
49 Q8D 0.9069
50 521 0.9068
51 MI2 0.9063
52 7ZO 0.9063
53 Q8G 0.9061
54 RGK 0.9060
55 613 0.9059
56 9FH 0.9057
57 7EL 0.9056
58 1OT 0.9054
59 5WK 0.9053
60 TEF 0.9051
61 L2K 0.9050
62 39R 0.9049
63 IQW 0.9049
64 LR2 0.9045
65 4NR 0.9044
66 WCU 0.9044
67 GJG 0.9043
68 ZTW 0.9040
69 397 0.9036
70 D64 0.9035
71 26C 0.9028
72 0DF 0.9028
73 BXZ 0.9018
74 AJ4 0.9017
75 5ZM 0.9006
76 JO5 0.9000
77 L02 0.9000
78 120 0.8999
79 E6Q 0.8997
80 90G 0.8996
81 RSV 0.8993
82 RF2 0.8992
83 6WL 0.8990
84 1R5 0.8988
85 G2V 0.8988
86 2OX 0.8988
87 H50 0.8987
88 6P3 0.8981
89 08C 0.8976
90 EI1 0.8971
91 7FZ 0.8966
92 8D6 0.8964
93 PQM 0.8960
94 PFT 0.8959
95 5S9 0.8955
96 7GY 0.8954
97 5VU 0.8950
98 1A5 0.8945
99 CBE 0.8943
100 2P3 0.8942
101 A4N 0.8935
102 Q11 0.8931
103 PQS 0.8931
104 OA4 0.8930
105 TFX 0.8930
106 HDI 0.8927
107 A05 0.8921
108 BSU 0.8918
109 15Q 0.8917
110 BC5 0.8916
111 DFL 0.8916
112 OSY 0.8914
113 SNJ 0.8913
114 72E 0.8910
115 38B 0.8903
116 JON 0.8903
117 6DQ 0.8900
118 4EU 0.8898
119 68C 0.8893
120 5OR 0.8891
121 CU8 0.8887
122 J27 0.8886
123 QME 0.8885
124 Y27 0.8885
125 C3P 0.8882
126 ESJ 0.8879
127 S45 0.8877
128 A4T 0.8872
129 BFL 0.8871
130 ZAR 0.8870
131 1Q1 0.8870
132 RKN 0.8869
133 L1T 0.8869
134 KP2 0.8869
135 U3P 0.8862
136 2JX 0.8857
137 MKN 0.8856
138 AJ8 0.8855
139 BGK 0.8853
140 KLE 0.8852
141 TC8 0.8852
142 1FL 0.8851
143 G14 0.8847
144 A4Q 0.8847
145 3CA 0.8845
146 KVN 0.8843
147 LOT 0.8842
148 P7V 0.8838
149 3QI 0.8838
150 PZ8 0.8836
151 VIB 0.8833
152 AUT 0.8824
153 EV2 0.8821
154 1GV 0.8816
155 A18 0.8815
156 MQR 0.8813
157 0X2 0.8811
158 TJM 0.8806
159 KUQ 0.8806
160 361 0.8804
161 FCD 0.8802
162 KMP 0.8797
163 72D 0.8794
164 1Q2 0.8788
165 68B 0.8786
166 7KE 0.8785
167 TCL 0.8784
168 BXS 0.8783
169 XYP XYP 0.8780
170 0ON 0.8779
171 1SF 0.8777
172 OSP 0.8775
173 7G0 0.8774
174 T11 0.8773
175 DES 0.8772
176 CT0 0.8771
177 2GE 0.8770
178 MQS 0.8769
179 6H2 0.8764
180 54E 0.8761
181 LU2 0.8761
182 XYS XYS 0.8760
183 7L4 0.8758
184 73E 0.8758
185 IPJ 0.8758
186 LZK 0.8756
187 KVW 0.8756
188 GF7 0.8754
189 DFV 0.8754
190 OJ7 0.8753
191 PIQ 0.8751
192 AP6 0.8751
193 9KL 0.8748
194 EEY 0.8744
195 UN3 0.8743
196 NPS 0.8739
197 7N8 0.8736
198 RFZ 0.8736
199 3K1 0.8735
200 FMQ 0.8734
201 5F4 0.8732
202 2L1 0.8731
203 4UM 0.8730
204 IKY 0.8728
205 A7K 0.8727
206 KVQ 0.8724
207 NYJ 0.8722
208 FYR 0.8721
209 6QT 0.8718
210 PV1 0.8717
211 LZ4 0.8716
212 M2E 0.8711
213 FT6 0.8710
214 AUE 0.8708
215 6MY 0.8702
216 ADN 0.8701
217 83D 0.8700
218 5H6 0.8698
219 5ET 0.8695
220 S0J 0.8693
221 0K7 0.8693
222 DCN 0.8693
223 MTA 0.8690
224 JSX 0.8689
225 U4J 0.8688
226 51Y 0.8686
227 FLP 0.8675
228 DBE 0.8674
229 KXN 0.8673
230 A9K 0.8672
231 5B2 0.8666
232 J1K 0.8665
233 5CX 0.8662
234 C5P 0.8659
235 1GM 0.8657
236 AU8 0.8655
237 EAT 0.8651
238 16Z 0.8651
239 C93 0.8650
240 AGI 0.8649
241 72H 0.8648
242 TLT 0.8646
243 LZ5 0.8645
244 XYP XDN 0.8642
245 XIF XYP 0.8642
246 W23 0.8640
247 NAR 0.8637
248 135 0.8635
249 UA3 0.8635
250 QUE 0.8635
251 EST 0.8633
252 LWS 0.8632
253 M16 0.8631
254 CC5 0.8630
255 J3B 0.8628
256 XDN XYP 0.8618
257 WDW 0.8617
258 K0G 0.8612
259 TYP 0.8611
260 ERZ 0.8607
261 A4B 0.8607
262 XYP XIF 0.8604
263 4AJ 0.8602
264 AJ1 0.8601
265 B1J 0.8601
266 3WL 0.8601
267 AVX 0.8600
268 GJB 0.8600
269 TID 0.8598
270 RVE 0.8596
271 1Q4 0.8594
272 5TU 0.8593
273 PNW 0.8589
274 92O 0.8589
275 U55 0.8588
276 5EU 0.8587
277 6WU 0.8582
278 4MP 0.8582
279 YZ9 0.8580
280 XDL XYP 0.8578
281 FM1 0.8569
282 GP6 0.8569
283 9W7 0.8567
284 TVZ 0.8562
285 BX4 0.8562
286 XIL 0.8561
287 DZ1 0.8560
288 TFQ 0.8558
289 5AD 0.8556
290 20N 0.8554
291 NZ4 0.8544
292 3JC 0.8543
293 FHI 0.8542
294 H4B 0.8541
295 JMM 0.8541
296 4L2 0.8539
297 Q4G 0.8535
298 1EB 0.8531
299 LWA 0.8516
300 QTD 0.8510
301 IMH 0.8508
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6D19; Ligand: YKG; 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: 6d19.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6D19; Ligand: YKG; 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: 6d19.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6D19; Ligand: YKG; 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: 6d19.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
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