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Receptor
PDB id Resolution Class Description Source Keywords
1KNY 2.5 Å EC: 2.7.7.- KANAMYCIN NUCLEOTIDYLTRANSFERASE STAPHYLOCOCCUS AUREUS ANTIBIOTIC RESISTANCE TRANSFERASE PLASMID
Ref.: STRUCTURAL INVESTIGATION OF THE ANTIBIOTIC AND ATP-BINDING SITES IN KANAMYCIN NUCLEOTIDYLTRANSFERASE. BIOCHEMISTRY V. 34 13305 1995
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
APC A:556;
B:557;
Valid;
Valid;
none;
none;
submit data
505.208 C11 H18 N5 O12 P3 c1nc(...
KAN A:558;
B:559;
Valid;
Valid;
none;
none;
submit data
484.499 C18 H36 N4 O11 C1[C@...
MG A:603;
B:604;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1KNY 2.5 Å EC: 2.7.7.- KANAMYCIN NUCLEOTIDYLTRANSFERASE STAPHYLOCOCCUS AUREUS ANTIBIOTIC RESISTANCE TRANSFERASE PLASMID
Ref.: STRUCTURAL INVESTIGATION OF THE ANTIBIOTIC AND ATP-BINDING SITES IN KANAMYCIN NUCLEOTIDYLTRANSFERASE. BIOCHEMISTRY V. 34 13305 1995
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 1KNY - KAN C18 H36 N4 O11 C1[C@H]([C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 1KNY - KAN C18 H36 N4 O11 C1[C@H]([C....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 1KNY - KAN C18 H36 N4 O11 C1[C@H]([C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: APC; Similar ligands found: 345
No: Ligand ECFP6 Tc MDL keys Tc
1 APC 1 1
2 ACQ 0.831169 0.986301
3 AP2 0.821918 1
4 A12 0.821918 1
5 ADV 0.805195 0.972973
6 RBY 0.805195 0.972973
7 AMP 0.777778 0.931507
8 A 0.777778 0.931507
9 ADP 0.763158 0.958904
10 ACP 0.75641 0.986301
11 6YZ 0.756098 0.986301
12 A2D 0.746667 0.932432
13 AP5 0.74026 0.932432
14 B4P 0.74026 0.932432
15 HEJ 0.734177 0.958904
16 ATP 0.734177 0.958904
17 BA3 0.727273 0.932432
18 5FA 0.725 0.958904
19 AQP 0.725 0.958904
20 ABM 0.723684 0.881579
21 AT4 0.708861 0.921053
22 AN2 0.708861 0.945946
23 M33 0.7 0.92
24 T99 0.698795 0.921053
25 TAT 0.698795 0.921053
26 SRA 0.697368 0.883117
27 AR6 0.682927 0.932432
28 APR 0.682927 0.932432
29 ADX 0.679012 0.841463
30 CA0 0.679012 0.907895
31 AU1 0.679012 0.933333
32 ANP 0.678571 0.933333
33 AD9 0.674699 0.933333
34 SAP 0.674699 0.909091
35 AGS 0.674699 0.909091
36 ADP PO3 0.674699 0.905405
37 50T 0.670732 0.92
38 PRX 0.662651 0.858974
39 ATF 0.643678 0.921053
40 MAP 0.640449 0.909091
41 A22 0.640449 0.945946
42 GAP 0.639535 0.858974
43 TAD 0.632653 0.923077
44 5AL 0.632184 0.894737
45 SON 0.626506 0.946667
46 ADQ 0.626374 0.907895
47 ALF ADP 0.625 0.8375
48 ADP ALF 0.625 0.8375
49 LMS 0.620253 0.797619
50 VO4 ADP 0.617977 0.894737
51 SRP 0.617977 0.896104
52 ADP VO4 0.617977 0.894737
53 9ZA 0.615385 0.873418
54 25A 0.615385 0.932432
55 9ZD 0.615385 0.873418
56 XYA 0.611111 0.810811
57 RAB 0.611111 0.810811
58 ADN 0.611111 0.810811
59 25L 0.610526 0.945946
60 4AD 0.608696 0.909091
61 A3R 0.608696 0.922078
62 A1R 0.608696 0.922078
63 DAL AMP 0.604396 0.87013
64 OOB 0.597826 0.894737
65 8QN 0.597826 0.894737
66 5SV 0.597826 0.839506
67 9X8 0.595745 0.884615
68 OAD 0.595745 0.907895
69 ADP BMA 0.595745 0.883117
70 AMO 0.591398 0.921053
71 PAJ 0.591398 0.851852
72 AOC 0.585366 0.789474
73 00A 0.585106 0.85
74 AHX 0.585106 0.886076
75 DLL 0.585106 0.894737
76 PTJ 0.583333 0.8625
77 3OD 0.583333 0.907895
78 BIS 0.583333 0.897436
79 3UK 0.578947 0.883117
80 DZD 0.577982 0.923077
81 5AS 0.576471 0.752809
82 5N5 0.573333 0.786667
83 PR8 0.572917 0.864198
84 WAQ 0.572917 0.897436
85 LAD 0.572917 0.875
86 B5V 0.572917 0.871795
87 4TC 0.571429 0.910256
88 TXA 0.56701 0.896104
89 NB8 0.56701 0.886076
90 1ZZ 0.56701 0.831325
91 FYA 0.56701 0.894737
92 ME8 0.56701 0.831325
93 A4D 0.565789 0.786667
94 5CD 0.565789 0.773333
95 ATP A A A 0.565657 0.893333
96 A3P 0.564706 0.931507
97 7D5 0.5625 0.868421
98 PAP 0.561798 0.945205
99 MYR AMP 0.561224 0.809524
100 G5P 0.558824 0.886076
101 M2T 0.556962 0.707317
102 A A 0.556701 0.906667
103 9SN 0.555556 0.839506
104 G2P 0.553191 0.923077
105 7D3 0.552941 0.894737
106 UP5 0.552381 0.884615
107 TXD 0.552381 0.873418
108 JB6 0.55102 0.873418
109 2A5 0.550562 0.907895
110 FA5 0.55 0.896104
111 YAP 0.55 0.884615
112 B5Y 0.55 0.860759
113 B5M 0.55 0.860759
114 G3A 0.54902 0.886076
115 3AM 0.548781 0.891892
116 A2P 0.546512 0.917808
117 7D4 0.545455 0.894737
118 XAH 0.544554 0.853659
119 ATR 0.544444 0.931507
120 EP4 0.544304 0.725
121 AFH 0.543689 0.875
122 GA7 0.543689 0.896104
123 4UV 0.539216 0.860759
124 TYR AMP 0.539216 0.860759
125 GTA 0.538462 0.853659
126 DQV 0.538462 0.92
127 G5A 0.538462 0.772727
128 NAI 0.537736 0.873418
129 DTA 0.5375 0.779221
130 3DH 0.536585 0.74359
131 LAQ 0.533333 0.831325
132 AHZ 0.533333 0.788235
133 MTA 0.530864 0.74359
134 ARG AMP 0.528846 0.821429
135 4UU 0.528846 0.860759
136 7MD 0.528846 0.853659
137 AR6 AR6 0.528846 0.881579
138 48N 0.528302 0.886076
139 LPA AMP 0.528302 0.809524
140 ITT 0.52809 0.905405
141 AMP DBH 0.524272 0.858974
142 NAX 0.523364 0.864198
143 4UW 0.523364 0.829268
144 DND 0.523364 0.896104
145 NXX 0.523364 0.896104
146 6V0 0.523364 0.8625
147 IMO 0.523256 0.891892
148 A4P 0.522936 0.813953
149 HFD 0.521739 0.909091
150 A5A 0.521277 0.77907
151 TSB 0.520833 0.790698
152 TXE 0.518519 0.873418
153 OMR 0.518519 0.843373
154 2AM 0.518072 0.905405
155 6RE 0.517647 0.753086
156 S4M 0.517241 0.681818
157 V3L 0.516129 0.932432
158 SSA 0.515789 0.793103
159 YLP 0.514019 0.833333
160 AP0 0.513761 0.8625
161 UPA 0.513761 0.873418
162 139 0.513514 0.864198
163 T5A 0.513514 0.855422
164 PPS 0.510638 0.841463
165 VMS 0.510417 0.761364
166 A2R 0.510417 0.945946
167 54H 0.510417 0.761364
168 52H 0.510417 0.752809
169 CNA 0.508929 0.896104
170 ZAS 0.505882 0.7375
171 J7C 0.505747 0.7625
172 A3N 0.505747 0.75641
173 5X8 0.505495 0.75641
174 8X1 0.505155 0.747253
175 53H 0.505155 0.752809
176 5CA 0.505155 0.793103
177 TYM 0.504587 0.896104
178 AF3 ADP 3PG 0.504587 0.829268
179 IOT 0.504505 0.845238
180 80F 0.504348 0.833333
181 ADJ 0.5 0.843373
182 7MC 0.5 0.833333
183 AMP NAD 0.5 0.87013
184 OVE 0.5 0.87013
185 YLC 0.5 0.853659
186 YLB 0.5 0.833333
187 P5A 0.49505 0.758242
188 NSS 0.494949 0.793103
189 DSZ 0.494949 0.793103
190 LSS 0.494949 0.755556
191 6AD 0.494737 0.875
192 MAO 0.494382 0.77381
193 DSH 0.494253 0.740741
194 A3D 0.491379 0.883117
195 F2R 0.491228 0.855422
196 9K8 0.490196 0.691489
197 NVA LMS 0.49 0.747253
198 AV2 0.489583 0.881579
199 COD 0.486957 0.825581
200 4TA 0.486957 0.821429
201 NAD 0.486957 0.894737
202 YLA 0.486726 0.833333
203 LEU LMS 0.485149 0.747253
204 NA7 0.485149 0.972973
205 3AT 0.484211 0.958904
206 GJV 0.483146 0.743902
207 AYB 0.482456 0.823529
208 5AD 0.480519 0.716216
209 KAA 0.480392 0.766667
210 GSU 0.480392 0.772727
211 71V 0.477778 0.873418
212 A3G 0.477273 0.792208
213 7D7 0.474359 0.736842
214 G A A A 0.474138 0.839506
215 BTX 0.474138 0.855422
216 6C6 0.473684 0.896104
217 SFG 0.473118 0.766234
218 DAT 0.473118 0.92
219 YSA 0.471698 0.772727
220 PO4 PO4 A A A A PO4 0.470588 0.866667
221 BT5 0.470085 0.845238
222 AVV 0.47 0.910256
223 SMM 0.469388 0.701149
224 SAM 0.46875 0.705882
225 6IA 0.46875 0.829268
226 DTP 0.46875 0.92
227 A7D 0.467391 0.792208
228 M24 0.466667 0.819277
229 SA8 0.463158 0.722892
230 A5D 0.463158 0.779221
231 NAE 0.46281 0.860759
232 MHZ 0.462366 0.712644
233 PGS 0.462366 0.85
234 8PZ 0.462264 0.793103
235 NAJ PZO 0.462185 0.817073
236 DA 0.460674 0.893333
237 D5M 0.460674 0.893333
238 NEC 0.460674 0.717949
239 EAD 0.459677 0.841463
240 2SA 0.459184 0.921053
241 NAQ 0.459016 0.839506
242 SAH 0.458333 0.759494
243 SAI 0.458333 0.75
244 Y3J 0.45679 0.697368
245 A A A 0.456311 0.92
246 AAM 0.455556 0.931507
247 6K6 0.455446 0.893333
248 ZID 0.455285 0.883117
249 S7M 0.454545 0.705882
250 YLY 0.454545 0.823529
251 4YB 0.454545 0.755556
252 AMZ 0.453488 0.88
253 C2R 0.453488 0.868421
254 A3S 0.451613 0.802632
255 Z5A 0.451613 0.772727
256 7DD 0.451613 0.945205
257 U A 0.45 0.873418
258 7C5 0.449541 0.7875
259 101 0.449438 0.868421
260 A G 0.449153 0.85
261 EEM 0.44898 0.705882
262 NAJ PYZ 0.447154 0.77907
263 N6P 0.446602 0.878378
264 ARU 0.446602 0.829268
265 AIR 0.445783 0.864865
266 U A G G 0.445378 0.85
267 P1H 0.445312 0.821429
268 NDE 0.445312 0.896104
269 N0B 0.443548 0.833333
270 A U 0.443478 0.8375
271 NIA 0.443182 0.792683
272 A3T 0.442105 0.789474
273 GEK 0.441176 0.753086
274 GP2 0.438776 0.923077
275 DDS 0.438776 0.868421
276 WSA 0.438596 0.781609
277 7DT 0.4375 0.945205
278 0WD 0.436975 0.886076
279 8BR 0.434783 0.871795
280 AAT 0.434343 0.722892
281 TXP 0.432203 0.886076
282 GGZ 0.431373 0.795181
283 NJP 0.428571 0.909091
284 A6D 0.428571 0.717647
285 FB0 0.427481 0.83908
286 NDC 0.427481 0.8625
287 649 0.426087 0.758242
288 7RA 0.423913 0.918919
289 NDP 0.423729 0.886076
290 0UM 0.423077 0.714286
291 8Q2 0.422414 0.766667
292 QQY 0.422222 0.78481
293 ACK 0.422222 0.826667
294 RGT 0.422018 0.921053
295 FDA 0.421053 0.825581
296 CC5 0.419753 0.808219
297 ANZ 0.419643 0.771084
298 62X 0.419048 0.681818
299 APU 0.418803 0.860759
300 6FA 0.41791 0.833333
301 128 0.417391 0.75
302 ODP 0.416667 0.875
303 3AD 0.416667 0.797297
304 TM1 0.416667 0.747126
305 K15 0.415094 0.697674
306 2BA 0.414894 0.878378
307 CMP 0.414894 0.864865
308 V1N 0.414414 0.881579
309 S8M 0.413462 0.775
310 7RP 0.413043 0.890411
311 2VA 0.412371 0.769231
312 12D 0.412281 0.758621
313 NPW 0.411765 0.876543
314 SFD 0.411765 0.729167
315 FAS 0.411765 0.843373
316 FAD 0.411765 0.843373
317 2FA 0.411765 0.782051
318 QQX 0.411111 0.775
319 62F 0.410072 0.853659
320 AS 0.408602 0.848101
321 FAI 0.408602 0.88
322 RMB 0.408602 0.837838
323 NZQ 0.408333 0.898734
324 GCP 0.407767 0.910256
325 SXZ 0.407407 0.72619
326 RP1 0.406593 0.810127
327 SP1 0.406593 0.810127
328 EO7 0.404255 0.761364
329 NVA 2AD 0.40404 0.753086
330 D3Y 0.403846 0.782051
331 KB1 0.40367 0.714286
332 A C A C 0.403226 0.817073
333 SLU 0.403226 0.744444
334 N01 0.403226 0.87013
335 G 0.402062 0.871795
336 5GP 0.402062 0.871795
337 XNP 0.401639 0.841463
338 NMN AMP PO4 0.401639 0.8375
339 DCA 0.4 0.837209
340 ETB 0.4 0.825581
341 FNK 0.4 0.797753
342 3D1 0.4 0.789474
343 3L1 0.4 0.789474
344 VRT 0.4 0.7625
345 SO8 0.4 0.759494
Ligand no: 2; Ligand: KAN; Similar ligands found: 10
No: Ligand ECFP6 Tc MDL keys Tc
1 KAN 1 1
2 9CS 0.75 1
3 TOY 0.661765 0.957447
4 KNC 0.661538 0.978261
5 AKN 0.607143 0.901961
6 7QM 0.519481 0.958333
7 RIO 0.460526 0.958333
8 7XP 0.417722 0.978261
9 XXX 0.416667 0.913043
10 84G 0.40404 0.849057
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1KNY; Ligand: KAN; Similar sites found with APoc: 51
This union binding pocket(no: 1) in the query (biounit: 1kny.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 3CMC NAD 1.58103
2 1OQC FAD 1.6
3 2CER PGI 1.97628
4 3HDY GDU 1.97628
5 3HDY FAD 1.97628
6 4OKZ 3E9 1.97628
7 1MO9 FAD 1.97628
8 1MO9 KPC 1.97628
9 2BW7 APC 2.28311
10 5IH1 GDP 2.37154
11 1T8U UAP SGN IDS SGN 2.37154
12 5O0B 9FE 2.46914
13 1CER NAD 2.7668
14 5UR0 NAD 2.7668
15 1PIE GLA 2.7668
16 1DSS NAD 3.16206
17 1U8X NAD 3.55731
18 4RI1 ACO 3.76344
19 4WT2 3UD 3.80952
20 2JFZ DGL 3.95257
21 2JFZ 003 3.95257
22 4ZGS NAD 3.95257
23 3ICS COA 3.95257
24 1FCH TYR GLN SER LYS LEU 4.34783
25 3EBL GA4 4.65753
26 6CI7 ACP 4.74308
27 1QNF FAD 4.74308
28 3ANP DCC 4.90196
29 1WUU GLA 5.5336
30 4ZBR NPS 5.92885
31 2R2L FPP 6.32411
32 1MZC BNE 6.32411
33 1MZC FPP 6.32411
34 2ZSH GA3 6.36364
35 1HDG NAD 6.71937
36 1QCI ADE 6.71937
37 6BC3 COA 8.3004
38 6BC3 SIS 8.3004
39 4QC6 30N 8.37989
40 1J6W MET 8.57143
41 3OV6 MK0 8.69565
42 5VEO AMP 8.69565
43 5ZQS BXP 9.09091
44 1QSN COA 9.25926
45 2ZCQ B65 9.88142
46 5NQR 958 10.5023
47 3MBG FAD 10.7914
48 2PTR 2SA 11.8577
49 1Q0H NDP 12.6482
50 1Q0H FOM 12.6482
51 5WCZ NOJ 12.6482
Pocket No.: 2; Query (leader) PDB : 1KNY; Ligand: KAN; Similar sites found with APoc: 18
This union binding pocket(no: 2) in the query (biounit: 1kny.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 5U5G NAP 2.37154
2 4GNI ATP 2.37154
3 1F3L SAH 2.7668
4 5N5U 7N8 2.7668
5 5IKR ID8 2.7668
6 5XFI NAG NAG BMA MAN MAN NAG GAL NAG 3.26797
7 1BZL GCG 3.55731
8 4DL8 UMP AF3 PO4 3.95257
9 4O1Z MXM 4.74308
10 4HPH SUC 4.74308
11 1LBZ FBP 6.74603
12 5DOZ NDP 7.90514
13 6EQ8 BQZ 8.3004
14 1RQJ RIS 8.3004
15 1YOK P6L 8.69565
16 4EIL NDP 9.48617
17 4X8O AP5 10.2804
18 1Z83 AP5 11.2245
Pocket No.: 3; Query (leader) PDB : 1KNY; Ligand: APC; Similar sites found with APoc: 28
This union binding pocket(no: 3) in the query (biounit: 1kny.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 2RI1 GLP 2.12766
2 1LVL FAD 2.37154
3 2Q0D ATP 3.16206
4 5BRE 4UZ 3.16206
5 4AP3 FAD 3.55731
6 4AP3 NAP 3.55731
7 3HIY UTP 4.34783
8 3HJ1 UTP 4.34783
9 3ER9 3AT 4.74308
10 2VK4 TPP 4.74308
11 1FEC FAD 4.74308
12 2H12 OAA 5.13834
13 1RGE 2GP 5.20833
14 5W0N 2KH 5.5336
15 4U03 TLL 5.92885
16 4U03 GTP 5.92885
17 1ZPD DPX 5.92885
18 4XJ6 GH3 6.32411
19 4WOP CTP 6.66667
20 5A2Z GTP 6.71937
21 4P4M D3T 7.11462
22 1Q79 3AT 7.90514
23 6F97 FAD 7.90514
24 3B0X DGT 8.3004
25 2B56 U5P 9.48617
26 2B56 UTP 9.48617
27 3JYY PPV 14.6245
28 3JZ0 APC 15.0198
Pocket No.: 4; Query (leader) PDB : 1KNY; Ligand: APC; Similar sites found with APoc: 11
This union binding pocket(no: 4) in the query (biounit: 1kny.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4JLS 3ZE 1.31579
2 4KQW NAP 1.97628
3 5J60 FAD 2.7668
4 1DL5 SAH 3.95257
5 4YNU FAD 3.95257
6 1M5B BN1 4.34783
7 1GPE FAD 4.34783
8 4D04 FAD 5.5336
9 4D04 NAP 5.5336
10 5HSA FAS 5.5336
11 6CI9 NAP 6.71937
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