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 18 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 17 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 17 families.
1 1KNY - KAN C18 H36 N4 O11 C1[C@H]([C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: APC; Similar ligands found: 330
No: Ligand ECFP6 Tc MDL keys Tc
1 APC 1 1
2 ACQ 0.831169 0.986301
3 A12 0.821918 1
4 AP2 0.821918 1
5 ADV 0.805195 0.972973
6 RBY 0.805195 0.972973
7 A 0.777778 0.931507
8 AMP 0.777778 0.931507
9 ADP 0.763158 0.958904
10 ACP 0.75641 0.986301
11 A2D 0.746667 0.932432
12 AP5 0.74026 0.932432
13 B4P 0.74026 0.932432
14 ATP 0.734177 0.958904
15 BA3 0.727273 0.932432
16 AQP 0.725 0.958904
17 5FA 0.725 0.958904
18 ABM 0.723684 0.881579
19 AMP MG 0.710526 0.857143
20 AN2 0.708861 0.945946
21 M33 0.7 0.92
22 TAT 0.698795 0.921053
23 SRA 0.697368 0.883117
24 AR6 0.682927 0.932432
25 APR 0.682927 0.932432
26 ADP MG 0.679012 0.87013
27 CA0 0.679012 0.907895
28 AU1 0.679012 0.933333
29 ADX 0.679012 0.841463
30 ANP 0.678571 0.933333
31 ADP PO3 0.674699 0.905405
32 SAP 0.674699 0.909091
33 AGS 0.674699 0.909091
34 AD9 0.674699 0.933333
35 BEF ADP 0.670732 0.848101
36 50T 0.670732 0.92
37 ADP BEF 0.670732 0.848101
38 ATP MG 0.666667 0.87013
39 PRX 0.662651 0.858974
40 ATF 0.643678 0.921053
41 MAP 0.640449 0.909091
42 A22 0.640449 0.945946
43 GAP 0.639535 0.858974
44 TAD 0.632653 0.923077
45 5AL 0.632184 0.894737
46 SON 0.626506 0.946667
47 ADQ 0.626374 0.907895
48 ADP ALF 0.625 0.8375
49 ALF ADP 0.625 0.8375
50 ANP MG 0.617977 0.860759
51 SRP 0.617977 0.896104
52 ADP VO4 0.617977 0.894737
53 VO4 ADP 0.617977 0.894737
54 25A 0.615385 0.932432
55 RAB 0.611111 0.810811
56 XYA 0.611111 0.810811
57 ADN 0.611111 0.810811
58 25L 0.610526 0.945946
59 A1R 0.608696 0.922078
60 4AD 0.608696 0.909091
61 DAL AMP 0.604396 0.87013
62 5SV 0.597826 0.839506
63 8QN 0.597826 0.894737
64 OOB 0.597826 0.894737
65 ADP BMA 0.595745 0.883117
66 OAD 0.595745 0.907895
67 PAJ 0.591398 0.851852
68 AMO 0.591398 0.921053
69 AOC 0.585366 0.789474
70 DLL 0.585106 0.894737
71 AHX 0.585106 0.886076
72 00A 0.585106 0.85
73 BIS 0.583333 0.897436
74 3OD 0.583333 0.907895
75 PTJ 0.583333 0.8625
76 3UK 0.578947 0.883117
77 DZD 0.577982 0.923077
78 5AS 0.576471 0.752809
79 5N5 0.573333 0.786667
80 PR8 0.572917 0.864198
81 WAQ 0.572917 0.897436
82 LAD 0.572917 0.875
83 4TC 0.571429 0.910256
84 ME8 0.56701 0.831325
85 TXA 0.56701 0.896104
86 1ZZ 0.56701 0.831325
87 FYA 0.56701 0.894737
88 NB8 0.56701 0.886076
89 5CD 0.565789 0.773333
90 A4D 0.565789 0.786667
91 ATP A A A 0.565657 0.893333
92 A3P 0.564706 0.931507
93 7D5 0.5625 0.868421
94 PAP 0.561798 0.945205
95 MYR AMP 0.561224 0.809524
96 G5P 0.558824 0.886076
97 M2T 0.556962 0.707317
98 A A 0.556701 0.906667
99 9SN 0.555556 0.839506
100 G2P 0.553191 0.923077
101 7D3 0.552941 0.894737
102 TXD 0.552381 0.873418
103 UP5 0.552381 0.884615
104 JB6 0.55102 0.873418
105 2A5 0.550562 0.907895
106 FA5 0.55 0.896104
107 YAP 0.55 0.884615
108 G3A 0.54902 0.886076
109 3AM 0.548781 0.891892
110 A2P 0.546512 0.917808
111 7D4 0.545455 0.894737
112 XAH 0.544554 0.853659
113 TYR AMP 0.544554 0.848101
114 ATR 0.544444 0.931507
115 EP4 0.544304 0.725
116 AFH 0.543689 0.875
117 4UV 0.539216 0.860759
118 G5A 0.538462 0.772727
119 GTA 0.538462 0.853659
120 NAI 0.537736 0.873418
121 DTA 0.5375 0.779221
122 3DH 0.536585 0.74359
123 AHZ 0.533333 0.788235
124 ARG AMP 0.533333 0.821429
125 LAQ 0.533333 0.831325
126 MTA 0.530864 0.74359
127 AR6 AR6 0.528846 0.881579
128 7MD 0.528846 0.853659
129 4UU 0.528846 0.860759
130 48N 0.528302 0.886076
131 LPA AMP 0.528302 0.809524
132 ITT 0.52809 0.905405
133 AMP DBH 0.524272 0.858974
134 NAX 0.523364 0.864198
135 DND 0.523364 0.896104
136 NXX 0.523364 0.896104
137 4UW 0.523364 0.829268
138 6V0 0.523364 0.8625
139 IMO 0.523256 0.891892
140 A4P 0.522936 0.813953
141 A5A 0.521277 0.77907
142 TSB 0.520833 0.790698
143 OMR 0.518519 0.843373
144 TXE 0.518519 0.873418
145 2AM 0.518072 0.905405
146 6RE 0.517647 0.753086
147 S4M 0.517241 0.681818
148 V3L 0.516129 0.932432
149 SSA 0.515789 0.793103
150 YLP 0.514019 0.833333
151 AP0 0.513761 0.8625
152 UPA 0.513761 0.873418
153 139 0.513514 0.864198
154 T5A 0.513514 0.855422
155 PPS 0.510638 0.841463
156 A2R 0.510417 0.945946
157 54H 0.510417 0.761364
158 VMS 0.510417 0.761364
159 52H 0.510417 0.752809
160 CNA 0.508929 0.896104
161 ZAS 0.505882 0.7375
162 A3N 0.505747 0.75641
163 J7C 0.505747 0.7625
164 5X8 0.505495 0.75641
165 53H 0.505155 0.752809
166 5CA 0.505155 0.793103
167 ALF ADP 3PG 0.504587 0.829268
168 LA8 ALF 3PG 0.504587 0.829268
169 AF3 ADP 3PG 0.504587 0.829268
170 TYM 0.504587 0.896104
171 IOT 0.504505 0.845238
172 YLC 0.5 0.853659
173 ADJ 0.5 0.843373
174 OVE 0.5 0.87013
175 YLB 0.5 0.833333
176 7MC 0.5 0.833333
177 P5A 0.49505 0.758242
178 NSS 0.494949 0.793103
179 LSS 0.494949 0.755556
180 DSZ 0.494949 0.793103
181 6AD 0.494737 0.875
182 MAO 0.494382 0.77381
183 DSH 0.494253 0.740741
184 A3D 0.491379 0.883117
185 NVA LMS 0.49 0.736264
186 AV2 0.489583 0.881579
187 COD 0.486957 0.825581
188 NAD 0.486957 0.894737
189 4TA 0.486957 0.821429
190 YLA 0.486726 0.833333
191 NA7 0.485149 0.972973
192 LEU LMS 0.485149 0.736264
193 3AT 0.484211 0.958904
194 GJV 0.483146 0.743902
195 AYB 0.482456 0.823529
196 5AD 0.480519 0.716216
197 GSU 0.480392 0.772727
198 KAA 0.480392 0.766667
199 NAD IBO 0.478261 0.8375
200 71V 0.477778 0.873418
201 A3G 0.477273 0.792208
202 7D7 0.474359 0.736842
203 BTX 0.474138 0.855422
204 G A A A 0.474138 0.839506
205 6C6 0.473684 0.896104
206 DAT 0.473118 0.92
207 SFG 0.473118 0.766234
208 YSA 0.471698 0.772727
209 PO4 PO4 A A A A PO4 0.470588 0.866667
210 BT5 0.470085 0.845238
211 AVV 0.47 0.910256
212 SMM 0.469388 0.701149
213 6IA 0.46875 0.829268
214 SAM 0.46875 0.705882
215 DTP 0.46875 0.92
216 A7D 0.467391 0.792208
217 AMP NAD 0.467213 0.848101
218 M24 0.466667 0.819277
219 SA8 0.463158 0.722892
220 A5D 0.463158 0.779221
221 NAE 0.46281 0.860759
222 PGS 0.462366 0.85
223 MHZ 0.462366 0.712644
224 NAJ PZO 0.462185 0.817073
225 DA 0.460674 0.893333
226 D5M 0.460674 0.893333
227 NEC 0.460674 0.717949
228 EAD 0.459677 0.841463
229 2SA 0.459184 0.921053
230 NAQ 0.459016 0.839506
231 NAJ PYZ 0.459016 0.819277
232 SAH 0.458333 0.759494
233 SAI 0.458333 0.75
234 Y3J 0.45679 0.697368
235 A A A 0.456311 0.92
236 AAM 0.455556 0.931507
237 6K6 0.455446 0.893333
238 ZID 0.455285 0.883117
239 4YB 0.454545 0.755556
240 S7M 0.454545 0.705882
241 YLY 0.454545 0.823529
242 PLP AAD 0.453782 0.736264
243 AMZ 0.453488 0.88
244 C2R 0.453488 0.868421
245 Z5A 0.451613 0.772727
246 7DD 0.451613 0.945205
247 A3S 0.451613 0.802632
248 7C5 0.449541 0.7875
249 101 0.449438 0.868421
250 EEM 0.44898 0.705882
251 N6P 0.446602 0.878378
252 ARU 0.446602 0.829268
253 AIR 0.445783 0.864865
254 U A G G 0.445378 0.85
255 P1H 0.445312 0.821429
256 NDE 0.445312 0.896104
257 N0B 0.443548 0.833333
258 A U 0.443478 0.8375
259 NIA 0.443182 0.792683
260 A3T 0.442105 0.789474
261 GEK 0.441176 0.753086
262 GP2 0.438776 0.923077
263 DDS 0.438776 0.868421
264 WSA 0.438596 0.781609
265 7DT 0.4375 0.945205
266 0WD 0.436975 0.886076
267 8BR 0.434783 0.871795
268 AAT 0.434343 0.722892
269 TXP 0.432203 0.886076
270 GGZ 0.431373 0.795181
271 NJP 0.428571 0.909091
272 A6D 0.428571 0.717647
273 FB0 0.427481 0.83908
274 NDC 0.427481 0.8625
275 649 0.426087 0.758242
276 7RA 0.423913 0.918919
277 NDP 0.423729 0.886076
278 0UM 0.423077 0.714286
279 ACK 0.422222 0.826667
280 QQY 0.422222 0.78481
281 RGT 0.422018 0.921053
282 FDA 0.421053 0.825581
283 CC5 0.419753 0.808219
284 ANZ 0.419643 0.771084
285 62X 0.419048 0.681818
286 APU 0.418803 0.860759
287 6FA 0.41791 0.833333
288 128 0.417391 0.75
289 ODP 0.416667 0.875
290 TM1 0.416667 0.747126
291 3AD 0.416667 0.797297
292 K15 0.415094 0.697674
293 2BA 0.414894 0.878378
294 CMP 0.414894 0.864865
295 V1N 0.414414 0.881579
296 S8M 0.413462 0.775
297 7RP 0.413043 0.890411
298 2VA 0.412371 0.769231
299 12D 0.412281 0.758621
300 SFD 0.411765 0.729167
301 NPW 0.411765 0.876543
302 FAS 0.411765 0.843373
303 2FA 0.411765 0.782051
304 FAD 0.411765 0.843373
305 QQX 0.411111 0.775
306 62F 0.410072 0.853659
307 FAI 0.408602 0.88
308 RMB 0.408602 0.837838
309 AS 0.408602 0.848101
310 NZQ 0.408333 0.898734
311 GCP 0.407767 0.910256
312 SXZ 0.407407 0.72619
313 SP1 0.406593 0.810127
314 RP1 0.406593 0.810127
315 U G A 0.404412 0.809524
316 D3Y 0.403846 0.782051
317 KB1 0.40367 0.714286
318 N01 0.403226 0.87013
319 SLU 0.403226 0.744444
320 5GP 0.402062 0.871795
321 G 0.402062 0.871795
322 NMN AMP PO4 0.401639 0.8375
323 XNP 0.401639 0.841463
324 SO8 0.4 0.759494
325 VRT 0.4 0.7625
326 DCA 0.4 0.837209
327 3L1 0.4 0.789474
328 3D1 0.4 0.789474
329 FNK 0.4 0.797753
330 ETB 0.4 0.825581
Ligand no: 2; Ligand: KAN; Similar ligands found: 5
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 RIO 0.460526 0.958333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1KNY; Ligand: KAN; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1kny.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1KNY; Ligand: KAN; Similar sites found: 16
This union binding pocket(no: 2) in the query (biounit: 1kny.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1OQC FAD 0.01261 0.42479 1.6
2 1T8U UAP SGN IDS SGN 0.01574 0.43175 2.37154
3 5U5G NAP 0.01411 0.4207 2.37154
4 4GNI ATP 0.01089 0.41951 2.37154
5 1F3L SAH 0.02378 0.40634 2.7668
6 5IKR ID8 0.01712 0.40031 2.7668
7 5AV7 MMA MAN NAG MAN NAG NAG 0.03538 0.40723 3.31126
8 2JFZ DGL 0.02498 0.43591 3.95257
9 2JFZ 003 0.03316 0.42542 3.95257
10 4DL8 UMP AF3 PO4 0.03204 0.40435 3.95257
11 4HPH SUC 0.03558 0.40027 4.74308
12 1LBZ FBP 0.01267 0.41463 6.74603
13 1RQJ RIS 0.02956 0.40073 8.3004
14 1YOK P6L 0.04612 0.40093 8.69565
15 4EIL NDP 0.01929 0.42213 9.48617
16 4X8O AP5 0.04411 0.40812 10.2804
Pocket No.: 3; Query (leader) PDB : 1KNY; Ligand: APC; Similar sites found: 19
This union binding pocket(no: 3) in the query (biounit: 1kny.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2Q0D ATP 0.002035 0.45254 3.16206
2 5BRE 4UZ 0.02515 0.40313 3.16206
3 4AP3 FAD 0.03708 0.41458 3.55731
4 4AP3 NAP 0.03708 0.41458 3.55731
5 3HIY UTP 0.0008433 0.44629 4.34783
6 3HJ1 UTP 0.001641 0.43563 4.34783
7 3ER9 3AT 0.005463 0.41193 4.74308
8 1FEC FAD 0.04679 0.40121 4.74308
9 2VK4 TPP 0.01928 0.40016 4.74308
10 5W0N 2KH 0.0004364 0.46171 5.5336
11 4XJ6 GH3 0.003313 0.42179 6.32411
12 5A2Z GTP 0.001776 0.41673 6.71937
13 4P4M D3T 0.004024 0.40327 7.11462
14 1Q79 3AT 0.005616 0.40485 7.90514
15 3B0X DGT 0.003028 0.41196 8.3004
16 2B56 UTP 0.00356 0.43506 9.48617
17 2B56 U5P 0.00356 0.43506 9.48617
18 3JYY PPV 0.0002705 0.49723 14.6245
19 3JZ0 APC 0.0001311 0.47532 15.0198
Pocket No.: 4; Query (leader) PDB : 1KNY; Ligand: APC; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1kny.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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