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Receptor
PDB id Resolution Class Description Source Keywords
5LMK 2.4 Å EC: 2.7.11.22 STRUCTURE OF PHOPSHO-CDK2-CYCLIN A IN COMPLEX WITH AN ATP-CO INHIBITOR HOMO SAPIENS CDK2; CYCLIN A CELL CYCLE TRANSFERASE INHIBITOR COMPLEX
Ref.: EXPLICIT TREATMENT OF ACTIVE-SITE WATERS ENHANCES Q MECHANICAL/IMPLICIT SOLVENT SCORING: INHIBITION OF NEW PYRAZOLO[1,5-A]PYRIMIDINES. EUR J MED CHEM V. 126 1118 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SGM B:501;
D:501;
Invalid;
Invalid;
none;
none;
submit data
108.159 C3 H8 O2 S C([C@...
6ZK A:301;
C:301;
Valid;
Valid;
none;
none;
submit data
499.362 C25 H19 Br N6 O c1cc(...
MG B:502;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5LMK 2.4 Å EC: 2.7.11.22 STRUCTURE OF PHOPSHO-CDK2-CYCLIN A IN COMPLEX WITH AN ATP-CO INHIBITOR HOMO SAPIENS CDK2; CYCLIN A CELL CYCLE TRANSFERASE INHIBITOR COMPLEX
Ref.: EXPLICIT TREATMENT OF ACTIVE-SITE WATERS ENHANCES Q MECHANICAL/IMPLICIT SOLVENT SCORING: INHIBITION OF NEW PYRAZOLO[1,5-A]PYRIMIDINES. EUR J MED CHEM V. 126 1118 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 5LMK - 6ZK C25 H19 Br N6 O c1cc(cnc1)....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 5LMK - 6ZK C25 H19 Br N6 O c1cc(cnc1)....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4BCN Ki = 0.012 uM T9N C16 H14 N6 O S Cc1c(sc(n1....
2 4BCM Ki = 0.123 uM T7Z C21 H23 N7 O3 S2 Cc1ccc(cc1....
3 6GUE Kd = 4 nM FB8 C18 H21 N5 O2 S Cc1ncc(n1C....
4 5LQF - 4SP C18 H22 N6 O3 S c1cc(ccc1N....
5 4Y72 ic50 = 10 nM LZ9 C17 H11 F3 N4 O2 c1cc(c(c(c....
6 6GU2 Kd = 23 nM F9Z C21 H20 Cl N O5 CN1CC[C@@H....
7 5HQ0 ic50 = 10 nM LZ9 C17 H11 F3 N4 O2 c1cc(c(c(c....
8 4BCQ Ki = 0.147 uM TJF C21 H21 N7 O2 S Cc1c(sc(n1....
9 5LMK - 6ZK C25 H19 Br N6 O c1cc(cnc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 6ZK; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 6ZK 1 1
2 SCJ 0.698795 0.877193
3 6SC 0.533333 0.877193
4 2SC 0.489583 0.786885
5 SCZ 0.464646 0.779661
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5LMK; Ligand: 6ZK; Similar sites found with APoc: 365
This union binding pocket(no: 1) in the query (biounit: 5lmk.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 5GZ9 ANP 2.3569
2 3SUC ATP 2.6936
3 3AKK ADP 2.71318
4 3PN1 IVH 3.10078
5 5OLK DTP 3.10078
6 3KJS NAP 3.10078
7 5COU ATP 3.367
8 4NJH SAM 3.47826
9 4NJH 2K8 3.47826
10 3BP1 GUN 3.48837
11 4GYI ADP 3.48837
12 3WO0 ALA 3.7037
13 3WO0 ADP 3.7037
14 3PDT ADP 3.87597
15 1J3I NDP 3.87597
16 1J3I WRA 3.87597
17 6EOM ALA LYS 3.87597
18 1ZX5 LFR 3.87597
19 1UI0 URA 3.90244
20 6FL8 TIY 4.01338
21 6FL8 ADP 4.01338
22 3UDZ ADP 4.01338
23 2W5P CL8 4.02685
24 5JBE MAL 4.0404
25 5JIL 6KL 4.0404
26 1HDR NAD 4.09836
27 1Y60 H4M 4.14201
28 2IF8 ADP 4.26357
29 5J60 FAD 4.26357
30 6DW2 HD4 4.31373
31 4PZ6 GMP 4.3771
32 2QX0 PH2 4.40252
33 5UWA 8ND 4.4335
34 5I35 ANP 4.65116
35 5IM3 DTP 4.65116
36 6G34 5ID 4.7138
37 4OUC 5ID 4.7138
38 4OCJ NDG 4.7138
39 4B0T ADP 4.7138
40 3RG9 WRA 5
41 3RG9 NDP 5
42 4XGX ADP 5.03876
43 2PYW ADP 5.05051
44 4OCV ANP 5.05051
45 4LI4 AMP 5.14706
46 3HAV ATP 5.38721
47 1IOW PHY 5.38721
48 1IOW ADP 5.38721
49 6BMN PAP 5.42373
50 5MW8 ATP 5.42636
51 2V58 LZJ 5.42636
52 1U6R IOM 5.72391
53 1GSA ADP 5.72391
54 1VRP IOM 5.72391
55 5AE9 OKO 5.81395
56 2UV4 AMP 5.92105
57 6C1S EFV 6.20155
58 1G51 AMP 6.20155
59 1PK8 ATP 6.39731
60 4DP3 MMV 6.39731
61 4DP3 NDP 6.39731
62 6E8I PTR 6.50888
63 3X01 AMP 6.58915
64 2PHN GDP 6.69291
65 4NFE BEN 6.75105
66 3VPD ANP 6.76157
67 1S68 AMP 6.82731
68 1IY8 NAD 6.97674
69 4AZW ATP 7.07071
70 1T36 ADP 7.07071
71 5VLQ ANP 7.40741
72 4LRJ ANP 7.69231
73 5OES ADP 7.75194
74 1I7L ATP 7.75194
75 3TY5 ATP 7.75194
76 4XZ3 ACP 7.82609
77 5ZCT ANP 8.13953
78 4O1P ANP 8.41751
79 5EQY 5RA 8.52713
80 4XMF HSM 8.69565
81 3I0O ADP 8.91473
82 6BSX E7S 8.98876
83 6MJ7 ARG 9.09091
84 2VQD AP2 9.09091
85 3VOZ 04A 9.09091
86 1AUX AGS 9.09091
87 1Z2P I3S 9.09091
88 1Z2P ACP 9.09091
89 3KAL ADP 9.30233
90 5YK1 ANP 9.42761
91 1W2D ADP 9.43396
92 5DMZ ADP 9.68992
93 4ZS4 ATP 9.68992
94 3WVR AMP 9.68992
95 4CC6 L5Y 9.74843
96 3NYQ AMP 9.76431
97 3NYQ MCA 9.76431
98 3VPB ADP 9.92908
99 3VPC ADP 9.92908
100 4TVD BGC 10.0775
101 4NZN 2OU 10.0775
102 4NZN ANP 10.0775
103 1ZTH ADP 10.4651
104 1ZP9 ATP 10.4651
105 3DLG GWE 10.4651
106 3R4S SIA 10.4651
107 3T1A 5MA 10.4651
108 1CBK ROI 10.625
109 3RE4 TO1 10.8527
110 1IA9 ANP 10.8527
111 1TQP ATP 10.9929
112 3A7R LAQ 11.1111
113 4Q5H ANP 11.4943
114 5DZT AMP 11.6279
115 3VOT ADP 12.0155
116 2IO8 ADP 12.0155
117 6CGD AKN 12.1212
118 6CGD GNP 12.1212
119 3B6R CRN 12.4031
120 4X3H ARG ILE PRO SER TYR ARG TYR ARG TYR 12.6582
121 3TDV GDP 12.7946
122 6AC9 ANP 12.7946
123 5CKW ANP 12.7946
124 3SJK LYS PRO VAL LEU ARG THR ALA 13.1579
125 3LF0 ATP 14.0351
126 5YW5 ADE 14.5251
127 5K2M ADP 15.0943
128 3WW2 SF9 16.0156
129 5UQW GDP 16.4021
130 4WW7 AMP 17.1123
131 2PUL ACP 17.1717
132 4DFU QUE 18.0124
133 5C4L 4XR 18.3801
134 1NU4 MLA 18.5567
135 4OAV ACP 18.8552
136 5LXT GTP 19.5804
137 5M06 ADP 19.9275
138 4CYI ATP 20.202
139 5FM0 WAQ 20.9302
140 6BFN DL1 22.8956
141 3LQV ADE 23.0769
142 5VC5 96M 23.1834
143 3Q60 ATP 24.2424
144 4WOV 3SM 24.5791
145 4BTK DTQ 24.5791
146 5KO1 6UY 25.4417
147 5W4W 9WG 25.5892
148 4NFN 2KC 25.5892
149 5OKT 9XK 25.5892
150 4KBA 1QM 25.5892
151 6GZD LCI 25.9259
152 3VHE 42Q 26.2626
153 5C03 AGS 26.5993
154 4XH0 ADP 28.9562
155 2CSN CKI 29.2929
156 5QIN J2V 29.9663
157 4IX4 ADP 29.9663
158 6GIN IR2 30.6397
159 3H9R TAK 30.6397
160 4Y0X ADP 30.6397
161 3KRL KRL 31.3131
162 4EUU BX7 31.3131
163 4IDT T28 31.3131
164 4FL3 ANP 31.6498
165 3KMW ATP 31.7343
166 3PP0 03Q 31.9865
167 6ES0 BW8 32.3232
168 4P5Z Q7M 32.6599
169 5HCY 60D 32.6599
170 5T8O 76Z 32.6599
171 1U59 STU 32.7526
172 4Y93 746 32.9966
173 5JFS 6K0 32.9966
174 4E93 GUI 32.9966
175 4UAL 3FV 32.9966
176 4YMJ 4EJ 32.9966
177 5CEO 50D 32.9966
178 6BXI ANP 32.9966
179 3UIM ANP 33.3333
180 4CLI 5P8 33.3333
181 2R5T ANP 33.3333
182 4Y8D 49J 33.67
183 1K3A ACP 33.67
184 5EOB 5QQ 33.67
185 3NW7 LGV 33.67
186 3DLS ADP 33.67
187 3C1X CKK 33.67
188 4YZN 4K5 33.7979
189 5TA6 79D 34.0067
190 3FC2 IBI 34.0067
191 3LXK MI1 34.0067
192 4AT3 LTI 34.0067
193 4U44 3D9 34.0067
194 1JPA ANP 34.0067
195 4FF8 14S 34.0067
196 5NKB 8ZT 34.3434
197 2F2U M77 34.3434
198 2XVD AS6 34.3434
199 2X2M X2M 34.3434
200 4I94 ANP 34.3434
201 1VJY 460 34.3434
202 5UIU 8CG 34.3434
203 2QLU ADE 34.3434
204 6F3G CJN 34.5763
205 5WO4 B7V 34.6801
206 4OH4 ANP 34.6801
207 5WNL STU 34.6801
208 5LPZ ADP 34.6801
209 5Y80 IRE 34.6801
210 5HES 032 34.6801
211 6C0T EE4 34.6801
212 4GJ3 0XP 34.6801
213 2Y6O 1N1 34.7079
214 5LPB ADP 34.7973
215 3TKI S25 35.0168
216 3LXN MI1 35.0168
217 5AX9 4KT 35.0168
218 2HY0 306 35.0168
219 4X7Q 3YR 35.0168
220 5U6C 7YS 35.3535
221 1U5R ATP 35.3535
222 5MJA 7O3 35.3535
223 5TO8 7FM 35.461
224 4F4P 0SB 35.5311
225 5JGA 6KC 35.6902
226 3V8S 0HD 35.6902
227 4G17 0VN 35.6902
228 4E1Z 0MX 35.7388
229 6C7Y ADP 36.014
230 3EKK GS2 36.0269
231 1IR3 ANP 36.0269
232 3BU5 ATP 36.0269
233 3PLS ANP 36.3636
234 1ZY5 ANP 36.3636
235 5USZ SKE 36.6782
236 1BYG STU 36.6906
237 3SLS ANP 36.7003
238 5HVJ ANP 36.7003
239 4N70 2HX 37.037
240 3CY2 MB9 37.037
241 4QMN DB8 37.037
242 4EWH T77 37.0909
243 4RFM 3P6 37.218
244 5FBN 5WF 37.2694
245 2GU8 796 37.3737
246 1RE8 BD2 37.3737
247 5LI1 ANP 37.3737
248 2QCS ANP 37.3737
249 1Y57 MPZ 37.3737
250 3IDB ANP 37.3737
251 2H8H H8H 37.3737
252 4U0I 0LI 37.3737
253 2PVF ACP 37.3737
254 2WQN ADP 37.3737
255 3FHI ANP 37.3737
256 2PZI AXX 37.3737
257 3RI1 3RH 37.3737
258 4A4X JUP 37.6344
259 4WB7 ATP 37.7104
260 4K33 ACP 37.7104
261 4WB6 ATP 38.0471
262 3ORK AGS 38.0471
263 2A19 ANP 38.3803
264 6CQF F97 38.3838
265 1OPK P16 38.3838
266 5MY8 RXZ 38.7205
267 3G5D 1N1 38.8112
268 3SRV S19 38.9892
269 3GQI ACP 39.0572
270 6GQM F8H 39.0572
271 5UR1 YY9 39.0572
272 4NW6 2NS 39.3939
273 5JKG 6LF 39.3939
274 5H2U 1N1 39.7004
275 2Z7R STU 39.7306
276 3GNI ATP 39.7306
277 3FHR P4O 39.7306
278 4G31 0WH 39.7306
279 4Y85 499 39.7306
280 2OO8 RAJ 39.7306
281 3E8N ATP 40.0673
282 3E8N VRA 40.0673
283 4OTH DRN 40.0673
284 4UXL 5P8 40.0673
285 3M2W L8I 40.0673
286 6CZ3 FLJ 40.1515
287 4AG8 AXI 40.404
288 4ASE AV9 40.404
289 4WNP 3RJ 40.4181
290 4I6H 1C8 40.7407
291 4XV1 904 40.7534
292 3BZ3 YAM 40.942
293 5VCV 1N1 41.4141
294 4M69 ANP 41.7508
295 4TWP AXI 42.0664
296 4PNI KQQ 42.0875
297 4L9I 8PR 42.0875
298 3VRY B43 42.4242
299 4BHN BH9 42.4242
300 6E2O S0L 42.7119
301 5N87 N66 42.7609
302 4CQE CQE 42.8058
303 3HMO STU 43.0976
304 4FG8 ATP 43.0976
305 3ALN ANP 43.4343
306 4CSV STI 43.6364
307 5IH9 6BF 43.771
308 5JZJ AN2 43.771
309 3RWP ABQ 44.1077
310 6GWR FEW 44.1077
311 4YZC STU 44.1077
312 2OFV 242 44.4043
313 3KN5 ANP 44.4444
314 5LVP ATP 44.4444
315 4JR7 GNP 44.7811
316 2V7O DRN 44.7811
317 5UPK ANP 44.8161
318 3MVH WFE 45.1178
319 2VZ6 FEF 45.1178
320 5LI9 ACP 45.1178
321 4DC2 ADE 45.1178
322 2VN9 GVD 45.4545
323 4BFM ANP 45.4545
324 3PVW QRX 45.4545
325 5DBX ANP 45.4545
326 2WEL K88 45.4545
327 5UKL SIX 45.4545
328 2F57 23D 45.485
329 5XVG 8FX 45.7338
330 4WNK 453 45.7912
331 3DAK ANP 46.2069
332 5DRB 5FJ 46.3918
333 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 46.4646
334 2JDR L20 46.4646
335 2XK9 XK9 46.4646
336 2HK5 1BM 46.6667
337 3AQV TAK 46.7391
338 1XJD STU 46.8013
339 3GGF GVD 46.8227
340 4KS7 X4Z 46.9178
341 1PHK ATP 47.138
342 5EH0 5NW 47.2868
343 4F9C 0SX 47.4747
344 2J7T 274 47.4747
345 2ZV2 609 47.651
346 4L3L 5FI 48.1481
347 1Q8Y ADP 48.1481
348 6FYV 3NG 48.1481
349 2YAB AMP 48.1481
350 1Q8Y ADE 48.1481
351 3TXO 07U 48.4848
352 3SXS PP2 48.5075
353 3C0G 3AM 48.8215
354 6CMJ F6J 49.1582
355 5DEY 59T 49.1582
356 5X8I SQZ 49.4949
357 6G33 5ID 49.4949
358 3IGO ANP 49.4949
359 4USF 6UI 49.4949
360 4ONA UW1 49.4949
361 4C2V YJA 49.8246
362 2YAK OSV 49.8246
363 2WU6 DKI 49.8316
364 4IJP 1EH 49.8316
365 6FYL 3NG 49.8316
Pocket No.: 2; Query (leader) PDB : 5LMK; Ligand: 6ZK; Similar sites found with APoc: 32
This union binding pocket(no: 2) in the query (biounit: 5lmk.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 2CBT TH2 2.67857
2 3DNT ATP 3.10078
3 2Z9I GLY ALA THR VAL 3.367
4 4UCF GLA 3.87597
5 3VX3 ADP 4.43548
6 5IGI ZIT 4.65116
7 5IGI GMP 4.65116
8 5WGR FAD 4.7138
9 2CJU PHX 4.95868
10 2YY8 MTA 5.47264
11 4OHU 2TK 6.22837
12 4OHU NAD 6.22837
13 5LRT ADP 6.58915
14 2IW3 ADP 6.73401
15 5A89 ADP 7.05128
16 5A89 FMN 7.05128
17 1SVM ATP 7.07071
18 1JG3 ADN 7.23404
19 4IP7 FLC 7.75194
20 3W0O HY0 8.41751
21 3W0O ADP 8.41751
22 4PU5 ANP 8.75421
23 3LXI CAM 10.0775
24 4BTI 7R9 10.2362
25 4OKD GLC GLC GLC 10.4377
26 1I8T FAD 10.7744
27 3NNF AKG 13.1783
28 4R78 AMP 14.8148
29 3IID APR 17.0616
30 5U98 1KX 18.1818
31 5C4L SIS 18.3801
32 1R1Q ACE ARG GLU PTR VAL ASN VAL 20
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