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 13 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 11 families.
1 5LMK - 6ZK C25 H19 Br N6 O c1cc(cnc1)....
50% Homology Family (7)
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 5LQF - 4SP C18 H22 N6 O3 S c1cc(ccc1N....
4 4Y72 ic50 = 10 nM LZ9 C17 H11 F3 N4 O2 c1cc(c(c(c....
5 5HQ0 ic50 = 10 nM LZ9 C17 H11 F3 N4 O2 c1cc(c(c(c....
6 4BCQ Ki = 0.147 uM TJF C21 H21 N7 O2 S Cc1c(sc(n1....
7 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: 248
This union binding pocket(no: 1) in the query (biounit: 5lmk.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5GZ9 ANP 0.000003591 0.56999 2.3569
2 3AKK ADP 0.002517 0.41703 2.71318
3 3KJS NAP 0.005489 0.43042 3.10078
4 5COU ATP 0.007741 0.40504 3.367
5 4GYI ADP 0.009901 0.40193 3.48837
6 3PDT ADP 0.001102 0.44105 3.87597
7 1UI0 URA 0.00778 0.43083 3.90244
8 3UDZ ADP 0.0002343 0.47883 4.01338
9 5JBE MAL 0.01041 0.42411 4.0404
10 2IF8 ADP 0.008055 0.41957 4.26357
11 2QX0 PH2 0.002499 0.45469 4.40252
12 5I35 ANP 0.0002545 0.46168 4.65116
13 4OUC 5ID 0.0000004517 0.59352 4.7138
14 4OCJ NDG 0.007598 0.432 4.7138
15 4B0T ADP 0.01065 0.41098 4.7138
16 3RG9 WRA 0.0162 0.41773 5
17 3RG9 NDP 0.0144 0.41722 5
18 2PYW ADP 0.0003262 0.43059 5.05051
19 4LI4 AMP 0.006691 0.4187 5.14706
20 4ZBY URA 0.01474 0.41709 5.15464
21 3HAV ATP 0.007404 0.42252 5.38721
22 5MW8 ATP 0.0001111 0.50043 5.42636
23 1VRP IOM 0.00803 0.41775 5.72391
24 3X01 AMP 0.01909 0.40323 6.58915
25 1S68 AMP 0.00264 0.40081 6.82731
26 4AZT LY2 0.004486 0.42235 7.07071
27 4AZW ATP 0.007964 0.41031 7.07071
28 4LRJ ANP 0.0005399 0.44813 7.69231
29 3TY5 ATP 0.007897 0.4107 7.75194
30 4O1P ANP 0.00001561 0.53012 8.41751
31 4XMF HSM 0.003476 0.4563 8.69565
32 3I0O ADP 0.003256 0.42894 8.91473
33 1W2D ADP 0.007171 0.41269 9.43396
34 5DMZ ADP 0.0003599 0.4488 9.68992
35 4ZS4 ATP 0.001107 0.42091 9.68992
36 3WVR AMP 0.008831 0.4003 9.68992
37 4CC6 L5Y 0.009214 0.41193 9.74843
38 3VPB ADP 0.0006563 0.40007 9.92908
39 1ZP9 ATP 0.0008524 0.44608 10.4651
40 1ZTH ADP 0.0004452 0.44434 10.4651
41 3R4S SIA 0.01292 0.40434 10.4651
42 3RE4 TO1 0.00005402 0.51315 10.8527
43 1IA9 ANP 0.002835 0.40298 10.8527
44 3A7R LAQ 0.027 0.40372 11.1111
45 4Q5H ANP 0.002442 0.41301 11.4943
46 5DZT AMP 0.006989 0.42441 11.6279
47 3VOT ADP 0.001119 0.4509 12.0155
48 5IQD GNP 0.009243 0.42672 12.1212
49 5IQD RIO 0.00972 0.42672 12.1212
50 3B6R CRN 0.003677 0.40823 12.4031
51 5CKW ANP 0.003524 0.42732 12.7946
52 3TDV GDP 0.003182 0.40998 12.7946
53 3SJK LYS PRO VAL LEU ARG THR ALA 0.004366 0.43722 13.1579
54 5K2M ADP 0.009022 0.41284 15.0943
55 4WW7 AMP 0.002123 0.43879 17.1123
56 2PUL ACP 0.0002256 0.46214 17.1717
57 4DFU QUE 0.01573 0.40498 18.0124
58 5C4L 4XR 0.0009451 0.46858 18.3801
59 1NU4 MLA 0.00416 0.43722 18.5567
60 4OAV ACP 0.00002422 0.50452 18.8552
61 5M06 ADP 0.00001203 0.52937 19.9275
62 4CYI ATP 0.00006802 0.50588 20.202
63 3LQV ADE 0.01088 0.40951 23.0769
64 5VC5 96M 0.0000003977 0.48601 23.1834
65 3Q60 ATP 0.0004937 0.44903 24.2424
66 4WOV 3SM 0.000001352 0.58024 24.5791
67 4BTK DTQ 0.00002048 0.52473 24.5791
68 5KO1 6UY 0.0001387 0.4714 25.4417
69 4NFN 2KC 0.0001552 0.46907 25.5892
70 4KBA 1QM 0.00001411 0.44429 25.5892
71 5W4W 9WG 0.00001483 0.42866 25.5892
72 3VHE 42Q 0.000005731 0.4347 26.2626
73 5C03 AGS 0.0000004828 0.56303 26.5993
74 4XH0 ADP 0.00006042 0.52923 28.9562
75 2CSN CKI 0.008424 0.44477 29.2929
76 4IX4 ADP 0.00002994 0.52234 29.9663
77 3H9R TAK 0.00001715 0.54453 30.6397
78 4Y0X ADP 0.0006729 0.45071 30.6397
79 4IDT T28 0.000000963 0.56557 31.3131
80 3KRL KRL 0.0000002342 0.53779 31.3131
81 4EUU BX7 0.000002704 0.4692 31.3131
82 4FL3 ANP 0.0000005541 0.52433 31.6498
83 3KMW ATP 0.0001986 0.46473 31.7343
84 3PP0 03Q 0.0000216 0.44094 31.9865
85 5T8O 76Z 0.0000118 0.48577 32.6599
86 4P5Z Q7M 0.0000007731 0.42784 32.6599
87 1U59 STU 0.000004356 0.52521 32.7526
88 4YMJ 4EJ 0.0000001367 0.66638 32.9966
89 5JFS 6K0 0.0000008552 0.62947 32.9966
90 5CEO 50D 0.000003543 0.55949 32.9966
91 4Y93 746 0.0000002223 0.51093 32.9966
92 4E93 GUI 0.0000005245 0.46053 32.9966
93 4CLI 5P8 0.000002548 0.61047 33.3333
94 3UIM ANP 0.0000001813 0.58107 33.3333
95 2R5T ANP 0.000000567 0.52855 33.3333
96 1K3A ACP 0.000001213 0.58241 33.67
97 5EOB 5QQ 0.00004974 0.55627 33.67
98 4Y8D 49J 0.0000007428 0.55529 33.67
99 3NW7 LGV 0.0000421 0.55216 33.67
100 3DLS ADP 0.0001585 0.47897 33.67
101 3C1X CKK 0.0007239 0.41165 33.67
102 4YZN 4K5 0.0000001459 0.53867 33.7979
103 1JPA ANP 0.0000001334 0.65948 34.0067
104 4U44 3D9 0.00001191 0.53548 34.0067
105 5TA6 79D 0.0000003075 0.48956 34.0067
106 3LXK MI1 0.0000007188 0.48254 34.0067
107 4FF8 14S 0.0007904 0.43544 34.0067
108 4AT3 LTI 0.00002408 0.4202 34.0067
109 5UIU 8CG 0.0000006246 0.61959 34.3434
110 2X2M X2M 0.000001026 0.59274 34.3434
111 2QLU ADE 0.000009204 0.57741 34.3434
112 4I94 ANP 0.0000168 0.52583 34.3434
113 1VJY 460 0.00000007245 0.48278 34.3434
114 2XVD AS6 0.000001346 0.47142 34.3434
115 5NKB 8ZT 0.000001267 0.40749 34.3434
116 4OH4 ANP 0.00000006143 0.60054 34.6801
117 5LPZ ADP 0.0000004319 0.56671 34.6801
118 5HES 032 0.00001212 0.54296 34.6801
119 5HX8 66P 0.00000004087 0.5291 34.6801
120 4GJ3 0XP 0.000000006359 0.51429 34.6801
121 2Y6O 1N1 0.000004609 0.49445 34.7079
122 5LPB ADP 0.00000177 0.58336 34.7973
123 3KRR DQX 0.00000006932 0.71197 34.9153
124 3TKI S25 0.0000002709 0.67044 35.0168
125 5AX9 4KT 0.00000006816 0.59869 35.0168
126 2HY0 306 0.000002223 0.57028 35.0168
127 3LXN MI1 0.0000002306 0.55228 35.0168
128 4X7Q 3YR 0.000006091 0.5194 35.0168
129 1U5R ATP 0.000001029 0.55123 35.3535
130 5U6C 7YS 0.00000947 0.47947 35.3535
131 5MJA 7O3 0.0002765 0.46809 35.3535
132 5TO8 7FM 0.000006971 0.40418 35.461
133 4F4P 0SB 0.0001278 0.53916 35.5311
134 3V8S 0HD 0.000002851 0.54298 35.6902
135 4G17 0VN 0.000119 0.48458 35.6902
136 5JGA 6KC 0.000005955 0.43326 35.6902
137 4E1Z 0MX 0.0000004146 0.52276 35.7388
138 3BU5 ATP 0.00001369 0.53271 36.0269
139 3EKK GS2 0.0000002233 0.44396 36.0269
140 1ZY5 ANP 0.000005198 0.54892 36.3636
141 3PLS ANP 0.000004934 0.53419 36.3636
142 5USZ SKE 0.0000001809 0.50038 36.6782
143 1BYG STU 0.0000001066 0.62176 36.6906
144 5HVJ ANP 0.000001059 0.62028 36.7003
145 3SLS ANP 0.000001708 0.51259 36.7003
146 4XLI 1N1 0.00003544 0.49678 36.9403
147 3CY2 MB9 0.000003743 0.49042 37.037
148 4QMN DB8 0.000002444 0.42209 37.037
149 4EWH T77 0.000006349 0.45361 37.0909
150 5FBN 5WF 0.000002323 0.59976 37.2694
151 1RE8 BD2 0.000001523 0.62445 37.3737
152 2QCS ANP 0.000001558 0.59411 37.3737
153 3FHI ANP 0.000001964 0.58935 37.3737
154 2H8H H8H 0.0000007406 0.55476 37.3737
155 3RI1 3RH 0.00004059 0.52708 37.3737
156 5LI1 ANP 0.0000008183 0.52067 37.3737
157 2WQN ADP 0.00003051 0.51783 37.3737
158 2PVF ACP 0.00001302 0.51601 37.3737
159 1Y57 MPZ 0.000001227 0.50621 37.3737
160 3IDB ANP 0.000001297 0.50305 37.3737
161 2PZI AXX 0.0008579 0.451 37.3737
162 4U0I 0LI 0.00001221 0.41509 37.3737
163 4A4X JUP 0.000004919 0.45987 37.6344
164 4K33 ACP 0.00002998 0.51981 37.7104
165 4WB7 ATP 0.000007371 0.40823 37.7104
166 4WB6 ATP 0.000001811 0.47688 38.0471
167 3ORK AGS 0.00006105 0.43442 38.0471
168 2A19 ANP 0.00003211 0.52383 38.3803
169 1OPK P16 0.00001348 0.41736 38.3838
170 5MY8 RXZ 0.00005203 0.43595 38.7205
171 3G5D 1N1 0.000007183 0.60025 38.8112
172 3SRV S19 0.000001508 0.57327 38.9892
173 5UR1 YY9 0.0000004753 0.6453 39.0572
174 3GQI ACP 0.000001125 0.54957 39.0572
175 5JKG 6LF 0.000004868 0.58905 39.3939
176 4NW6 2NS 0.00000002852 0.48965 39.3939
177 5H2U 1N1 0.00004875 0.48254 39.7004
178 2Z7R STU 0.00000006972 0.56329 39.7306
179 3GNI ATP 0.0000005558 0.54036 39.7306
180 3FHR P4O 0.000001786 0.52746 39.7306
181 4Y85 499 0.00003224 0.49951 39.7306
182 5DA3 58V 0.0000008513 0.59838 40
183 4OTH DRN 0.000001527 0.51011 40.0673
184 3M2W L8I 0.00006806 0.48821 40.0673
185 4ASE AV9 0.000006606 0.44383 40.404
186 4AG8 AXI 0.000002328 0.41717 40.404
187 4WNP 3RJ 0.0000006865 0.59382 40.4181
188 4I6H 1C8 0.000001244 0.54814 40.7407
189 4XV1 904 0.000007358 0.57368 40.7534
190 5VCV 1N1 0.000001609 0.49261 41.4141
191 4M69 ANP 0.000001806 0.52038 41.7508
192 4L9I 8PR 0.0008217 0.43979 42.0875
193 4BHN BH9 0.000001821 0.51814 42.4242
194 3VRY B43 0.00001351 0.45133 42.4242
195 5N87 N66 0.00000004027 0.46328 42.7609
196 4CQE CQE 0.0004013 0.41907 42.8058
197 3HMO STU 0.00000005473 0.61788 43.0976
198 4FG8 ATP 0.0001398 0.4503 43.0976
199 3ALN ANP 0.0000005687 0.54158 43.4343
200 4CSV STI 0.0001743 0.42316 43.6364
201 4D2S DYK 0.00000004722 0.64742 43.662
202 5IH9 6BF 0.00002716 0.54935 43.771
203 5JZJ AN2 0.000004498 0.53617 43.771
204 4YZC STU 0.0000001697 0.65887 44.1077
205 2OFV 242 0.0000001688 0.45392 44.4043
206 3KN5 ANP 0.0000006688 0.57541 44.4444
207 5LVP ATP 0.000003235 0.5456 44.4444
208 4JR7 GNP 0.0000007518 0.55553 44.7811
209 2V7O DRN 0.000003272 0.52118 44.7811
210 4JDI ANP 0.000001054 0.52767 44.8161
211 2VZ6 FEF 0.000003671 0.56024 45.1178
212 4DC2 ADE 0.000002563 0.48163 45.1178
213 5LI9 ACP 0.00003646 0.47773 45.1178
214 3MVH WFE 0.000004194 0.4414 45.1178
215 2X4Z X4Z 0.000004746 0.42425 45.2703
216 2VN9 GVD 0.000001264 0.54018 45.4545
217 4BFM ANP 0.000003386 0.50718 45.4545
218 5DBX ANP 0.00003894 0.49775 45.4545
219 2WEL K88 0.00000345 0.49225 45.4545
220 5UKL SIX 0.00229 0.4457 45.4545
221 3PVW QRX 0.00007589 0.42324 45.4545
222 2F57 23D 0.000003591 0.553 45.485
223 4WNK 453 0.00005771 0.4136 45.7912
224 3DAK ANP 0.00007841 0.49273 46.2069
225 2XK9 XK9 0.02748 0.42771 46.4646
226 2HK5 1BM 0.00009206 0.49981 46.6667
227 3AQV TAK 0.00003359 0.51493 46.7391
228 1XJD STU 0.00000006387 0.58612 46.8013
229 3GGF GVD 0.000002407 0.56083 46.8227
230 4KS7 X4Z 0.0000004847 0.51816 46.9178
231 1PHK ATP 0.0000008614 0.59056 47.138
232 5UOX 8GY 0.000001517 0.51202 47.2325
233 4F9C 0SX 0.000003946 0.55434 47.4747
234 2ZV2 609 0.00002216 0.53145 47.651
235 4L3L 5FI 0.000001111 0.60759 48.1481
236 1Q8Y ADP 0.00001142 0.54165 48.1481
237 1Q8Y ADE 0.00007767 0.47081 48.1481
238 2YAB AMP 0.00005853 0.47047 48.1481
239 3TXO 07U 0.000006327 0.54193 48.4848
240 3SXS PP2 0.000004284 0.50565 48.5075
241 3C0G 3AM 0.0000009399 0.58752 48.8215
242 5X8I SQZ 0.000003868 0.52772 49.4949
243 4USF 6UI 0.0001438 0.49724 49.4949
244 3IGO ANP 0.00008624 0.44834 49.4949
245 4C2V YJA 0.0000003889 0.47371 49.8246
246 2YAK OSV 0.00002022 0.42022 49.8246
247 4IJP 1EH 0.000001733 0.57945 49.8316
248 2WU6 DKI 0.000001859 0.50534 49.8316
Pocket No.: 2; Query (leader) PDB : 5LMK; Ligand: 6ZK; Similar sites found: 19
This union binding pocket(no: 2) in the query (biounit: 5lmk.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2CBT TH2 0.01812 0.4019 2.67857
2 2Z9I GLY ALA THR VAL 0.02127 0.40188 3.367
3 5IGI ZIT 0.0243 0.407 4.65116
4 5IGI GMP 0.02319 0.407 4.65116
5 2CJU PHX 0.02124 0.40484 4.95868
6 4OCV ANP 0.004003 0.40015 5.05051
7 2YY8 MTA 0.005335 0.41436 5.47264
8 5LRT ADP 0.01033 0.41161 6.58915
9 2IW3 ADP 0.005472 0.41826 6.73401
10 3LXI CAM 0.008751 0.41953 10.0775
11 4BTI 7R9 0.0126 0.40752 10.2362
12 4OKD GLC GLC GLC 0.01798 0.40131 10.4377
13 4R78 AMP 0.001747 0.44706 14.8148
14 3IID APR 0.01896 0.4032 17.0616
15 5U98 1KX 0.03969 0.41116 18.1818
16 5C4L SIS 0.02011 0.40446 18.3801
17 1R1Q ACE ARG GLU PTR VAL ASN VAL 0.02603 0.40116 20
18 4N70 2HX 0.0000001138 0.40467 37.037
19 3SXF BK5 0.00001728 0.40202 49.4949
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