Receptor
PDB id Resolution Class Description Source Keywords
5X8I 1.9 Å EC: 2.7.12.1 CRYSTAL STRUCTURE OF HUMAN CLK1 IN COMPLEX WITH COMPOUND 25 HOMO SAPIENS INHIBITOR COMPLEX KINASE CLK1 TRANSFERASE-TRANSFERASE INCOMPLEX
Ref.: DISCOVERY OF POTENT AND SELECTIVE INHIBITORS OF CDC KINASE 1 (CLK1) AS A NEW CLASS OF AUTOPHAGY INDUCER J. MED. CHEM. V. 60 6337 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SQZ B:501;
A:501;
 Valid;
Valid;
 none;
none;
 ic50 = 2 nM
409.415 C24 H16 F N5 O C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5X8I 1.9 Å EC: 2.7.12.1 CRYSTAL STRUCTURE OF HUMAN CLK1 IN COMPLEX WITH COMPOUND 25 HOMO SAPIENS INHIBITOR COMPLEX KINASE CLK1 TRANSFERASE-TRANSFERASE INCOMPLEX
Ref.: DISCOVERY OF POTENT AND SELECTIVE INHIBITORS OF CDC KINASE 1 (CLK1) AS A NEW CLASS OF AUTOPHAGY INDUCER J. MED. CHEM. V. 60 6337 2017
Members (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 6I5I - H3E C21 H17 N5 O Cn1cc(cn1)....
2 2VAG ic50 = 19.7 nM V25 C15 H13 Cl2 N3 O2 CCOC(=O)c1....
3 6YTG Ki = 0.136 uM KHC C17 H16 Cl2 N4 O Cn1c2c(ccc....
4 6I5H - H3N C23 H17 N3 O2 Cn1cc(cn1)....
5 6ZLN Ki = 0.036 uM PKB C20 H17 F3 N6 O2 CCOc1ccc2c....
6 5X8I ic50 = 2 nM SQZ C24 H16 F N5 O C[C@@H](c1....
7 6FT9 - E6W C16 H9 Br N2 O c1ccc(cc1)....
8 1Z57 - DBQ C11 H11 N5 O2 c1c[nH]c2c....
9 6FYO - EAQ C20 H21 N6 O CC(C)(C)c1....
10 6YTA Ki = 0.229 uM IYZ C18 H18 N4 O CC(=O)c1cc....
11 6YTE Kd = 0.075 uM EAE C13 H15 N O2 S CCN1c2cc(c....
12 6FT8 - E6T C16 H10 N2 O2 c1cc(cc(c1....
13 7AK3 - RH8 C21 H21 F N8 CN1CCN(CC1....
14 6YTI - 7A7 C18 H14 F N5 O2 S [H]/N=C(c1....
15 6Q8K ic50 = 290 nM FG9 C18 H22 N6 O c1cncc2c1c....
16 5J1W ic50 = 0.19 uM 6FB C11 H8 N4 c1cncc2c1c....
17 6I5K - H3H C20 H19 N3 O2 CC(C)Oc1cc....
18 6TW2 - V25 C15 H13 Cl2 N3 O2 CCOC(=O)c1....
19 6YTD Ki = 0.671 uM EAE C13 H15 N O2 S CCN1c2cc(c....
70% Homology Family (30)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 6FYV ic50 = 11 nM 3NG C19 H12 Cl N3 O2 c1cc(cc(c1....
2 6YTY - EAE C13 H15 N O2 S CCN1c2cc(c....
3 2WU7 ic50 = 530 nM V25 C15 H13 Cl2 N3 O2 CCOC(=O)c1....
4 2WU6 ic50 = 29.2 nM DKI C15 H13 F2 N7 O2 S2 c1cc(c(c(c....
5 6FYR - EAQ C20 H21 N6 O CC(C)(C)c1....
6 6YU1 - KHC C17 H16 Cl2 N4 O Cn1c2c(ccc....
7 6FT7 - E6Q C16 H10 N2 O c1ccc(cc1)....
8 6YTW Kd = 7.78 uM EAE C13 H15 N O2 S CCN1c2cc(c....
9 6FYP ic50 = 143 nM 3NG C19 H12 Cl N3 O2 c1cc(cc(c1....
10 6I5I - H3E C21 H17 N5 O Cn1cc(cn1)....
11 2VAG ic50 = 19.7 nM V25 C15 H13 Cl2 N3 O2 CCOC(=O)c1....
12 6YTG Ki = 0.136 uM KHC C17 H16 Cl2 N4 O Cn1c2c(ccc....
13 6I5H - H3N C23 H17 N3 O2 Cn1cc(cn1)....
14 6ZLN Ki = 0.036 uM PKB C20 H17 F3 N6 O2 CCOc1ccc2c....
15 5X8I ic50 = 2 nM SQZ C24 H16 F N5 O C[C@@H](c1....
16 6FT9 - E6W C16 H9 Br N2 O c1ccc(cc1)....
17 1Z57 - DBQ C11 H11 N5 O2 c1c[nH]c2c....
18 6FYO - EAQ C20 H21 N6 O CC(C)(C)c1....
19 6YTA Ki = 0.229 uM IYZ C18 H18 N4 O CC(=O)c1cc....
20 6YTE Kd = 0.075 uM EAE C13 H15 N O2 S CCN1c2cc(c....
21 6FT8 - E6T C16 H10 N2 O2 c1cc(cc(c1....
22 7AK3 - RH8 C21 H21 F N8 CN1CCN(CC1....
23 6YTI - 7A7 C18 H14 F N5 O2 S [H]/N=C(c1....
24 6Q8K ic50 = 290 nM FG9 C18 H22 N6 O c1cncc2c1c....
25 5J1W ic50 = 0.19 uM 6FB C11 H8 N4 c1cncc2c1c....
26 6I5K - H3H C20 H19 N3 O2 CC(C)Oc1cc....
27 6TW2 - V25 C15 H13 Cl2 N3 O2 CCOC(=O)c1....
28 6YTD Ki = 0.671 uM EAE C13 H15 N O2 S CCN1c2cc(c....
29 6FYK ic50 = 3 nM EAZ C19 H24 N4 O Cc1c2cc(cc....
30 6FYL ic50 = 7 nM 3NG C19 H12 Cl N3 O2 c1cc(cc(c1....
50% Homology Family (45)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5A4T ic50 = 1.3 uM AJG C10 H7 N3 O S CC(=O)N=C1....
2 5A4Q ic50 = 2.9 uM Y3L C9 H7 Cl N2 O S CC(=O)Nc1n....
3 6EIQ Ki = 383 nM B6Z C22 H25 N5 O2 S CN1CCN(CC1....
4 6EIF Ki = 104 nM B5T C18 H14 N4 O2 S c1cc(cnc1)....
5 6A1F ic50 = 0.33 uM 9OF C15 H17 N3 O CC1(Cc2cc(....
6 5A3X ic50 = 0.8 uM QIV C9 H8 N2 O2 S CC(=O)Nc1n....
7 4YLK ic50 = 0.18 uM 4E2 C16 H8 Cl I N2 O2 c1cc2c3c(c....
8 6A1G ic50 = 0.054 uM 9OL C21 H26 N4 CC1(Cc2cc(....
9 6EIL - B6B C17 H15 N5 O2 COc1ccc(cc....
10 6EIS Ki = 252 nM B6N C22 H12 F4 N4 O c1cc2c(cc1....
11 4MQ1 - 2C3 C25 H22 Cl2 N6 O4 COc1ncc2c(....
12 6EIJ Ki = 1680 nM B5Z C23 H26 N6 O3 S c1cc(cc(c1....
13 4YLL ic50 = 0.12 uM 4E3 C16 H8 Br I N2 O2 c1cc2c3c(c....
14 6EIR Ki = 575 nM B6H C25 H30 N6 O3 S CCC(=O)Nc1....
15 5LXC ic50 = 10.8 nM 7AA C17 H11 Cl2 N5 O S COC(=N)c1n....
16 6FYV ic50 = 11 nM 3NG C19 H12 Cl N3 O2 c1cc(cc(c1....
17 2WU7 ic50 = 530 nM V25 C15 H13 Cl2 N3 O2 CCOC(=O)c1....
18 2WU6 ic50 = 29.2 nM DKI C15 H13 F2 N7 O2 S2 c1cc(c(c(c....
19 6FYR - EAQ C20 H21 N6 O CC(C)(C)c1....
20 6YU1 - KHC C17 H16 Cl2 N4 O Cn1c2c(ccc....
21 6FT7 - E6Q C16 H10 N2 O c1ccc(cc1)....
22 6YTW Kd = 7.78 uM EAE C13 H15 N O2 S CCN1c2cc(c....
23 6FYP ic50 = 143 nM 3NG C19 H12 Cl N3 O2 c1cc(cc(c1....
24 6YTG Ki = 0.136 uM KHC C17 H16 Cl2 N4 O Cn1c2c(ccc....
25 6I5H - H3N C23 H17 N3 O2 Cn1cc(cn1)....
26 6ZLN Ki = 0.036 uM PKB C20 H17 F3 N6 O2 CCOc1ccc2c....
27 5X8I ic50 = 2 nM SQZ C24 H16 F N5 O C[C@@H](c1....
28 6FT9 - E6W C16 H9 Br N2 O c1ccc(cc1)....
29 1Z57 - DBQ C11 H11 N5 O2 c1c[nH]c2c....
30 6FYO - EAQ C20 H21 N6 O CC(C)(C)c1....
31 6YTA Ki = 0.229 uM IYZ C18 H18 N4 O CC(=O)c1cc....
32 6YTE Kd = 0.075 uM EAE C13 H15 N O2 S CCN1c2cc(c....
33 6FT8 - E6T C16 H10 N2 O2 c1cc(cc(c1....
34 7AK3 - RH8 C21 H21 F N8 CN1CCN(CC1....
35 6YTI - 7A7 C18 H14 F N5 O2 S [H]/N=C(c1....
36 6Q8K ic50 = 290 nM FG9 C18 H22 N6 O c1cncc2c1c....
37 5J1W ic50 = 0.19 uM 6FB C11 H8 N4 c1cncc2c1c....
38 6I5K - H3H C20 H19 N3 O2 CC(C)Oc1cc....
39 6TW2 - V25 C15 H13 Cl2 N3 O2 CCOC(=O)c1....
40 6YTD Ki = 0.671 uM EAE C13 H15 N O2 S CCN1c2cc(c....
41 6FYL ic50 = 7 nM 3NG C19 H12 Cl N3 O2 c1cc(cc(c1....
42 4IFC - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
43 4IIR - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
44 4IJP ic50 = 0.016 uM 1EH C20 H14 Cl N3 O2 S2 c1cc(c2cc(....
45 6K0J ic50 = 13 nM CQO C18 H20 N2 O2 S COc1ccc2c(....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: SQZ; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 SQZ 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: SQZ; Similar ligands found: 2
No: Ligand Similarity coefficient
1 5VS 0.8705
2 H72 0.8667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5X8I; Ligand: SQZ; Similar sites found with APoc: 40
This union binding pocket(no: 1) in the query (biounit: 5x8i.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 4OUC 5ID 6.16247
2 1U5R ATP 15.0289
3 2CSN CKI 22.5589
4 3TXO 07U 28.3237
5 6HMR GE5 28.3439
6 3RWP ABQ 29.2605
7 3RWP ABQ 29.2605
8 5LPB ADP 29.3919
9 3ALN ANP 30.581
10 6QF4 ADP 30.8869
11 5IZF 6J9 AZ1 DAR ACA DAR NH2 31.2139
12 5AX9 4KT 31.8182
13 6F3G CJN 31.8644
14 2GU8 796 32.0475
15 3GGF GVD 32.2259
16 3TKI S25 32.8173
17 3DLS ADP 34.6269
18 3DLS ADP 34.6269
19 3DLS ADP 34.6269
20 3DLS ADP 34.6269
21 3SRV S19 35.0181
22 2YAB AMP 37.8613
23 1BYG STU 38.4892
24 4NST ADP 39.0173
25 3KN5 ANP 40
26 4WNP 3RJ 40.7666
27 4WNP 3RJ 40.7666
28 2VN9 GVD 41.8605
29 4H3Q ANP 42.4855
30 4H3P ANP 42.7746
31 3M2W L8I 42.8094
32 5H8E 5Y3 44.7447
33 4UX9 ANP 45.0867
34 5LXM ADP 45.2297
35 2PVN P63 46.3068
36 5JZJ AN2 46.4646
37 2B9H ADP 46.8208
38 2BPM 529 47.5728
39 4CFU 2WC 48.5149
40 6XX7 ANP 48.538
41 1V0O INR 50
Pocket No.: 2; Query (leader) PDB : 5X8I; Ligand: SQZ; Similar sites found with APoc: 51
This union binding pocket(no: 2) in the query (biounit: 5x8i.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 6G34 5ID 6.16247
2 4OUC 5ID 6.16247
3 1U5R ATP 15.0289
4 6VRF ADP 22.408
5 2CSN CKI 22.5589
6 5VCV 1N1 27.3312
7 3TXO 07U 28.3237
8 6F1W CG5 28.3439
9 6F1W CG5 28.3439
10 6HMR GE5 28.3439
11 6HMR GE5 28.3439
12 4OTH DRN 28.4457
13 5UIU 8CG 28.7926
14 3RWP ABQ 29.2605
15 3RWP ABQ 29.2605
16 5LPB ADP 29.3919
17 6OVA N9G 29.5681
18 7JNT VFA 30.0578
19 6QF4 ADP 30.8869
20 6LVK EVC 30.9904
21 4N70 2HX 31.0976
22 5IZF 6J9 AZ1 DAR ACA DAR NH2 31.2139
23 3IOK 1P6 31.3099
24 6F3G CJN 31.8644
25 3GGF GVD 32.2259
26 3TKI S25 32.8173
27 3MVH WFE 33.0409
28 4X7Q 3YR 33.6538
29 3DLS ADP 34.6269
30 2Z7R STU 34.891
31 3SRV S19 35.0181
32 1XJD STU 35.6522
33 2YAB AMP 37.8613
34 2VZ6 FEF 39.9361
35 3KN5 ANP 40
36 4WNP 3RJ 40.7666
37 4WNP 3RJ 40.7666
38 2VN9 GVD 41.8605
39 4QTB 38Z 41.9075
40 4H3P ANP 42.7746
41 3M2W L8I 42.8094
42 1PHK ATP 43.2886
43 5H8E 5Y3 44.7447
44 5JZJ AN2 46.4646
45 2B9H ADP 46.8208
46 2BPM 529 47.5728
47 1Q8Y ADP 47.9769
48 4CFU 2WC 48.5149
49 6XX7 ANP 48.538
50 5HQ0 LZ9 49.0066
51 6GUE FB8 49.0066
52 1V0O INR 50
APoc FAQ
Feedback