Receptor
PDB id Resolution Class Description Source Keywords
6FYV 2.46 Å EC: 2.7.12.1 X-RAY STRUCTURE OF CLK4-KD(146-480)/CX-4945 AT 2.46A HOMO SAPIENS SPLICING KINASE PHOSPHOTRANSFERASE TRANSFERASE
Ref.: X-RAY STRUCTURES AND FEASIBILITY ASSESSMENT OF CLK2 INHIBITORS FOR PHELAN-MCDERMID SYNDROME. CHEMMEDCHEM V. 13 1997 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3NG A:501;
 Valid;
 none;
 ic50 = 11 nM
349.77 C19 H12 Cl N3 O2 c1cc(...
SO4 A:502;
A:503;
A:504;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6FYV 2.46 Å EC: 2.7.12.1 X-RAY STRUCTURE OF CLK4-KD(146-480)/CX-4945 AT 2.46A HOMO SAPIENS SPLICING KINASE PHOSPHOTRANSFERASE TRANSFERASE
Ref.: X-RAY STRUCTURES AND FEASIBILITY ASSESSMENT OF CLK2 INHIBITORS FOR PHELAN-MCDERMID SYNDROME. CHEMMEDCHEM V. 13 1997 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 6FYV ic50 = 11 nM 3NG C19 H12 Cl N3 O2 c1cc(cc(c1....
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: 3NG; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 3NG 1 1
2 E1B 0.461538 0.769231
Similar Ligands (3D)
Ligand no: 1; Ligand: 3NG; Similar ligands found: 37
No: Ligand Similarity coefficient
1 O74 0.9160
2 74U 0.9119
3 855 0.9047
4 25Q 0.9038
5 L0F 0.8964
6 2A6 0.8920
7 HM4 0.8907
8 QIG 0.8897
9 D58 0.8895
10 5F3 0.8865
11 WUL 0.8855
12 8OH 0.8810
13 6A1 0.8810
14 D4Z 0.8757
15 RBF 0.8743
16 ZRM 0.8725
17 36I 0.8709
18 JYM 0.8705
19 9KQ 0.8701
20 YDK 0.8699
21 057 0.8678
22 23D 0.8678
23 1VO 0.8674
24 E2X 0.8672
25 DZJ 0.8652
26 HXP 0.8651
27 E2F 0.8648
28 TE7 0.8647
29 7AA 0.8622
30 1VM 0.8621
31 HM5 0.8609
32 NE8 0.8604
33 C70 0.8586
34 BHF 0.8565
35 LBD 0.8562
36 C9Q 0.8556
37 B64 0.8545
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6FYV; Ligand: 3NG; Similar sites found with APoc: 48
This union binding pocket(no: 1) in the query (biounit: 6fyv.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 6G34 5ID 5.63798
2 5UIU 8CG 15.4799
3 4YZC STU 25.5193
4 4YZC STU 25.5193
5 6LUB EUX 25.8359
6 5VCV 1N1 27.0096
7 6I82 H6W 28.0255
8 3RWP ABQ 28.6174
9 3RWP ABQ 28.6174
10 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 29.0801
11 2JDR L20 29.0801
12 4QMN DB8 29.6774
13 2BDJ HET 29.7491
14 6NSP L0P 29.9663
15 4CLI 5P8 29.9694
16 6LVK EVC 30.9904
17 6LVK EVC 30.9904
18 4N70 2HX 31.4024
19 3MVH WFE 31.454
20 2GU8 796 31.7507
21 5IZF 6J9 AZ1 DAR ACA DAR NH2 31.7507
22 3TKI S25 32.8173
23 2CSN CKI 34.0067
24 6F1W CG5 34.0764
25 6F1W CG5 34.0764
26 4L3L 5FI 34.8684
27 3C0G 3AM 37.6855
28 4CRL C1I 40.3561
29 4WNP 3RJ 41.115
30 4QTB 38Z 42.1365
31 4QTB 38Z 42.1365
32 7A22 QWW 42.73
33 2JLD AG1 42.73
34 2JLD AG1 42.73
35 2JLD AG1 42.73
36 2JLD AG1 42.73
37 2XK9 XK9 43.4783
38 1PHK ATP 43.6242
39 5HQ0 LZ9 45.3642
40 1OUK 084 45.4006
41 2PVN P63 45.4545
42 2YAK OSV 45.614
43 5H8E 5Y3 45.6456
44 5H8E 5Y3 45.6456
45 2BPM 529 45.9547
46 2BPM 529 45.9547
47 6K3L 3NG 47.929
48 6XX7 ANP 48.2456
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