Receptor
PDB id Resolution Class Description Source Keywords
4BCP 2.26 Å EC: 2.7.11.22 STRUCTURE OF CDK2 IN COMPLEX WITH CYCLIN A AND A 2-AMINO-4- HETEROARYL-PYRIMIDINE INHIBITOR HOMO SAPIENS TRANSFERASE-CELL CYCLE COMPLEX CDK-CYCLIN COMPLEX CYCLIN-INHIBITOR STRUCTURE-BASED DRUG DESIGN
Ref.: SUBSTITUTED 4-(THIAZOL-5-YL)-2-(PHENYLAMINO)PYRIMID HIGHLY ACTIVE CDK9 INHIBITORS: SYNTHESIS, X-RAY CRY STRUCTURE, SAR AND ANTI-CANCER ACTIVITIES. J.MED.CHEM. V. 56 640 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
T3C C:1297;
A:1299;
 Valid;
Valid;
 none;
none;
 Ki = 568 nM
420.534 C21 H24 N8 S Cc1c(...
SGM B:1434;
B:1435;
D:1434;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
108.159 C3 H8 O2 S C([C@...
SO4 D:1433;
B:1433;
 Invalid;
Invalid;
 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
2BPM 2.4 Å EC: 2.7.11.22 STRUCTURE OF CDK2-CYCLIN A WITH PHA-630529 HOMO SAPIENS PROTEIN KINASE TRANSFERASE SERINE/THREONINE-PROTEIN KINASEPHOSPHORYLATION CELL DIVISION CYCLIN
Ref.: 3-AMINOPYRAZOLE INHIBITORS OF CDK2-CYCLIN A AS ANTI AGENTS. 2. LEAD OPTIMIZATION J.MED.CHEM. V. 48 2944 2005
Members (57)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 4CFN ic50 = 49 uM JYM C13 H16 F3 N5 O C1CCC(CC1)....
2 3BHU ic50 = 0.003 uM MHR C14 H15 N5 O CCCOc1ccnc....
3 1E9H ic50 = 35 nM INR C16 H10 N2 O5 S c1ccc2c(c1....
4 4EOL - 1RO C18 H13 N3 O S2 c1cc2cc(cc....
5 1OIU ic50 = 0.21 uM N76 C18 H22 N6 O3 S c1cc(cc(c1....
6 3BHV ic50 = 0.08 uM VAR C14 H11 N7 O c1cnc(n2c1....
7 4EOQ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
8 2G9X ic50 = 45 nM NU5 C23 H32 N6 O4 S c1cc(ccc1N....
9 3MY5 ic50 = 65 uM RFZ C12 H12 Cl2 N2 O4 c1c2c(cc(c....
10 1P5E - TBS C6 H Br4 N3 c12c(c(c(c....
11 2IW6 ic50 = 0.14 uM QQ2 C24 H27 Cl N6 O2 Cc1ccc(c(c....
12 1OKV ic50 = 0.68 uM ARG ARG LEU ILE PHE NH2 n/a n/a
13 1H1R ic50 = 2.3 uM 6CP C18 H20 Cl N5 O c1cc(cc(c1....
14 1OKW ic50 = 5.6 uM ACE ARG ARG LEU ASN FCL NH2 n/a n/a
15 1OI9 ic50 = 69 nM N20 C18 H21 N5 O2 c1cc(ccc1N....
16 4EON - 1RO C18 H13 N3 O S2 c1cc2cc(cc....
17 4EOJ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
18 2UZE ic50 = 47 uM C95 C15 H10 N2 O4 S [H]/N=C/1N....
19 1PKD - UCN C28 H26 N4 O4 C[C@@]12[C....
20 4CFV ic50 = 23.5 uM 75X C19 H23 N5 O2 Cc1c(cccc1....
21 6GUC Kd = 25 nM SU9 C13 H11 N3 O2 COc1ccc2c(....
22 3BHT ic50 = 0.011 uM MFR C12 H11 N5 O COc1ccnc2c....
23 2IW8 ic50 = 103 nM 4SP C18 H22 N6 O3 S c1cc(ccc1N....
24 4BCO Ki = 0.131 uM T6Q C23 H26 N8 O S Cc1c(sc(n1....
25 2UUE ic50 = 1.3 uM ARG LEU ILE PFF NH2 GVC n/a n/a
26 1FIN - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
27 4EOI - 1RO C18 H13 N3 O S2 c1cc2cc(cc....
28 4II5 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
29 1VYW ic50 = 37 nM 292 C18 H17 N3 O c1ccc2cc(c....
30 2UZL ic50 = 0.61 uM C94 C15 H10 F3 N3 O4 S2 [H]/N=C/1N....
31 1H24 Kd = 0.5 uM PRO VAL LYS ARG ARG LEU ASP LEU GLU n/a n/a
32 1H1Q ic50 = 1 uM 2A6 C18 H21 N5 O c1ccc(cc1)....
33 3DDQ ic50 = 0.21 uM RRC C19 H26 N6 O CC[C@H](CO....
34 2WEV ic50 = 30 uM ACE ARG ARG B3L MEA NH2 n/a n/a
35 1OIY ic50 = 64 nM N41 C19 H22 N6 O2 c1cc(ccc1C....
36 4I3Z Kd = 51.3 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
37 4EOP - 1RO C18 H13 N3 O S2 c1cc2cc(cc....
38 6GVA ic50 = 5 nM FCQ C22 H25 N7 S CC(C)c1c2c....
39 2C5O ic50 = 6.5 uM CK2 C9 H10 N4 S Cc1c(sc(n1....
40 2WIH ic50 = 0.045 uM P48 C25 H32 N8 O CC1(Cc2cnc....
41 2IW9 ic50 = 8.9 nM 4SP C18 H22 N6 O3 S c1cc(ccc1N....
42 4EOO - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
43 2BPM ic50 = 2 nM 529 C18 H19 N5 O2 C[C@@H](c1....
44 1H1S Ki = 6 nM 4SP C18 H22 N6 O3 S c1cc(ccc1N....
45 2C5N ic50 = 0.22 uM CK8 C17 H19 N5 S Cc1c(sc(n1....
46 4BCP Ki = 568 nM T3C C21 H24 N8 S Cc1c(sc(n1....
47 3F5X ic50 = 1040 nM EZV C25 H25 N7 CN1CCN(CC1....
48 3QHR - PRO LYS THR PRO LYS LYS ALA LYS LYS LEU n/a n/a
49 4BCK Ki = 0.004 uM T3E C16 H15 N7 O2 S2 Cc1c(sc(n1....
50 1H1P Ki = 12 uM CMG C12 H17 N5 O c1[nH]c2c(....
51 4EOR Ki = 500 nM 4SP C18 H22 N6 O3 S c1cc(ccc1N....
52 1QMZ - HIS HIS ALA SER PRO ARG LYS n/a n/a
53 4EOM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
54 2CJM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
55 3QHW - PRO LYS THR PRO LYS LYS ALA LYS LYS LEU n/a n/a
56 3TNW - F18 C9 H10 N6 O c1cc(ccc1/....
57 4CFW ic50 = 0.51 uM SQ9 C19 H24 N6 O3 S Cc1c(cccc1....
70% Homology Family (57)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 4CFN ic50 = 49 uM JYM C13 H16 F3 N5 O C1CCC(CC1)....
2 3BHU ic50 = 0.003 uM MHR C14 H15 N5 O CCCOc1ccnc....
3 1E9H ic50 = 35 nM INR C16 H10 N2 O5 S c1ccc2c(c1....
4 4EOL - 1RO C18 H13 N3 O S2 c1cc2cc(cc....
5 1OIU ic50 = 0.21 uM N76 C18 H22 N6 O3 S c1cc(cc(c1....
6 3BHV ic50 = 0.08 uM VAR C14 H11 N7 O c1cnc(n2c1....
7 4EOQ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
8 2G9X ic50 = 45 nM NU5 C23 H32 N6 O4 S c1cc(ccc1N....
9 3MY5 ic50 = 65 uM RFZ C12 H12 Cl2 N2 O4 c1c2c(cc(c....
10 1P5E - TBS C6 H Br4 N3 c12c(c(c(c....
11 2IW6 ic50 = 0.14 uM QQ2 C24 H27 Cl N6 O2 Cc1ccc(c(c....
12 1OKV ic50 = 0.68 uM ARG ARG LEU ILE PHE NH2 n/a n/a
13 1H1R ic50 = 2.3 uM 6CP C18 H20 Cl N5 O c1cc(cc(c1....
14 1OKW ic50 = 5.6 uM ACE ARG ARG LEU ASN FCL NH2 n/a n/a
15 1OI9 ic50 = 69 nM N20 C18 H21 N5 O2 c1cc(ccc1N....
16 4EON - 1RO C18 H13 N3 O S2 c1cc2cc(cc....
17 4EOJ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
18 2UZE ic50 = 47 uM C95 C15 H10 N2 O4 S [H]/N=C/1N....
19 1PKD - UCN C28 H26 N4 O4 C[C@@]12[C....
20 4CFV ic50 = 23.5 uM 75X C19 H23 N5 O2 Cc1c(cccc1....
21 6GUC Kd = 25 nM SU9 C13 H11 N3 O2 COc1ccc2c(....
22 3BHT ic50 = 0.011 uM MFR C12 H11 N5 O COc1ccnc2c....
23 2IW8 ic50 = 103 nM 4SP C18 H22 N6 O3 S c1cc(ccc1N....
24 4BCO Ki = 0.131 uM T6Q C23 H26 N8 O S Cc1c(sc(n1....
25 2UUE ic50 = 1.3 uM ARG LEU ILE PFF NH2 GVC n/a n/a
26 1FIN - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
27 4EOI - 1RO C18 H13 N3 O S2 c1cc2cc(cc....
28 4II5 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
29 1VYW ic50 = 37 nM 292 C18 H17 N3 O c1ccc2cc(c....
30 2UZL ic50 = 0.61 uM C94 C15 H10 F3 N3 O4 S2 [H]/N=C/1N....
31 1H24 Kd = 0.5 uM PRO VAL LYS ARG ARG LEU ASP LEU GLU n/a n/a
32 1H1Q ic50 = 1 uM 2A6 C18 H21 N5 O c1ccc(cc1)....
33 3DDQ ic50 = 0.21 uM RRC C19 H26 N6 O CC[C@H](CO....
34 2WEV ic50 = 30 uM ACE ARG ARG B3L MEA NH2 n/a n/a
35 1OIY ic50 = 64 nM N41 C19 H22 N6 O2 c1cc(ccc1C....
36 4I3Z Kd = 51.3 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
37 4EOP - 1RO C18 H13 N3 O S2 c1cc2cc(cc....
38 6GVA ic50 = 5 nM FCQ C22 H25 N7 S CC(C)c1c2c....
39 2C5O ic50 = 6.5 uM CK2 C9 H10 N4 S Cc1c(sc(n1....
40 2WIH ic50 = 0.045 uM P48 C25 H32 N8 O CC1(Cc2cnc....
41 2IW9 ic50 = 8.9 nM 4SP C18 H22 N6 O3 S c1cc(ccc1N....
42 4EOO - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
43 2BPM ic50 = 2 nM 529 C18 H19 N5 O2 C[C@@H](c1....
44 1H1S Ki = 6 nM 4SP C18 H22 N6 O3 S c1cc(ccc1N....
45 2C5N ic50 = 0.22 uM CK8 C17 H19 N5 S Cc1c(sc(n1....
46 4BCP Ki = 568 nM T3C C21 H24 N8 S Cc1c(sc(n1....
47 3F5X ic50 = 1040 nM EZV C25 H25 N7 CN1CCN(CC1....
48 3QHR - PRO LYS THR PRO LYS LYS ALA LYS LYS LEU n/a n/a
49 4BCK Ki = 0.004 uM T3E C16 H15 N7 O2 S2 Cc1c(sc(n1....
50 1H1P Ki = 12 uM CMG C12 H17 N5 O c1[nH]c2c(....
51 4EOR Ki = 500 nM 4SP C18 H22 N6 O3 S c1cc(ccc1N....
52 1QMZ - HIS HIS ALA SER PRO ARG LYS n/a n/a
53 4EOM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
54 2CJM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
55 3QHW - PRO LYS THR PRO LYS LYS ALA LYS LYS LEU n/a n/a
56 3TNW - F18 C9 H10 N6 O c1cc(ccc1/....
57 4CFW ic50 = 0.51 uM SQ9 C19 H24 N6 O3 S Cc1c(cccc1....
50% Homology Family (57)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 4CFN ic50 = 49 uM JYM C13 H16 F3 N5 O C1CCC(CC1)....
2 3BHU ic50 = 0.003 uM MHR C14 H15 N5 O CCCOc1ccnc....
3 1E9H ic50 = 35 nM INR C16 H10 N2 O5 S c1ccc2c(c1....
4 4EOL - 1RO C18 H13 N3 O S2 c1cc2cc(cc....
5 1OIU ic50 = 0.21 uM N76 C18 H22 N6 O3 S c1cc(cc(c1....
6 3BHV ic50 = 0.08 uM VAR C14 H11 N7 O c1cnc(n2c1....
7 4EOQ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
8 2G9X ic50 = 45 nM NU5 C23 H32 N6 O4 S c1cc(ccc1N....
9 3MY5 ic50 = 65 uM RFZ C12 H12 Cl2 N2 O4 c1c2c(cc(c....
10 1P5E - TBS C6 H Br4 N3 c12c(c(c(c....
11 2IW6 ic50 = 0.14 uM QQ2 C24 H27 Cl N6 O2 Cc1ccc(c(c....
12 1OKV ic50 = 0.68 uM ARG ARG LEU ILE PHE NH2 n/a n/a
13 1H1R ic50 = 2.3 uM 6CP C18 H20 Cl N5 O c1cc(cc(c1....
14 1OKW ic50 = 5.6 uM ACE ARG ARG LEU ASN FCL NH2 n/a n/a
15 1OI9 ic50 = 69 nM N20 C18 H21 N5 O2 c1cc(ccc1N....
16 4EON - 1RO C18 H13 N3 O S2 c1cc2cc(cc....
17 4EOJ - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
18 2UZE ic50 = 47 uM C95 C15 H10 N2 O4 S [H]/N=C/1N....
19 1PKD - UCN C28 H26 N4 O4 C[C@@]12[C....
20 4CFV ic50 = 23.5 uM 75X C19 H23 N5 O2 Cc1c(cccc1....
21 6GUC Kd = 25 nM SU9 C13 H11 N3 O2 COc1ccc2c(....
22 3BHT ic50 = 0.011 uM MFR C12 H11 N5 O COc1ccnc2c....
23 2IW8 ic50 = 103 nM 4SP C18 H22 N6 O3 S c1cc(ccc1N....
24 4BCO Ki = 0.131 uM T6Q C23 H26 N8 O S Cc1c(sc(n1....
25 2UUE ic50 = 1.3 uM ARG LEU ILE PFF NH2 GVC n/a n/a
26 1FIN - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
27 4EOI - 1RO C18 H13 N3 O S2 c1cc2cc(cc....
28 4II5 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
29 1VYW ic50 = 37 nM 292 C18 H17 N3 O c1ccc2cc(c....
30 2UZL ic50 = 0.61 uM C94 C15 H10 F3 N3 O4 S2 [H]/N=C/1N....
31 1H24 Kd = 0.5 uM PRO VAL LYS ARG ARG LEU ASP LEU GLU n/a n/a
32 1H1Q ic50 = 1 uM 2A6 C18 H21 N5 O c1ccc(cc1)....
33 3DDQ ic50 = 0.21 uM RRC C19 H26 N6 O CC[C@H](CO....
34 2WEV ic50 = 30 uM ACE ARG ARG B3L MEA NH2 n/a n/a
35 1OIY ic50 = 64 nM N41 C19 H22 N6 O2 c1cc(ccc1C....
36 4I3Z Kd = 51.3 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
37 4EOP - 1RO C18 H13 N3 O S2 c1cc2cc(cc....
38 6GVA ic50 = 5 nM FCQ C22 H25 N7 S CC(C)c1c2c....
39 2C5O ic50 = 6.5 uM CK2 C9 H10 N4 S Cc1c(sc(n1....
40 2WIH ic50 = 0.045 uM P48 C25 H32 N8 O CC1(Cc2cnc....
41 2IW9 ic50 = 8.9 nM 4SP C18 H22 N6 O3 S c1cc(ccc1N....
42 4EOO - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
43 2BPM ic50 = 2 nM 529 C18 H19 N5 O2 C[C@@H](c1....
44 1H1S Ki = 6 nM 4SP C18 H22 N6 O3 S c1cc(ccc1N....
45 2C5N ic50 = 0.22 uM CK8 C17 H19 N5 S Cc1c(sc(n1....
46 4BCP Ki = 568 nM T3C C21 H24 N8 S Cc1c(sc(n1....
47 3F5X ic50 = 1040 nM EZV C25 H25 N7 CN1CCN(CC1....
48 3QHR - PRO LYS THR PRO LYS LYS ALA LYS LYS LEU n/a n/a
49 4BCK Ki = 0.004 uM T3E C16 H15 N7 O2 S2 Cc1c(sc(n1....
50 1H1P Ki = 12 uM CMG C12 H17 N5 O c1[nH]c2c(....
51 4EOR Ki = 500 nM 4SP C18 H22 N6 O3 S c1cc(ccc1N....
52 1QMZ - HIS HIS ALA SER PRO ARG LYS n/a n/a
53 4EOM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
54 2CJM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
55 3QHW - PRO LYS THR PRO LYS LYS ALA LYS LYS LEU n/a n/a
56 3TNW - F18 C9 H10 N6 O c1cc(ccc1/....
57 4CFW ic50 = 0.51 uM SQ9 C19 H24 N6 O3 S Cc1c(cccc1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: T3C; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 T3C 1 1
2 T6Q 0.708738 0.833333
3 T9N 0.583333 0.61194
4 TJF 0.526786 0.757143
Similar Ligands (3D)
Ligand no: 1; Ligand: T3C; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2BPM; Ligand: 529; Similar sites found with APoc: 30
This union binding pocket(no: 1) in the query (biounit: 2bpm.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
1 6AC9 ANP 12.2977
2 6AC9 ANP 12.2977
3 6JKM ADP 24.2718
4 3H9R TAK 29.4498
5 4Y8D 49J 32.3625
6 1JPA ANP 33.3333
7 1U5R ATP 33.657
8 6F3G CJN 34.2373
9 6F3G CJN 34.2373
10 5LPB ADP 34.4595
11 5HVJ ANP 35.2751
12 3CY2 MB9 35.9223
13 1BYG STU 37.4101
14 3SRV S19 38.9892
15 3M2W L8I 39.1304
16 5LVP ATP 42.7184
17 3KN5 ANP 42.7184
18 2WEL K88 43.6893
19 4DC2 ADE 43.6893
20 6PJX SGV 44.0129
21 2VN9 GVD 44.8505
22 2VN9 GVD 44.8505
23 6QF4 ADP 45.3074
24 6FYV 3NG 45.9547
25 1Q8Y ADE 46.6019
26 3C0G 3AM 46.9256
27 6FYL 3NG 46.9256
28 4IJP 1EH 48.2201
29 2YAB AMP 48.2201
30 6A1G 9OL 48.8673
Pocket No.: 2; Query (leader) PDB : 2BPM; Ligand: 529; Similar sites found with APoc: 44
This union binding pocket(no: 2) in the query (biounit: 2bpm.bio2) has 53 residues
No: Leader PDB Ligand Sequence Similarity
1 6AC9 ANP 12.2977
2 6AC9 ANP 12.2977
3 6JKM ADP 24.2718
4 3H9R TAK 29.4498
5 4Y8D 49J 32.3625
6 3FC2 IBI 32.6861
7 1JPA ANP 33.3333
8 5Y80 IRE 33.3333
9 1U5R ATP 33.657
10 2HY0 306 33.657
11 5WNL STU 33.9806
12 6F3G CJN 34.2373
13 6F3G CJN 34.2373
14 5LPB ADP 34.4595
15 3BU5 ATP 34.9673
16 5HVJ ANP 35.2751
17 3CY2 MB9 35.9223
18 6LVK EVC 36.246
19 1BYG STU 37.4101
20 2A19 ANP 38.3803
21 3SRV S19 38.9892
22 3M2W L8I 39.1304
23 3KN5 ANP 42.7184
24 5LVP ATP 42.7184
25 5LVP ATP 42.7184
26 5LVP ATP 42.7184
27 2WEL K88 43.6893
28 5UPK ANP 43.6893
29 5DBX ANP 43.6893
30 2VN9 GVD 44.8505
31 2VN9 GVD 44.8505
32 6QF4 ADP 45.3074
33 6FYV 3NG 45.9547
34 1Q8Y ADE 46.6019
35 3DAK ANP 46.8966
36 3DAK ANP 46.8966
37 6FYL 3NG 46.9256
38 3C0G 3AM 46.9256
39 1PHK ATP 46.9799
40 5X8I SQZ 47.5728
41 5X8I SQZ 47.5728
42 4IJP 1EH 48.2201
43 6A1G 9OL 48.8673
44 2YAK OSV 49.8246
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