Receptor
PDB id Resolution Class Description Source Keywords
1UU9 1.95 Å EC: 2.7.11.1 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-3 SPODOPTERA FRUGIPERDA PROTEIN KINASE PKB PDK1 INHIBITOR LY333531 BISINDOLYL MBIM-1 DIABETES CANCER TRANSFERASE SERINE/THREONINE-PROTKINASE
Ref.: INTERACTIONS OF LY333531 AND OTHER BISINDOLYL MALEI INHIBITORS WITH PDK1 STRUCTURE V. 12 215 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BI3 A:1370;
Valid;
none;
ic50 = 3.8 uM
384.431 C23 H20 N4 O2 c1ccc...
GOL A:1357;
A:1358;
A:1359;
A:1360;
A:1361;
A:1362;
A:1363;
A:1364;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:1365;
A:1366;
A:1367;
A:1368;
A:1369;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
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
3RWP 1.92 Å EC: 2.7.11.1 DISCOVERY OF A NOVEL, POTENT AND SELECTIVE INHIBITOR OF 3- PHOSPHOINOSITIDE DEPENDENT KINASE (PDK1) HOMO SAPIENS KINASE DOMAIN TRANSFERASE PHOSPHOSERINE: SEP TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: DISCOVERY OF NOVEL, POTENT, AND SELECTIVE INHIBITOR 3-PHOSPHOINOSITIDE-DEPENDENT KINASE (PDK1). J.MED.CHEM. V. 54 8490 2011
Members (45)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 125 families.
1 2BIY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 1UU9 ic50 = 3.8 uM BI3 C23 H20 N4 O2 c1ccc2c(c1....
3 5LVO - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 4XX9 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 2XCK ic50 = 713 nM MH4 C29 H33 N9 O Cc1cc(ccn1....
6 3QD4 IC50 = 6.31 nM 3Q6 C22 H30 N8 O2 C[C@@H]1C[....
7 3RCJ ic50 = 0.8 uM 3RC C16 H13 N5 c1ccc(cc1)....
8 2PE0 - 39Z C14 H12 N2 O2 CC(c1ccc[n....
9 4CT2 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
10 5ACK - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
11 3HRC - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
12 5LVM - ADE C5 H5 N5 c1[nH]c2c(....
13 5MRD ic50 = 36.4 uM S26 C18 H13 Cl N2 O4 S2 CCOC(=O)C1....
14 3ION ic50 = 8 nM 8H1 C28 H27 N5 O3 COc1cc2c3c....
15 1UU7 ic50 = 14 uM BI2 C27 H26 N4 O2 C[N@@]1CCC....
16 3HRF Kd = 10.3 uM P47 C17 H15 Cl O2 c1ccc(cc1)....
17 3QCS IC50 = 0.316 uM 3Q1 C15 H17 N7 O c1cc2c(cc1....
18 1H1W - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
19 4AW1 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
20 2PE2 - 464 C28 H30 N6 O3 c1cc(cc(c1....
21 3H9O ic50 = 70 nM 9BD C19 H19 N5 O3 COCCOc1cc2....
22 3QD3 ic50 = 0.00000001 M 3Q5 C22 H30 N8 O2 C[C@H]1CC[....
23 1OKY ic50 = 6.5 nM STU C28 H26 N4 O3 C[C@@]12[C....
24 3IOP ic50 = 17 nM 8I1 C28 H27 N5 O3 COc1cc2c3c....
25 2PE1 ic50 = 6 nM 517 C15 H14 N4 O2 CC(c1ccc[n....
26 3RWP Ki = 0.6 nM ABQ C24 H24 F N7 O2 CC(C)n1cc(....
27 3NAX - MP7 C28 H22 F2 N4 O4 c1ccc(cc1)....
28 3QCQ IC50 = 0.158 uM 3Q0 C13 H15 N7 CCNc1cc(nc....
29 4A06 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
30 1Z5M ic50 = 30 nM LI8 C23 H31 Br N8 O3 CC(C)(C(=O....
31 5HKM ic50 = 0.013 uM 61Y C16 H15 N7 CCc1cc(nc(....
32 3QD0 IC50 = 3.16 nM 3Q4 C24 H26 N8 O C[C@@H]1CC....
33 3ORZ - BI4 C27 H26 N4 O2 C[N@]1CCC[....
34 5LVN Kd = 20 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
35 2XCH ic50 = 374 nM CKG C22 H25 N7 O c1c2c(nc(n....
36 4AW0 - MJF C18 H15 Cl O5 c1ccc(cc1)....
37 3OTU - BI4 C27 H26 N4 O2 C[N@]1CCC[....
38 3QCX ic50 = 63 nM 3Q2 C16 H19 N7 O C[C@@H]1CO....
39 1UU3 ic50 = 0.75 uM LY4 C28 H28 N4 O3 CN(C)C[C@@....
40 5LVL Kd = 1.25 uM 537 C14 H8 N2 O c1ccc2c(c1....
41 3QC4 ic50 = 0.002 uM MP7 C28 H22 F2 N4 O4 c1ccc(cc1)....
42 3QCY ic50 = 20 nM 3Q3 C22 H22 N8 O2 c1ccc(cc1)....
43 1UU8 ic50 = 9 uM BI1 C25 H24 N4 O2 CN(C)CCCn1....
44 4CT1 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
45 4A07 - AZ7 C17 H13 Cl3 N2 O2 c1cc(ccc1[....
70% Homology Family (45)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 95 families.
1 2BIY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 1UU9 ic50 = 3.8 uM BI3 C23 H20 N4 O2 c1ccc2c(c1....
3 5LVO - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 4XX9 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 2XCK ic50 = 713 nM MH4 C29 H33 N9 O Cc1cc(ccn1....
6 3QD4 IC50 = 6.31 nM 3Q6 C22 H30 N8 O2 C[C@@H]1C[....
7 3RCJ ic50 = 0.8 uM 3RC C16 H13 N5 c1ccc(cc1)....
8 2PE0 - 39Z C14 H12 N2 O2 CC(c1ccc[n....
9 4CT2 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
10 5ACK - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
11 3HRC - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
12 5LVM - ADE C5 H5 N5 c1[nH]c2c(....
13 5MRD ic50 = 36.4 uM S26 C18 H13 Cl N2 O4 S2 CCOC(=O)C1....
14 3ION ic50 = 8 nM 8H1 C28 H27 N5 O3 COc1cc2c3c....
15 1UU7 ic50 = 14 uM BI2 C27 H26 N4 O2 C[N@@]1CCC....
16 3HRF Kd = 10.3 uM P47 C17 H15 Cl O2 c1ccc(cc1)....
17 3QCS IC50 = 0.316 uM 3Q1 C15 H17 N7 O c1cc2c(cc1....
18 1H1W - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
19 4AW1 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
20 2PE2 - 464 C28 H30 N6 O3 c1cc(cc(c1....
21 3H9O ic50 = 70 nM 9BD C19 H19 N5 O3 COCCOc1cc2....
22 3QD3 ic50 = 0.00000001 M 3Q5 C22 H30 N8 O2 C[C@H]1CC[....
23 1OKY ic50 = 6.5 nM STU C28 H26 N4 O3 C[C@@]12[C....
24 3IOP ic50 = 17 nM 8I1 C28 H27 N5 O3 COc1cc2c3c....
25 2PE1 ic50 = 6 nM 517 C15 H14 N4 O2 CC(c1ccc[n....
26 3RWP Ki = 0.6 nM ABQ C24 H24 F N7 O2 CC(C)n1cc(....
27 3NAX - MP7 C28 H22 F2 N4 O4 c1ccc(cc1)....
28 3QCQ IC50 = 0.158 uM 3Q0 C13 H15 N7 CCNc1cc(nc....
29 4A06 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
30 1Z5M ic50 = 30 nM LI8 C23 H31 Br N8 O3 CC(C)(C(=O....
31 5HKM ic50 = 0.013 uM 61Y C16 H15 N7 CCc1cc(nc(....
32 3QD0 IC50 = 3.16 nM 3Q4 C24 H26 N8 O C[C@@H]1CC....
33 3ORZ - BI4 C27 H26 N4 O2 C[N@]1CCC[....
34 5LVN Kd = 20 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
35 2XCH ic50 = 374 nM CKG C22 H25 N7 O c1c2c(nc(n....
36 4AW0 - MJF C18 H15 Cl O5 c1ccc(cc1)....
37 3OTU - BI4 C27 H26 N4 O2 C[N@]1CCC[....
38 3QCX ic50 = 63 nM 3Q2 C16 H19 N7 O C[C@@H]1CO....
39 1UU3 ic50 = 0.75 uM LY4 C28 H28 N4 O3 CN(C)C[C@@....
40 5LVL Kd = 1.25 uM 537 C14 H8 N2 O c1ccc2c(c1....
41 3QC4 ic50 = 0.002 uM MP7 C28 H22 F2 N4 O4 c1ccc(cc1)....
42 3QCY ic50 = 20 nM 3Q3 C22 H22 N8 O2 c1ccc(cc1)....
43 1UU8 ic50 = 9 uM BI1 C25 H24 N4 O2 CN(C)CCCn1....
44 4CT1 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
45 4A07 - AZ7 C17 H13 Cl3 N2 O2 c1cc(ccc1[....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1REK Ki = 200 nM B8L C32 H36 N2 O7 CC[C@H](C)....
2 2Z7S - P01 C19 H25 Cl N6 O CC(C)[C@H]....
3 2BIY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 1UU9 ic50 = 3.8 uM BI3 C23 H20 N4 O2 c1ccc2c(c1....
5 1O6L - GLY ARG PRO ARG THR THR SER PHE ALA GLU n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BI3; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 BI3 1 1
2 BI1 0.808219 0.8
3 BI2 0.655172 0.8
4 BI4 0.655172 0.8
5 DRN 0.511364 0.777778
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3RWP; Ligand: ABQ; Similar sites found with APoc: 86
This union binding pocket(no: 1) in the query (biounit: 3rwp.bio2) has 77 residues
No: Leader PDB Ligand Sequence Similarity
1 4OAV ACP 7.71704
2 4OAV ACP 7.71704
3 4O1P ANP 8.03859
4 4O1P ANP 8.03859
5 4O1P ANP 8.03859
6 4O1P ANP 8.03859
7 6FYL 3NG 20.2572
8 6FYV 3NG 28.6174
9 4GJ3 0XP 29.1391
10 5X8I SQZ 29.2605
11 5X8I SQZ 29.2605
12 5DBX ANP 29.9035
13 3LXN MI1 29.9035
14 5DBX ANP 29.9035
15 4QTB 38Z 29.9035
16 4H3P ANP 30.2251
17 4H3P ANP 30.2251
18 4E1Z 0MX 30.2405
19 5WNL STU 30.5466
20 5WNL STU 30.5466
21 6JKM ADP 30.5466
22 4K33 ACP 31.1897
23 6K0J CQO 31.5113
24 5Y86 HRM 32.4759
25 2WU6 DKI 32.4759
26 2Y6O 1N1 32.9897
27 5MJA 7O3 33.4426
28 5MJA 7O3 33.4426
29 3PLS ANP 33.557
30 3RI1 3RH 33.7621
31 2PVF ACP 34.0836
32 3SRV S19 34.296
33 3SRV S19 34.296
34 3GQI ACP 34.4051
35 3HMO STU 34.4051
36 3HMO STU 34.4051
37 1U5R ATP 34.7267
38 1U5R ATP 34.7267
39 1U5R ATP 34.7267
40 1U59 STU 35.5401
41 2A19 ANP 35.5634
42 2X2M X2M 35.6913
43 2X2M X2M 35.6913
44 6N33 622 36.6559
45 3BU5 ATP 38.2353
46 1IR3 ANP 38.2353
47 4BHN BH9 40.5145
48 1BYG STU 40.6475
49 6K3L 3NG 40.8284
50 6JQR C6F 41.4791
51 3IGO ANP 41.4791
52 4YZC STU 41.8006
53 4YZC STU 41.8006
54 2B9I ADP 41.8006
55 2B9H ADP 41.8006
56 2B9J ADP 41.8006
57 1UNH IXM 42.4658
58 1UNH IXM 42.4658
59 3O0G 3O0 42.4658
60 3PTG 932 42.7653
61 4UX9 ANP 43.0868
62 4UX9 ANP 43.0868
63 4UX9 ANP 43.0868
64 6CMJ F6J 43.0868
65 6CMJ F6J 43.0868
66 4CFU 2WC 43.2343
67 4CFU 2WC 43.2343
68 6GUE FB8 43.3775
69 6GUE FB8 43.3775
70 2V7O DRN 43.4084
71 4BCM T7Z 43.5216
72 4BCQ TJF 43.5216
73 4BCN T9N 43.6667
74 4BCN T9N 43.6667
75 5LMK 6ZK 44.1077
76 5HQ0 LZ9 44.3709
77 2VN9 GVD 45.1827
78 2VN9 GVD 45.1827
79 2ZV2 609 45.302
80 2F57 23D 45.3376
81 6HK4 G8E 45.6592
82 4NM5 ADP 45.9807
83 4NM5 ADP 45.9807
84 1PHK ATP 48.3221
85 4L9I 8PR 48.8746
86 4L9I 8PR 48.8746
Pocket No.: 2; Query (leader) PDB : 3RWP; Ligand: ABQ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3rwp.bio2) has 77 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3RWP; Ligand: ABQ; Similar sites found with APoc: 94
This union binding pocket(no: 3) in the query (biounit: 3rwp.bio1) has 77 residues
No: Leader PDB Ligand Sequence Similarity
1 4OAV ACP 7.71704
2 4OAV ACP 7.71704
3 4O1P ANP 8.03859
4 4O1P ANP 8.03859
5 4O1P ANP 8.03859
6 4O1P ANP 8.03859
7 6FYL 3NG 20.2572
8 6FYV 3NG 28.6174
9 4GJ3 0XP 29.1391
10 5X8I SQZ 29.2605
11 5X8I SQZ 29.2605
12 5DBX ANP 29.9035
13 3LXN MI1 29.9035
14 5DBX ANP 29.9035
15 4QTB 38Z 29.9035
16 4H3P ANP 30.2251
17 4H3P ANP 30.2251
18 4E1Z 0MX 30.2405
19 5WNL STU 30.5466
20 5WNL STU 30.5466
21 6JKM ADP 30.5466
22 2CSN CKI 30.9764
23 4K33 ACP 31.1897
24 6K0J CQO 31.5113
25 5JGA 6KC 32.4759
26 5Y86 HRM 32.4759
27 2WU6 DKI 32.4759
28 2Y6O 1N1 32.9897
29 5MJA 7O3 33.4426
30 5MJA 7O3 33.4426
31 3PLS ANP 33.557
32 3RI1 3RH 33.7621
33 3RI1 3RH 33.7621
34 2PVF ACP 34.0836
35 3SRV S19 34.296
36 3SRV S19 34.296
37 3GQI ACP 34.4051
38 3HMO STU 34.4051
39 3HMO STU 34.4051
40 4EWH T77 34.5455
41 4EWH T77 34.5455
42 1U5R ATP 34.7267
43 1U5R ATP 34.7267
44 1U5R ATP 34.7267
45 1U59 STU 35.5401
46 2A19 ANP 35.5634
47 2X2M X2M 35.6913
48 2X2M X2M 35.6913
49 6N33 622 36.6559
50 6A1G 9OL 37.9421
51 3BU5 ATP 38.2353
52 1IR3 ANP 38.2353
53 4BHN BH9 40.5145
54 1BYG STU 40.6475
55 6K3L 3NG 40.8284
56 6JQR C6F 41.4791
57 5BYZ 4WE 41.4791
58 3IGO ANP 41.4791
59 4YZC STU 41.8006
60 4YZC STU 41.8006
61 2B9I ADP 41.8006
62 2B9H ADP 41.8006
63 2B9J ADP 41.8006
64 1UNH IXM 42.4658
65 1UNH IXM 42.4658
66 3O0G 3O0 42.4658
67 3PTG 932 42.7653
68 4UX9 ANP 43.0868
69 4UX9 ANP 43.0868
70 4UX9 ANP 43.0868
71 6CMJ F6J 43.0868
72 6CMJ F6J 43.0868
73 4CFU 2WC 43.2343
74 4CFU 2WC 43.2343
75 6GUE FB8 43.3775
76 6GUE FB8 43.3775
77 2V7O DRN 43.4084
78 4BCM T7Z 43.5216
79 4BCQ TJF 43.5216
80 4BCN T9N 43.6667
81 4BCN T9N 43.6667
82 5LMK 6ZK 44.1077
83 5HQ0 LZ9 44.3709
84 2VN9 GVD 45.1827
85 2VN9 GVD 45.1827
86 2ZV2 609 45.302
87 2F57 23D 45.3376
88 6HK4 G8E 45.6592
89 4NM5 ADP 45.9807
90 4NM5 ADP 45.9807
91 2JLD AG1 45.9807
92 1PHK ATP 48.3221
93 4L9I 8PR 48.8746
94 4L9I 8PR 48.8746
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