Receptor
PDB id Resolution Class Description Source Keywords
3WC5 1.7 Å EC: 3.4.17.2 CARBOXYPEPTIDASE B IN COMPLEX WITH DD9 SUS SCROFA SELEN ORGANOSELENIUM SELENIUM SELENOL CPB INHIBITOR SECHYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: STRUCTURAL BASIS FOR INHIBITION OF CARBOXYPEPTIDASE SELENIUM-CONTAINING INHIBITOR: SELENIUM COORDINATES IN ENZYME J.MED.CHEM. 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:401;
A:404;
A:402;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
CAC A:405;
Invalid;
none;
submit data
136.989 C2 H6 As O2 C[As]...
DDK A:403;
Valid;
none;
submit data
238.186 C8 H17 N O2 Se C(CC[...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4UIB 1.94 Å EC: 3.4.17.2 CRYSTAL STRUCTURE OF 3P IN COMPLEX WITH TAFCPB SUS SCROFA HYDROLASE TAFI THROMBOSIS FIBRINOLYSIS DRUG DISCOVERY
Ref.: NOVEL SMALL MOLECULE INHIBITORS OF ACTIVATED THROMB ACTIVATABLE FIBRINOLYSIS INHIBITOR (TAFIA) FROM NAT PRODUCT ANABAENOPEPTIN. J.MED.CHEM. V. 58 4839 2015
Members (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4UIB ic50 = 0.001 uM GWX C26 H46 N4 O4 C[C@@]12CC....
2 2PIZ ic50 = 170 nM 606 C19 H24 N3 O4 P [H]/N=C(/N....
3 5LRG - 73N DLY VAL 73O MAA PHE n/a n/a
4 1ZG7 - P20 C10 H12 Cl N3 O2 S c1cc(c(cc1....
5 2PJ4 ic50 = 13 nM 414 C24 H31 N4 O7 P [H]/N=C(/N....
6 2PJ8 ic50 = 18 nM 17A C26 H31 N2 O6 P S CC(C)[C@H]....
7 4UIA ic50 = 0.19 uM FH9 C21 H40 N4 O4 CC(C)CCNC(....
8 2PJ9 ic50 = 12 nM 281 C20 H25 N4 O6 P S2 CC(C)[C@H]....
9 1ZG9 - L06 C7 H15 N3 O2 S C(C[C@@H](....
10 2JEW Ki = 206 nM 720 C12 H21 N3 O2 CCCn1cc(nc....
11 2PJ5 ic50 = 15 nM 11B C23 H31 N4 O7 P [H]/N=C(/N....
12 3WC5 - DDK C8 H17 N O2 Se C(CC[C@@H]....
13 2PJC ic50 = 1.9 nM 343 C30 H36 N5 O9 P [H]/N=C(/N....
14 2PJA ic50 = 2.2 nM 33Z C31 H38 N5 O7 P [H]/N=C(/N....
15 1ZG8 - L98 C10 H13 N3 O2 S c1cc(cc(c1....
16 3WC7 - EF1 C21 H35 N2 O5 P CC(C)[C@H]....
17 2PJ2 ic50 = 12 nM 864 C22 H29 N2 O6 P CC(C)[C@H]....
18 5LRK - 73N DLY IIL 73O MAA PHE n/a n/a
19 2PJ3 ic50 = 6.6 nM 86A C22 H29 N4 O6 P [H]/N=C(/N....
20 2PIY ic50 = 20 nM 528 C23 H33 N2 O6 P S CC(C)[C@H]....
21 2PJ0 ic50 = 8.1 nM 922 C21 H27 N4 O7 P [H]/N=C(/N....
22 3WAB - DDW C8 H17 N O2 S C(CC[C@@H]....
23 2PJB ic50 = 19 nM 983 C31 H40 N3 O8 P S CC(C)[C@H]....
24 2PJ1 ic50 = 9.7 nM 578 C21 H27 N2 O7 P CC(C)[C@H]....
25 5LRJ - 73P DLY VAL 73O MAA PHE n/a n/a
26 2PJ6 ic50 = 49 nM 059 C22 H31 N2 O6 P S CC(C)[C@H]....
27 5ZEQ - 9B3 C9 H11 Cl N2 O2 Se c1c(cnc(c1....
28 2PJ7 ic50 = 17 nM 235 C20 H27 N2 O6 P S CC(C)[C@H]....
70% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 271 families.
1 1NSA - BEN C7 H8 N2 [H]/N=C(c1....
2 4UIB ic50 = 0.001 uM GWX C26 H46 N4 O4 C[C@@]12CC....
3 2PIZ ic50 = 170 nM 606 C19 H24 N3 O4 P [H]/N=C(/N....
4 5LRG - 73N DLY VAL 73O MAA PHE n/a n/a
5 1ZG7 - P20 C10 H12 Cl N3 O2 S c1cc(c(cc1....
6 2PJ4 ic50 = 13 nM 414 C24 H31 N4 O7 P [H]/N=C(/N....
7 2PJ8 ic50 = 18 nM 17A C26 H31 N2 O6 P S CC(C)[C@H]....
8 4UIA ic50 = 0.19 uM FH9 C21 H40 N4 O4 CC(C)CCNC(....
9 2PJ9 ic50 = 12 nM 281 C20 H25 N4 O6 P S2 CC(C)[C@H]....
10 1ZG9 - L06 C7 H15 N3 O2 S C(C[C@@H](....
11 2JEW Ki = 206 nM 720 C12 H21 N3 O2 CCCn1cc(nc....
12 2PJ5 ic50 = 15 nM 11B C23 H31 N4 O7 P [H]/N=C(/N....
13 3WC5 - DDK C8 H17 N O2 Se C(CC[C@@H]....
14 2PJC ic50 = 1.9 nM 343 C30 H36 N5 O9 P [H]/N=C(/N....
15 2PJA ic50 = 2.2 nM 33Z C31 H38 N5 O7 P [H]/N=C(/N....
16 1ZG8 - L98 C10 H13 N3 O2 S c1cc(cc(c1....
17 3WC7 - EF1 C21 H35 N2 O5 P CC(C)[C@H]....
18 2PJ2 ic50 = 12 nM 864 C22 H29 N2 O6 P CC(C)[C@H]....
19 5LRK - 73N DLY IIL 73O MAA PHE n/a n/a
20 2PJ3 ic50 = 6.6 nM 86A C22 H29 N4 O6 P [H]/N=C(/N....
21 2PIY ic50 = 20 nM 528 C23 H33 N2 O6 P S CC(C)[C@H]....
22 2PJ0 ic50 = 8.1 nM 922 C21 H27 N4 O7 P [H]/N=C(/N....
23 3WAB - DDW C8 H17 N O2 S C(CC[C@@H]....
24 2PJB ic50 = 19 nM 983 C31 H40 N3 O8 P S CC(C)[C@H]....
25 2PJ1 ic50 = 9.7 nM 578 C21 H27 N2 O7 P CC(C)[C@H]....
26 5LRJ - 73P DLY VAL 73O MAA PHE n/a n/a
27 2PJ6 ic50 = 49 nM 059 C22 H31 N2 O6 P S CC(C)[C@H]....
28 5ZEQ - 9B3 C9 H11 Cl N2 O2 Se c1c(cnc(c1....
29 2PJ7 ic50 = 17 nM 235 C20 H27 N2 O6 P S CC(C)[C@H]....
50% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 223 families.
1 1NSA - BEN C7 H8 N2 [H]/N=C(c1....
2 4UIB ic50 = 0.001 uM GWX C26 H46 N4 O4 C[C@@]12CC....
3 2PIZ ic50 = 170 nM 606 C19 H24 N3 O4 P [H]/N=C(/N....
4 5LRG - 73N DLY VAL 73O MAA PHE n/a n/a
5 1ZG7 - P20 C10 H12 Cl N3 O2 S c1cc(c(cc1....
6 2PJ4 ic50 = 13 nM 414 C24 H31 N4 O7 P [H]/N=C(/N....
7 2PJ8 ic50 = 18 nM 17A C26 H31 N2 O6 P S CC(C)[C@H]....
8 4UIA ic50 = 0.19 uM FH9 C21 H40 N4 O4 CC(C)CCNC(....
9 2PJ9 ic50 = 12 nM 281 C20 H25 N4 O6 P S2 CC(C)[C@H]....
10 1ZG9 - L06 C7 H15 N3 O2 S C(C[C@@H](....
11 2JEW Ki = 206 nM 720 C12 H21 N3 O2 CCCn1cc(nc....
12 2PJ5 ic50 = 15 nM 11B C23 H31 N4 O7 P [H]/N=C(/N....
13 3WC5 - DDK C8 H17 N O2 Se C(CC[C@@H]....
14 2PJC ic50 = 1.9 nM 343 C30 H36 N5 O9 P [H]/N=C(/N....
15 2PJA ic50 = 2.2 nM 33Z C31 H38 N5 O7 P [H]/N=C(/N....
16 1ZG8 - L98 C10 H13 N3 O2 S c1cc(cc(c1....
17 3WC7 - EF1 C21 H35 N2 O5 P CC(C)[C@H]....
18 2PJ2 ic50 = 12 nM 864 C22 H29 N2 O6 P CC(C)[C@H]....
19 5LRK - 73N DLY IIL 73O MAA PHE n/a n/a
20 2PJ3 ic50 = 6.6 nM 86A C22 H29 N4 O6 P [H]/N=C(/N....
21 2PIY ic50 = 20 nM 528 C23 H33 N2 O6 P S CC(C)[C@H]....
22 2PJ0 ic50 = 8.1 nM 922 C21 H27 N4 O7 P [H]/N=C(/N....
23 3WAB - DDW C8 H17 N O2 S C(CC[C@@H]....
24 2PJB ic50 = 19 nM 983 C31 H40 N3 O8 P S CC(C)[C@H]....
25 2PJ1 ic50 = 9.7 nM 578 C21 H27 N2 O7 P CC(C)[C@H]....
26 5LRJ - 73P DLY VAL 73O MAA PHE n/a n/a
27 2PJ6 ic50 = 49 nM 059 C22 H31 N2 O6 P S CC(C)[C@H]....
28 5ZEQ - 9B3 C9 H11 Cl N2 O2 Se c1c(cnc(c1....
29 2PJ7 ic50 = 17 nM 235 C20 H27 N2 O6 P S CC(C)[C@H]....
30 3CPA - GLY TYR n/a n/a
31 1F57 Ki = 2.3 uM DCY C3 H7 N O2 S C([C@H](C(....
32 1CPS Ki = 0.22 uM CPM C11 H16 N2 O2 S CS(=N)(=N)....
33 2CTC Ki = 0.13 mM HFA C9 H10 O3 c1ccc(cc1)....
34 2RFH Ki = 0.15 uM 23N C10 H11 N O4 c1ccc(cc1)....
35 1HDQ Ki = 1.5 uM INF C10 H12 N2 O4 c1ccc(cc1)....
36 1IY7 Ki = 0.64 uM CXA C9 H12 N2 O4 S c1ccc(cc1)....
37 3FX6 Ki = 0.16 uM BPX C12 H15 N O6 c1ccc(cc1)....
38 8CPA Ki = 710 pM AGF C21 H25 N2 O8 P C[C@@H](C(....
39 1HEE Ki = 4.6 uM LHY C10 H12 N2 O4 c1ccc(cc1)....
40 1HDU Ki = 19 uM ING C10 H12 N2 O3 c1ccc(cc1)....
41 7CPA Ki = 11 fM FVF C30 H35 N2 O8 P CC(C)[C@H]....
42 6CPA Ki = 3 pM ZAF C22 H27 N2 O8 P C[C@@H](C(....
43 1CBX Ki = 0.45 uM BZS C11 H12 O4 c1ccc(cc1)....
44 1PCA - VAL C5 H11 N O2 CC(C)[C@@H....
45 4P10 - 2B8 C14 H23 N3 O2 CCCn1cnc2c....
46 2PCU - PHE ASN ARG PRO VAL n/a n/a
47 2V77 Ki = 8.7 uM PAY C12 H18 O8 C[C@@H](C[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DDK; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 DDK 1 1
2 DDW 0.621622 0.892857
3 DLY 0.410256 0.709677
Similar Ligands (3D)
Ligand no: 1; Ligand: DDK; Similar ligands found: 47
No: Ligand Similarity coefficient
1 L06 0.9445
2 MLZ 0.9331
3 ARG 0.9230
4 SER THR 0.9171
5 IAR 0.9129
6 UN1 0.9047
7 CIR 0.9015
8 MLY 0.9013
9 EXY 0.9011
10 SN0 0.8991
11 NOT 0.8971
12 NPI 0.8961
13 NMH 0.8956
14 LYS 0.8954
15 FXY 0.8947
16 VAL VAL 0.8878
17 LPA 0.8848
18 FB6 0.8815
19 HOC 0.8814
20 PBN 0.8805
21 DIR 0.8802
22 LYN 0.8800
23 FB5 0.8796
24 SYM 0.8781
25 API 0.8750
26 3OL 0.8737
27 GGB 0.8733
28 8SZ 0.8730
29 6Q3 0.8730
30 G3H 0.8709
31 HL4 0.8685
32 ONH 0.8674
33 Z70 0.8671
34 NWH 0.8659
35 BHH 0.8653
36 1HS 0.8647
37 NNH 0.8646
38 3OM 0.8630
39 ENW 0.8621
40 G3P 0.8596
41 13P 0.8580
42 N6C 0.8575
43 C6L 0.8559
44 263 0.8533
45 9GB 0.8529
46 SEP 0.8526
47 5XA 0.8520
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4UIB; Ligand: GWX; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4uib.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
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