Receptor
PDB id Resolution Class Description Source Keywords
1QLL 2.04 Å EC: 3.1.1.4 PIRATOXIN-II (PRTX-II) - A K49 PLA2 FROM BOTHROPS PIRAJAI BOTHROPS PIRAJAI NEUROTOXIN K49 PHOSPHOLIPASE A2 (PLA2)
Ref.: STRUCTURAL BASIS FOR LOW CATALYTIC ACTIVITY IN LYS4 PHOSPHOLIPASES A2-A HYPOTHESIS: THE CRYSTAL STRUCTU PIRATOXIN II COMPLEXED TO FATTY ACID BIOCHEMISTRY V. 40 28 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
TDA A:122;
B:122;
 Valid;
Valid;
 none;
none;
 submit data
214.344 C13 H26 O2 CCCCC...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4YV5 1.9 Å EC: 3.1.1.4 CRYSTAL STRUCTURE OF MYOTOXIN II FROM BOTHROPS MOOJENI COMPL SURAMIN BOTHROPS MOOJENI BOTHROPS MOOJENI MYOTOXIN II LYS49-PLA2 SURAMIN TOXIN
Ref.: STRUCTURAL AND FUNCTIONAL EVIDENCE FOR MEMBRANE DOC DISRUPTION SITES ON PHOSPHOLIPASE A2-LIKE PROTEINS BY COMPLEXATION WITH THE INHIBITOR SURAMIN. ACTA CRYSTALLOGR. D BIOL. V. 71 2066 2015 CRYSTALLOGR.
Members (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 5VFM Kd = 150 uM HC4 C9 H8 O3 c1cc(ccc1C....
2 1QLL - TDA C13 H26 O2 CCCCCCCCCC....
3 6MQD - ROA C18 H16 O8 c1cc(c(cc1....
4 4YU7 - DHC C9 H8 O4 c1cc(c(cc1....
5 3MLM - MYR C14 H28 O2 CCCCCCCCCC....
6 3CXI - VIT C29 H50 O2 Cc1c(c2c(c....
7 1XXS - STE C18 H36 O2 CCCCCCCCCC....
8 6PWH - VRD C21 H20 N2 O5 CCc1c(c2c(....
9 3CYL - VIT C29 H50 O2 Cc1c(c2c(c....
10 6MQF - AIN C9 H8 O4 CC(=O)Oc1c....
11 6B81 - OCA C8 H16 O2 CCCCCCCC(=....
12 6DIK - GKP C22 H18 O12 c1c(cc(c(c....
13 6B80 - MYR C14 H28 O2 CCCCCCCCCC....
14 5VFJ Kd = 20 uM DHC C9 H8 O4 c1cc(c(cc1....
15 6B83 - 6NA C6 H12 O2 CCCCCC(=O)....
16 4YV5 Kd = 0.6 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
17 4YZ7 - 9AR C17 H11 N O8 COc1c(ccc2....
18 3QNL - ROA C18 H16 O8 c1cc(c(cc1....
19 1Y4L - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 5VFM Kd = 150 uM HC4 C9 H8 O3 c1cc(ccc1C....
2 1QLL - TDA C13 H26 O2 CCCCCCCCCC....
3 6MQD - ROA C18 H16 O8 c1cc(c(cc1....
4 4YU7 - DHC C9 H8 O4 c1cc(c(cc1....
5 3MLM - MYR C14 H28 O2 CCCCCCCCCC....
6 3CXI - VIT C29 H50 O2 Cc1c(c2c(c....
7 1XXS - STE C18 H36 O2 CCCCCCCCCC....
8 6PWH - VRD C21 H20 N2 O5 CCc1c(c2c(....
9 3CYL - VIT C29 H50 O2 Cc1c(c2c(c....
10 6MQF - AIN C9 H8 O4 CC(=O)Oc1c....
11 6B81 - OCA C8 H16 O2 CCCCCCCC(=....
12 6DIK - GKP C22 H18 O12 c1c(cc(c(c....
13 6B80 - MYR C14 H28 O2 CCCCCCCCCC....
14 5VFJ Kd = 20 uM DHC C9 H8 O4 c1cc(c(cc1....
15 6B83 - 6NA C6 H12 O2 CCCCCC(=O)....
16 4YV5 Kd = 0.6 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
17 4YZ7 - 9AR C17 H11 N O8 COc1c(ccc2....
18 3QNL - ROA C18 H16 O8 c1cc(c(cc1....
19 1Y4L - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
20 6CE2 Kd = 0.5 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
21 1S8G - DAO C12 H24 O2 CCCCCCCCCC....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 5VFM Kd = 150 uM HC4 C9 H8 O3 c1cc(ccc1C....
2 1QLL - TDA C13 H26 O2 CCCCCCCCCC....
3 6MQD - ROA C18 H16 O8 c1cc(c(cc1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: TDA; Similar ligands found: 64
No: Ligand ECFP6 Tc MDL keys Tc
1 PLM 1 1
2 STE 1 1
3 MYR 1 1
4 TDA 1 1
5 F23 1 1
6 DAO 1 1
7 X90 1 1
8 DCR 1 1
9 KNA 1 1
10 11A 1 1
11 EW8 1 1
12 F15 1 1
13 DKA 1 1
14 OCA 0.956522 1
15 SHV 0.833333 0.952381
16 KTC 0.793103 0.875
17 AZ1 0.73913 0.64
18 6NA 0.72 0.904762
19 ELA 0.71875 0.954545
20 NER 0.71875 0.954545
21 OLA 0.71875 0.954545
22 PAM 0.666667 0.954545
23 VCA 0.666667 0.954545
24 PML 0.625 0.6
25 3LA 0.606061 0.8
26 LEA 0.6 0.809524
27 MYZ 0.588235 0.909091
28 12H 0.586207 0.615385
29 ODD 0.567568 0.913043
30 BRC 0.566667 0.666667
31 14V 0.555556 0.740741
32 M12 0.545455 0.869565
33 14U 0.542857 0.703704
34 EOD 0.538462 0.7
35 EIC 0.538462 0.913043
36 BMJ 0.5 0.954545
37 BNV 0.5 0.954545
38 D0G 0.5 0.954545
39 BUA 0.48 0.666667
40 RCL 0.468085 0.84
41 FTT 0.459459 0.807692
42 56S 0.459459 0.653846
43 HXD 0.459459 0.807692
44 T4T 0.459459 0.8
45 ODT 0.452381 0.782609
46 3X1 0.444444 0.818182
47 LNL 0.44186 0.826087
48 9J6 0.441176 0.666667
49 OOA 0.441176 0.76
50 CUY 0.435897 0.68
51 CNS 0.435897 0.68
52 6UL 0.435897 0.68
53 5UF 0.432432 0.807692
54 243 0.428571 0.807692
55 EKG 0.418605 0.606061
56 GYM 0.418605 0.606061
57 1QW 0.418605 0.606061
58 OC9 0.413793 0.75
59 PL3 0.413793 0.75
60 F09 0.413793 0.75
61 DE1 0.413793 0.75
62 1DO 0.413793 0.75
63 O8N 0.413793 0.75
64 T25 0.403846 0.677419
Similar Ligands (3D)
Ligand no: 1; Ligand: TDA; Similar ligands found: 9
No: Ligand Similarity coefficient
1 TER 0.9287
2 SSV 0.9257
3 C14 0.9227
4 BDD 0.9222
5 ACA ACA 0.9214
6 MD2 0.9067
7 SP5 0.9028
8 SPM 0.8980
9 Q9C 0.8617
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YV5; Ligand: SVR; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 4yv5.bio1) has 118 residues
No: Leader PDB Ligand Sequence Similarity
1 6LM1 OCT 18.8525
2 6LM1 D10 18.8525
Pocket No.: 2; Query (leader) PDB : 4YV5; Ligand: SVR; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 4yv5.bio1) has 124 residues
No: Leader PDB Ligand Sequence Similarity
1 6LM1 OCT 18.8525
2 6LM1 D10 18.8525
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