Receptor
PDB id Resolution Class Description Source Keywords
6B80 1.95 Å EC: 3.1.1.4 CRYSTAL STRUCTURE OF MYOTOXIN II FROM BOTHROPS MOOJENI COMPL MYRISTIC ACID BOTHROPS MOOJENI MYOTOXIN II PHOSPHOLIPASE A2-LIKE BOTHROPS MOOJENI TOXIN
Ref.: STRUCTURAL EVIDENCE FOR A FATTY ACID-INDEPENDENT MY MECHANISM FOR A PHOSPHOLIPASE A2-LIKE TOXIN. BIOCHIM BIOPHYS ACTA V.1866 473 2018 PROTEINS PROTEOM
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PRO PHE CYS LYS LYS ALA ASP PRO CYS B:125;
A:125;
Invalid;
Invalid;
none;
none;
submit data n/a n/a n/a n/a
SO4 B:204;
A:202;
A:204;
A:203;
B:203;
B:205;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
PE4 B:202;
Invalid;
none;
submit data
354.436 C16 H34 O8 CCOCC...
MYR A:201;
B:201;
Valid;
Valid;
none;
none;
submit data
228.371 C14 H28 O2 CCCCC...
View in 3D viewer
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 (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 5VFM Kd = 150 uM HC4 C9 H8 O3 c1cc(ccc1C....
2 1QLL - TDA C13 H26 O2 CCCCCCCCCC....
3 4YU7 - DHC C9 H8 O4 c1cc(c(cc1....
4 3MLM - MYR C14 H28 O2 CCCCCCCCCC....
5 3CXI - VIT C29 H50 O2 Cc1c(c2c(c....
6 1XXS - STE C18 H36 O2 CCCCCCCCCC....
7 3CYL - VIT C29 H50 O2 Cc1c(c2c(c....
8 6B81 - OCA C8 H16 O2 CCCCCCCC(=....
9 6DIK - GKP C22 H18 O12 c1c(cc(c(c....
10 6B80 - MYR C14 H28 O2 CCCCCCCCCC....
11 5VFJ Kd = 20 uM DHC C9 H8 O4 c1cc(c(cc1....
12 6B83 - 6NA C6 H12 O2 CCCCCC(=O)....
13 4YV5 Kd = 6.2 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
14 4YZ7 - 9AR C17 H11 N O8 COc1c(ccc2....
15 3QNL - ROA C18 H16 O8 c1cc(c(cc1....
16 1Y4L - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
70% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 5VFM Kd = 150 uM HC4 C9 H8 O3 c1cc(ccc1C....
2 1QLL - TDA C13 H26 O2 CCCCCCCCCC....
3 4YU7 - DHC C9 H8 O4 c1cc(c(cc1....
4 3MLM - MYR C14 H28 O2 CCCCCCCCCC....
5 3CXI - VIT C29 H50 O2 Cc1c(c2c(c....
6 1XXS - STE C18 H36 O2 CCCCCCCCCC....
7 3CYL - VIT C29 H50 O2 Cc1c(c2c(c....
8 6B81 - OCA C8 H16 O2 CCCCCCCC(=....
9 6DIK - GKP C22 H18 O12 c1c(cc(c(c....
10 6B80 - MYR C14 H28 O2 CCCCCCCCCC....
11 5VFJ Kd = 20 uM DHC C9 H8 O4 c1cc(c(cc1....
12 6B83 - 6NA C6 H12 O2 CCCCCC(=O)....
13 4YV5 Kd = 6.2 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
14 4YZ7 - 9AR C17 H11 N O8 COc1c(ccc2....
15 3QNL - ROA C18 H16 O8 c1cc(c(cc1....
16 1Y4L - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
17 6CE2 Kd = 0.5 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
18 1S8G - DAO C12 H24 O2 CCCCCCCCCC....
50% Homology Family (84)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 1U4J - MAN C6 H12 O6 C([C@@H]1[....
2 4YU7 - DHC C9 H8 O4 c1cc(c(cc1....
3 3MLM - MYR C14 H28 O2 CCCCCCCCCC....
4 3CXI - VIT C29 H50 O2 Cc1c(c2c(c....
5 1XXS - STE C18 H36 O2 CCCCCCCCCC....
6 3CYL - VIT C29 H50 O2 Cc1c(c2c(c....
7 6B81 - OCA C8 H16 O2 CCCCCCCC(=....
8 6DIK - GKP C22 H18 O12 c1c(cc(c(c....
9 6B80 - MYR C14 H28 O2 CCCCCCCCCC....
10 5VFJ Kd = 20 uM DHC C9 H8 O4 c1cc(c(cc1....
11 6B83 - 6NA C6 H12 O2 CCCCCC(=O)....
12 4YV5 Kd = 6.2 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
13 4YZ7 - 9AR C17 H11 N O8 COc1c(ccc2....
14 3QNL - ROA C18 H16 O8 c1cc(c(cc1....
15 1Y4L - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
16 1FDK - GLE C16 H32 F3 O6 P CCCCCCCCCC....
17 1MKV - GEL C20 H45 N O8 P2 CCCCCCCCOC....
18 2B96 - ANN C8 H8 O3 COc1ccc(cc....
19 5OW8 ic50 = 6.9 uM AYN C16 H11 F3 N2 O c1ccc2c(c1....
20 4UY1 ic50 = 20 uM TJM C10 H11 N3 O S Cc1cc(c(s1....
21 5OWC ic50 = 0.026 uM AYZ C19 H15 F3 N2 O4 c1cc(cc(c1....
22 5G3M ic50 = 24 uM 9JH C14 H13 N O c1ccc(cc1)....
23 2AZY - CHD C24 H40 O5 C[C@H](CCC....
24 1HN4 Kd = 0.15 mM MJI C22 H44 F3 O6 P CCCCCCCCCC....
25 2B01 - TUD C26 H45 N O6 S C[C@H](CCC....
26 1Y6O - MJI C22 H44 F3 O6 P CCCCCCCCCC....
27 2AZZ - TCH C26 H45 N O7 S C[C@H](CCC....
28 2B04 - CHO C26 H43 N O5 C[C@H](CCC....
29 2B00 - GCH C26 H43 N O6 C[C@H](CCC....
30 5P2P - DHG C20 H42 N O6 P CCCCCCCCCC....
31 3O4M - CAQ C6 H6 O2 c1ccc(c(c1....
32 2B03 - TUD C26 H45 N O6 S C[C@H](CCC....
33 1L8S - LPE C26 H57 N O6 P CCCCCCCCCC....
34 1FXF - MJI C22 H44 F3 O6 P CCCCCCCCCC....
35 1FX9 - MJI C22 H44 F3 O6 P CCCCCCCCCC....
36 3QLM Ki = 15.8 uM PLM C16 H32 O2 CCCCCCCCCC....
37 1POE - GEL C20 H45 N O8 P2 CCCCCCCCOC....
38 1DB4 - 8IN C21 H25 N2 O5 P Cc1c(c2cc(....
39 1KQU - BR4 C25 H33 N O3 c1ccc(cc1)....
40 5G3N ic50 = 0.012 uM X28 C23 H21 N O3 c1ccc(cc1)....
41 1KVO ic50 = 0.013 uM OAP C31 H37 N O3 S c1ccc(cc1)....
42 1J1A ic50 = 0.029 uM BHP C31 H37 N O4 c1ccc(cc1)....
43 6CE2 Kd = 0.5 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
44 2QVD Kd = 0.00000145 M BER C20 H18 N O4 COc1ccc2cc....
45 1ZWP - NIM C13 H12 N2 O5 S CS(=O)(=O)....
46 1OXL - IDA C15 H18 N2 O3 CCCc1cc2cc....
47 1TG4 - PHE LEU ALA TYR LYS n/a n/a
48 1SKG - VAL ALA PHE ARG SER n/a n/a
49 1JQ9 Kd = 3.57 nM PHE LEU SER TYR LYS n/a n/a
50 2ARM Ki = 7.4 nM OIN C17 H23 N O3 CN1[C@H]2C....
51 1FV0 Kd = 1.18 uM 9AR C17 H11 N O8 COc1c(ccc2....
52 1Q7A Kd = 0.064 uM OPB C19 H20 N2 O3 CCCC[C@H]1....
53 1TG1 - PHQ LEU VAL ARG TYR n/a n/a
54 1ZYX - LCF C23 H22 Cl N O2 CC1(Cc2c(c....
55 1TJK - PHE LEU SER THR LYS n/a n/a
56 1KPM Ki = 1.59 uM VIT C29 H50 O2 Cc1c(c2c(c....
57 1TP2 - TDA C13 H26 O2 CCCCCCCCCC....
58 1TDV - TYR TRP ALA ALA ALA ALA n/a n/a
59 1TJ9 - VAL ALA ARG SER n/a n/a
60 1JQ8 Ki = 1.01 uM LEU ALA ILE TYR SER n/a n/a
61 1SQZ - PHQ ILE ALA ARG SER n/a n/a
62 1TGM - AIN C9 H8 O4 CC(=O)Oc1c....
63 1ZR8 - AJM C18 H22 N2 O2 C[N@]1c2cc....
64 1TH6 - OIN C17 H23 N O3 CN1[C@H]2C....
65 1Y38 - G3P C3 H9 O6 P C([C@H](CO....
66 3H1X Kd = 0.00000145 M IMN C19 H16 Cl N O4 Cc1c(c2cc(....
67 1SXK - BHA C7 H7 N O3 c1cc(c(cc1....
68 1TK4 - ALA ILE ARG SER n/a n/a
69 1SV3 - ANN C8 H8 O3 COc1ccc(cc....
70 5WZW ic50 = 1.23 uM U8D C22 H27 N2 O5 P CCc1c(c2cc....
71 5WZU ic50 = 0.1 uM 7W3 C21 H17 F3 N2 O5 Cc1c(c2c(n....
72 5WZT ic50 = 0.22 uM 7W6 C20 H17 Br N2 O5 Cc1c(c2c(n....
73 5WZS ic50 = 0.28 uM 7W9 C24 H20 N2 O5 Cc1c(c2c(n....
74 5Y5E - 7W3 C21 H17 F3 N2 O5 Cc1c(c2c(n....
75 5WZV ic50 = 0.21 uM 7W0 C26 H22 N2 O5 Cc1c(c2c(n....
76 6G5J ic50 = 15 nM EM8 C20 H17 F3 N2 O4 C[C@H](CC(....
77 2QHD - DAO C12 H24 O2 CCCCCCCCCC....
78 3BJW - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
79 1S8G - DAO C12 H24 O2 CCCCCCCCCC....
80 1POB - GEL C20 H45 N O8 P2 CCCCCCCCOC....
81 1TD7 Kd = 43 uM NFL C13 H9 F3 N2 O2 c1cc(cc(c1....
82 1OXR Kd = 0.00000145 M AIN C9 H8 O4 CC(=O)Oc1c....
83 2WQ5 Kd = 180 uM MIY C23 H27 N3 O7 CN(C)c1ccc....
84 1MF4 Ki = 10.2 nM VAL ALA PHE ARG SER n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MYR; Similar ligands found: 62
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 EW8 1 1
3 TDA 1 1
4 F15 1 1
5 PLM 1 1
6 STE 1 1
7 X90 1 1
8 DAO 1 1
9 KNA 1 1
10 DCR 1 1
11 F23 1 1
12 11A 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 OLA 0.71875 0.954545
21 NER 0.71875 0.954545
22 VCA 0.666667 0.954545
23 PAM 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 EIC 0.538462 0.913043
35 EOD 0.538462 0.7
36 D0G 0.5 0.954545
37 BMJ 0.5 0.954545
38 BNV 0.5 0.954545
39 BUA 0.48 0.666667
40 RCL 0.468085 0.84
41 FTT 0.459459 0.807692
42 HXD 0.459459 0.807692
43 56S 0.459459 0.653846
44 ODT 0.452381 0.782609
45 3X1 0.444444 0.818182
46 LNL 0.44186 0.826087
47 9J6 0.441176 0.666667
48 OOA 0.441176 0.76
49 CUY 0.435897 0.68
50 6UL 0.435897 0.68
51 CNS 0.435897 0.68
52 5UF 0.432432 0.807692
53 243 0.428571 0.807692
54 1QW 0.418605 0.606061
55 GYM 0.418605 0.606061
56 O8N 0.413793 0.75
57 1DO 0.413793 0.75
58 PL3 0.413793 0.75
59 OC9 0.413793 0.75
60 DE1 0.413793 0.75
61 F09 0.413793 0.75
62 T25 0.403846 0.677419
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4yv5.bio1) has 108 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4YV5; Ligand: SVR; 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: 4yv5.bio1) has 117 residues
No: Leader PDB Ligand Sequence Similarity
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