Receptor
PDB id Resolution Class Description Source Keywords
3MLM 2.21 Å EC: 3.1.1.4 CRYSTAL STRUCTURE OF BN IV IN COMPLEX WITH MYRISTIC ACID: A MYOTOXIC PHOSPHOLIPASE A2 FROM BOTHROPS NEUWIEDI VENOM BOTHROPS NEUWIEDI PAULOENSIS MYOTOXIN PHOSPHOLIPASE-LIKE PROTEIN HYDROLASE
Ref.: CRYSTAL STRUCTURE OF BN IV IN COMPLEX WITH MYRISTIC LYS49 MYOTOXIC PHOSPHOLIPASE A2 FROM BOTHROPS NEUWI VENOM. BIOCHIMIE V. 93 513 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MYR A:124;
B:125;
Valid;
Valid;
none;
none;
submit data
228.371 C14 H28 O2 CCCCC...
SO4 A:122;
A:123;
B:122;
B:123;
Invalid;
Invalid;
Invalid;
Invalid;
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
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.,SECT.D V. 71 2066 2015
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 1QLL - TDA C13 H26 O2 CCCCCCCCCC....
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 4YV5 Kd = 6.2 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
8 4YZ7 - 9AR C17 H11 N O8 COc1c(ccc2....
9 3QNL - ROA C18 H16 O8 c1cc(c(cc1....
10 1Y4L - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 1QLL - TDA C13 H26 O2 CCCCCCCCCC....
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 4YV5 Kd = 6.2 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
8 4YZ7 - 9AR C17 H11 N O8 COc1c(ccc2....
9 3QNL - ROA C18 H16 O8 c1cc(c(cc1....
10 1Y4L - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
11 1S8G - DAO C12 H24 O2 CCCCCCCCCC....
50% Homology Family (68)
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 1FDK - GLE C16 H32 F3 O6 P CCCCCCCCCC....
3 1MKV - GEL C20 H45 N O8 P2 CCCCCCCCOC....
4 2B96 - ANN C8 H8 O3 COc1ccc(cc....
5 4YU7 - DHC C9 H8 O4 c1cc(c(cc1....
6 3MLM - MYR C14 H28 O2 CCCCCCCCCC....
7 3CXI - VIT C29 H50 O2 Cc1c(c2c(c....
8 1XXS - STE C18 H36 O2 CCCCCCCCCC....
9 3CYL - VIT C29 H50 O2 Cc1c(c2c(c....
10 4YV5 Kd = 6.2 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
11 4YZ7 - 9AR C17 H11 N O8 COc1c(ccc2....
12 3QNL - ROA C18 H16 O8 c1cc(c(cc1....
13 1Y4L - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
14 2AZY - CHD C24 H40 O5 C[C@H](CCC....
15 1HN4 Kd = 0.15 mM MJI C22 H44 F3 O6 P CCCCCCCCCC....
16 2B01 - TUD C26 H45 N O6 S C[C@H](CCC....
17 1Y6O - MJI C22 H44 F3 O6 P CCCCCCCCCC....
18 2AZZ - TCH C26 H45 N O7 S C[C@H](CCC....
19 2B04 - CHO C26 H43 N O5 C[C@H](CCC....
20 2B00 - GCH C26 H43 N O6 C[C@H](CCC....
21 5P2P - DHG C20 H42 N O6 P CCCCCCCCCC....
22 3O4M - CAQ C6 H6 O2 c1ccc(c(c1....
23 2B03 - TUD C26 H45 N O6 S C[C@H](CCC....
24 1L8S - LPE C26 H57 N O6 P CCCCCCCCCC....
25 1FXF - MJI C22 H44 F3 O6 P CCCCCCCCCC....
26 1FX9 - MJI C22 H44 F3 O6 P CCCCCCCCCC....
27 3QLM Ki = 15.8 uM PLM C16 H32 O2 CCCCCCCCCC....
28 1POE - GEL C20 H45 N O8 P2 CCCCCCCCOC....
29 1DB4 - 8IN C21 H25 N2 O5 P Cc1c(c2cc(....
30 1KQU - BR4 C25 H33 N O3 c1ccc(cc1)....
31 5G3N ic50 = 0.012 uM X28 C23 H21 N O3 c1ccc(cc1)....
32 1KVO ic50 = 0.013 uM OAP C31 H37 N O3 S c1ccc(cc1)....
33 1J1A ic50 = 0.029 uM BHP C31 H37 N O4 c1ccc(cc1)....
34 4UY1 ic50 = 20 uM TJM C10 H11 N3 O S Cc1cc(c(s1....
35 5G3M ic50 = 24 uM 9JH C14 H13 N O c1ccc(cc1)....
36 2QVD Kd = 0.00000145 M BER C20 H18 N O4 COc1ccc2cc....
37 1ZWP - NIM C13 H12 N2 O5 S CS(=O)(=O)....
38 1OXL - IDA C15 H18 N2 O3 CCCc1cc2cc....
39 1TG4 - PHE LEU ALA TYR LYS n/a n/a
40 1SKG - VAL ALA PHE ARG SER n/a n/a
41 1JQ9 Kd = 3.57 nM PHE LEU SER TYR LYS n/a n/a
42 2ARM Ki = 7.4 nM OIN C17 H23 N O3 CN1[C@H]2C....
43 1FV0 Kd = 1.18 uM 9AR C17 H11 N O8 COc1c(ccc2....
44 1Q7A Kd = 0.064 uM OPB C19 H20 N2 O3 CCCC[C@H]1....
45 1TG1 - PHQ LEU VAL ARG TYR n/a n/a
46 1ZYX - LCF C23 H22 Cl N O2 CC1(Cc2c(c....
47 1TJK - PHE LEU SER THR LYS n/a n/a
48 1KPM Ki = 1.59 uM VIT C29 H50 O2 Cc1c(c2c(c....
49 1TDV - TYR TRP ALA ALA ALA ALA n/a n/a
50 1TJ9 - VAL ALA ARG SER n/a n/a
51 1JQ8 Ki = 1.01 uM LEU ALA ILE TYR SER n/a n/a
52 1SQZ - PHQ ILE ALA ARG SER n/a n/a
53 1TGM - AIN C9 H8 O4 CC(=O)Oc1c....
54 1ZR8 - AJM C18 H22 N2 O2 C[N@]1c2cc....
55 1TH6 - OIN C17 H23 N O3 CN1[C@H]2C....
56 1Y38 - G3P C3 H9 O6 P C([C@H](CO....
57 3H1X Kd = 0.00000145 M IMN C19 H16 Cl N O4 Cc1c(c2cc(....
58 1SXK - BHA C7 H7 N O3 c1cc(c(cc1....
59 1TK4 - ALA ILE ARG SER n/a n/a
60 1SV3 - ANN C8 H8 O3 COc1ccc(cc....
61 2QHD - DAO C12 H24 O2 CCCCCCCCCC....
62 3BJW - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
63 1S8G - DAO C12 H24 O2 CCCCCCCCCC....
64 1POB - GEL C20 H45 N O8 P2 CCCCCCCCOC....
65 1TD7 Kd = 43 uM NFL C13 H9 F3 N2 O2 c1cc(cc(c1....
66 1OXR Kd = 0.00000145 M AIN C9 H8 O4 CC(=O)Oc1c....
67 2WQ5 Kd = 180 uM MIY C23 H27 N3 O7 CN(C)c1ccc....
68 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: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 F23 1 1
3 11A 1 1
4 STE 1 1
5 KNA 1 1
6 TDA 1 1
7 DCR 1 1
8 DAO 1 1
9 DKA 1 1
10 PLM 1 1
11 F15 1 1
12 OCA 0.956522 1
13 SHV 0.833333 0.952381
14 KTC 0.793103 0.875
15 AZ1 0.73913 0.64
16 6NA 0.72 0.904762
17 NER 0.71875 0.954545
18 OLA 0.71875 0.954545
19 ELA 0.71875 0.954545
20 VCA 0.666667 0.954545
21 PAM 0.666667 0.954545
22 PML 0.625 0.6
23 3LA 0.606061 0.8
24 LEA 0.6 0.809524
25 MYZ 0.588235 0.909091
26 12H 0.586207 0.615385
27 ODD 0.567568 0.913043
28 BRC 0.566667 0.666667
29 14V 0.555556 0.740741
30 M12 0.545455 0.869565
31 14U 0.542857 0.703704
32 EIC 0.538462 0.913043
33 EOD 0.538462 0.7
34 BUA 0.48 0.666667
35 RCL 0.468085 0.84
36 HXD 0.459459 0.807692
37 56S 0.459459 0.653846
38 ODT 0.452381 0.782609
39 3X1 0.444444 0.818182
40 LNL 0.44186 0.826087
41 CNS 0.435897 0.68
42 6UL 0.435897 0.68
43 5UF 0.432432 0.807692
44 243 0.428571 0.807692
45 GYM 0.418605 0.606061
46 PL3 0.413793 0.75
47 O8N 0.413793 0.75
48 1DO 0.413793 0.75
49 F09 0.413793 0.75
50 OC9 0.413793 0.75
51 DE1 0.413793 0.75
52 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: 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 95 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4YV5; Ligand: SVR; Similar sites found: 47
This union binding pocket(no: 2) in the query (biounit: 4yv5.bio1) has 105 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4OAS 2SW 0.0001702 0.56374 None
2 4LWU 20U 0.0005282 0.53666 None
3 4HBM 0Y7 0.002358 0.49656 None
4 1LNX URI 0.009244 0.48844 None
5 4WT2 3UD 0.002923 0.45853 None
6 4WG0 CHD 0.02837 0.45721 None
7 2GBB CIT 0.03749 0.44849 None
8 3KMZ EQO 0.0157 0.42719 None
9 2EV1 OLA 0.03185 0.42164 None
10 4OAR 2S0 0.008709 0.45575 1.63934
11 2HHP FLC 0.00007757 0.60233 4.09836
12 3I6B KDO 0.04732 0.4423 4.09836
13 2PZI AXX 0.04015 0.43583 4.09836
14 5K0S 0OU 0.04857 0.42227 4.09836
15 3E2M E2M 0.04352 0.40631 4.09836
16 3TDC 0EU 0.0006837 0.59349 4.91803
17 1NHZ 486 0.003487 0.47615 4.91803
18 2WPX ACO 0.02235 0.43748 4.91803
19 4ITH RCM 0.04485 0.41892 4.91803
20 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 0.01816 0.47594 5.7377
21 2JHP GUN 0.0154 0.45965 5.7377
22 1DKF BMS 0.007695 0.45244 5.7377
23 4XPL ACO 0.02818 0.43505 5.7377
24 3FEI CTM 0.01789 0.43163 5.7377
25 4EIL FOL 0.04775 0.42546 5.7377
26 3SP6 IL2 0.03945 0.42444 5.7377
27 5B4B LP5 0.01945 0.41855 5.7377
28 4I67 G G G RPC 0.01449 0.46491 5.74713
29 1J78 OLA 0.01963 0.4687 6.55738
30 2YOO K2B 0.04852 0.41965 6.55738
31 3L9R L9Q 0.01667 0.41367 8.16327
32 3B6C SDN 0.0006816 0.55324 8.19672
33 1XVB 3BR 0.03689 0.44136 8.19672
34 1TMX HGX 0.03976 0.41917 8.19672
35 3QCP FAD 0.0331 0.41403 8.19672
36 1M2Z BOG 0.0007373 0.57003 9.01639
37 1TV5 N8E 0.02181 0.46716 9.83607
38 5IXK 6EW 0.02865 0.40706 9.83607
39 4YSX E23 0.01791 0.46797 10.6557
40 2BJ4 OHT 0.006571 0.46204 10.6557
41 4TV1 36M 0.03645 0.44924 10.6557
42 3W54 RNB 0.02122 0.44166 10.6557
43 2CNT COA 0.04367 0.40824 13.1148
44 3QKD HI0 0.02921 0.41885 17.2131
45 3RV5 DXC 0.01673 0.40392 24.7191
46 1K7L 544 0.01501 0.43043 28.5714
47 2NPA MMB 0.0245 0.42992 40
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