Receptor
PDB id Resolution Class Description Source Keywords
1TK4 1.1 Å EC: 3.1.1.4 CRYSTAL STRUCTURE OF RUSSELLS VIPER PHOSPHOLIPASE A2 IN COMPLEX WITH A SPECIFICALLY DESIGNED TETRAPEPTIDE ALA-ILE- A RG-SER AT 1.1 A RESOLUTION DABOIA RUSSELLII PULCHELLA CRYSTAL STRUCTURE TETRAPEPTIDE PHOSPHOLIPASE A2 HYDROLASE
Ref.: CRYSTAL STRUCTURE OF RUSSELLS VIPER PHOSPHOLIPASE A2 WITH A SPECIFICALLY DESIGNED TETRAPEPTIDE ALA-ILE-ARG-SER AT 1.1 A RESOLUTION TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ALA ILE ARG SER B:1;
 Valid;
 none;
 submit data
431.538 n/a O=C(N...
SO4 A:301;
A:302;
A:303;
 Invalid;
Invalid;
Invalid;
 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
1JQ9 1.8 Å EC: 3.1.1.4 CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN PHOSPHOLIPASE DABOIA RUSSELLI PULCHELLA AND A DESIGNED PENTAPEPTIDE PHE-LT YR-LYS AT 1.8 RESOLUTION DABOIA RUSSELLII PULCHELLA PHOSPHOLIPASE A2 DABOIA RUSSELLI PULCHELLA NEUROTOXIC DESPEPTIDE HYDROLASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN A SNA PHOSPHOLIPASE A2 AND A POTENT PEPTIDE INHIBITOR PHE-LEU-SER-TYR-LYS AT 1.8 A RESOLUTION J.BIOL.CHEM. V. 277 41079 2002
Members (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 2QVD Kd = 0.000000064 M BER C20 H18 N O4 COc1ccc2cc....
2 1ZWP - NIM C13 H12 N2 O5 S CS(=O)(=O)....
3 1OXL - IDA C15 H18 N2 O3 CCCc1cc2cc....
4 1TG4 - PHE LEU ALA TYR LYS n/a n/a
5 1SKG - VAL ALA PHE ARG SER n/a n/a
6 1JQ9 Kd = 3.57 nM PHE LEU SER TYR LYS n/a n/a
7 2ARM Kd = 0.000000064 M OIN C17 H23 N O3 CN1[C@H]2C....
8 1FV0 Ki = 1.18 uM 9AR C17 H11 N O8 COc1c(ccc2....
9 1Q7A Kd = 0.000000064 M OPB C19 H20 N2 O3 CCCC[C@H]1....
10 1TG1 - PHQ LEU VAL ARG TYR n/a n/a
11 1ZYX - LCF C23 H22 Cl N O2 CC1(Cc2c(c....
12 1TJK - PHE LEU SER THR LYS n/a n/a
13 1KPM Ki = 1.59 uM VIT C29 H50 O2 Cc1c(c2c(c....
14 1TP2 - TDA C13 H26 O2 CCCCCCCCCC....
15 1TDV - TYR TRP ALA ALA ALA ALA n/a n/a
16 1TJ9 - VAL ALA ARG SER n/a n/a
17 1JQ8 Ki = 1.01 uM LEU ALA ILE TYR SER n/a n/a
18 1SQZ - PHQ ILE ALA ARG SER n/a n/a
19 1TGM - AIN C9 H8 O4 CC(=O)Oc1c....
20 1ZR8 - AJM C18 H22 N2 O2 C[N@]1c2cc....
21 1TH6 - OIN C17 H23 N O3 CN1[C@H]2C....
22 1Y38 - G3P C3 H9 O6 P C([C@H](CO....
23 3H1X Kd = 0.000000064 M IMN C19 H16 Cl N O4 Cc1c(c2cc(....
24 1SXK - BHA C7 H7 N O3 c1cc(c(cc1....
25 1TK4 - ALA ILE ARG SER n/a n/a
26 1SV3 - ANN C8 H8 O3 COc1ccc(cc....
70% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 2QVD Kd = 0.000000064 M BER C20 H18 N O4 COc1ccc2cc....
2 1ZWP - NIM C13 H12 N2 O5 S CS(=O)(=O)....
3 1OXL - IDA C15 H18 N2 O3 CCCc1cc2cc....
4 1TG4 - PHE LEU ALA TYR LYS n/a n/a
5 1SKG - VAL ALA PHE ARG SER n/a n/a
6 1JQ9 Kd = 3.57 nM PHE LEU SER TYR LYS n/a n/a
7 2ARM Kd = 0.000000064 M OIN C17 H23 N O3 CN1[C@H]2C....
8 1FV0 Ki = 1.18 uM 9AR C17 H11 N O8 COc1c(ccc2....
9 1Q7A Kd = 0.000000064 M OPB C19 H20 N2 O3 CCCC[C@H]1....
10 1TG1 - PHQ LEU VAL ARG TYR n/a n/a
11 1ZYX - LCF C23 H22 Cl N O2 CC1(Cc2c(c....
12 1TJK - PHE LEU SER THR LYS n/a n/a
13 1KPM Ki = 1.59 uM VIT C29 H50 O2 Cc1c(c2c(c....
14 1TP2 - TDA C13 H26 O2 CCCCCCCCCC....
15 1TDV - TYR TRP ALA ALA ALA ALA n/a n/a
16 1TJ9 - VAL ALA ARG SER n/a n/a
17 1JQ8 Ki = 1.01 uM LEU ALA ILE TYR SER n/a n/a
18 1SQZ - PHQ ILE ALA ARG SER n/a n/a
19 1TGM - AIN C9 H8 O4 CC(=O)Oc1c....
20 1ZR8 - AJM C18 H22 N2 O2 C[N@]1c2cc....
21 1TH6 - OIN C17 H23 N O3 CN1[C@H]2C....
22 1Y38 - G3P C3 H9 O6 P C([C@H](CO....
23 3H1X Kd = 0.000000064 M IMN C19 H16 Cl N O4 Cc1c(c2cc(....
24 1SXK - BHA C7 H7 N O3 c1cc(c(cc1....
25 1TK4 - ALA ILE ARG SER n/a n/a
26 1SV3 - ANN C8 H8 O3 COc1ccc(cc....
27 2QHD - DAO C12 H24 O2 CCCCCCCCCC....
28 3BJW - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
50% Homology Family (86)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 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 6PWH - VRD C21 H20 N2 O5 CCc1c(c2c(....
7 3CYL - VIT C29 H50 O2 Cc1c(c2c(c....
8 6MQF - AIN C9 H8 O4 CC(=O)Oc1c....
9 6B81 - OCA C8 H16 O2 CCCCCCCC(=....
10 6DIK - GKP C22 H18 O12 c1c(cc(c(c....
11 6B80 - MYR C14 H28 O2 CCCCCCCCCC....
12 5VFJ Kd = 20 uM DHC C9 H8 O4 c1cc(c(cc1....
13 6B83 - 6NA C6 H12 O2 CCCCCC(=O)....
14 4YV5 Kd = 0.6 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
15 4YZ7 - 9AR C17 H11 N O8 COc1c(ccc2....
16 3QNL - ROA C18 H16 O8 c1cc(c(cc1....
17 1Y4L - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
18 1FDK - GLE C16 H32 F3 O6 P CCCCCCCCCC....
19 1MKV - GEL C20 H45 N O8 P2 CCCCCCCCOC....
20 2B96 - ANN C8 H8 O3 COc1ccc(cc....
21 5OW8 ic50 = 6.9 uM AYN C16 H11 F3 N2 O c1ccc2c(c1....
22 4UY1 ic50 = 20 uM TJM C10 H11 N3 O S Cc1cc(c(s1....
23 5OWC ic50 = 0.026 uM AYZ C19 H15 F3 N2 O4 c1cc(cc(c1....
24 5G3M ic50 = 2.2 uM 9JH C14 H13 N O c1ccc(cc1)....
25 2AZY - CHD C24 H40 O5 C[C@H](CCC....
26 1HN4 Kd = 0.15 mM MJI C22 H44 F3 O6 P CCCCCCCCCC....
27 2B01 - TUD C26 H45 N O6 S C[C@H](CCC....
28 1Y6O - MJI C22 H44 F3 O6 P CCCCCCCCCC....
29 2AZZ - TCH C26 H45 N O7 S C[C@H](CCC....
30 2B04 - CHO C26 H43 N O5 C[C@H](CCC....
31 2B00 - GCH C26 H43 N O6 C[C@H](CCC....
32 5P2P - DHG C20 H42 N O6 P CCCCCCCCCC....
33 3O4M - CAQ C6 H6 O2 c1ccc(c(c1....
34 2B03 - TUD C26 H45 N O6 S C[C@H](CCC....
35 1L8S - LPE C26 H57 N O6 P CCCCCCCCCC....
36 1FXF - MJI C22 H44 F3 O6 P CCCCCCCCCC....
37 1FX9 - MJI C22 H44 F3 O6 P CCCCCCCCCC....
38 3QLM Ki = 0.0000158 M PLM C16 H32 O2 CCCCCCCCCC....
39 1POE - GEL C20 H45 N O8 P2 CCCCCCCCOC....
40 1DB4 - 8IN C21 H25 N2 O5 P Cc1c(c2cc(....
41 1KQU - BR4 C25 H33 N O3 c1ccc(cc1)....
42 5G3N ic50 = 0.012 uM X28 C23 H21 N O3 c1ccc(cc1)....
43 1KVO ic50 = 0.013 uM OAP C31 H37 N O3 S c1ccc(cc1)....
44 1J1A ic50 = 0.029 uM BHP C31 H37 N O4 c1ccc(cc1)....
45 6CE2 Kd = 0.5 uM SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
46 2QVD Kd = 0.000000064 M BER C20 H18 N O4 COc1ccc2cc....
47 1ZWP - NIM C13 H12 N2 O5 S CS(=O)(=O)....
48 1OXL - IDA C15 H18 N2 O3 CCCc1cc2cc....
49 1TG4 - PHE LEU ALA TYR LYS n/a n/a
50 1SKG - VAL ALA PHE ARG SER n/a n/a
51 1JQ9 Kd = 3.57 nM PHE LEU SER TYR LYS n/a n/a
52 2ARM Kd = 0.000000064 M OIN C17 H23 N O3 CN1[C@H]2C....
53 1FV0 Ki = 1.18 uM 9AR C17 H11 N O8 COc1c(ccc2....
54 1Q7A Kd = 0.000000064 M OPB C19 H20 N2 O3 CCCC[C@H]1....
55 1TG1 - PHQ LEU VAL ARG TYR n/a n/a
56 1ZYX - LCF C23 H22 Cl N O2 CC1(Cc2c(c....
57 1TJK - PHE LEU SER THR LYS n/a n/a
58 1KPM Ki = 1.59 uM VIT C29 H50 O2 Cc1c(c2c(c....
59 1TP2 - TDA C13 H26 O2 CCCCCCCCCC....
60 1TDV - TYR TRP ALA ALA ALA ALA n/a n/a
61 1TJ9 - VAL ALA ARG SER n/a n/a
62 1JQ8 Ki = 1.01 uM LEU ALA ILE TYR SER n/a n/a
63 1SQZ - PHQ ILE ALA ARG SER n/a n/a
64 1TGM - AIN C9 H8 O4 CC(=O)Oc1c....
65 1ZR8 - AJM C18 H22 N2 O2 C[N@]1c2cc....
66 1TH6 - OIN C17 H23 N O3 CN1[C@H]2C....
67 1Y38 - G3P C3 H9 O6 P C([C@H](CO....
68 3H1X Kd = 0.000000064 M IMN C19 H16 Cl N O4 Cc1c(c2cc(....
69 1SXK - BHA C7 H7 N O3 c1cc(c(cc1....
70 1TK4 - ALA ILE ARG SER n/a n/a
71 1SV3 - ANN C8 H8 O3 COc1ccc(cc....
72 5WZW ic50 = 1.23 uM U8D C22 H27 N2 O5 P CCc1c(c2cc....
73 5WZU ic50 = 0.1 uM 7W3 C21 H17 F3 N2 O5 Cc1c(c2c(n....
74 5WZT ic50 = 0.22 uM 7W6 C20 H17 Br N2 O5 Cc1c(c2c(n....
75 5WZS ic50 = 0.28 uM 7W9 C24 H20 N2 O5 Cc1c(c2c(n....
76 5Y5E - 7W3 C21 H17 F3 N2 O5 Cc1c(c2c(n....
77 5WZV ic50 = 0.21 uM 7W0 C26 H22 N2 O5 Cc1c(c2c(n....
78 6G5J ic50 = 0.2 uM EM8 C20 H17 F3 N2 O4 C[C@H](CC(....
79 2QHD - DAO C12 H24 O2 CCCCCCCCCC....
80 3BJW - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
81 1S8G - DAO C12 H24 O2 CCCCCCCCCC....
82 1POB - GEL C20 H45 N O8 P2 CCCCCCCCOC....
83 1TD7 Kd = 43 uM NFL C13 H9 F3 N2 O2 c1cc(cc(c1....
84 1OXR Kd = 0.000000064 M AIN C9 H8 O4 CC(=O)Oc1c....
85 2WQ5 Kd = 180 uM MIY C23 H27 N3 O7 CN(C)c1ccc....
86 1MF4 Ki = 10.2 nM VAL ALA PHE ARG SER n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ALA ILE ARG SER; Similar ligands found: 81
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA ILE ARG SER 1 1
2 ALA ARG M3L SER 0.6375 0.762712
3 ARG ILE PHE SER 0.611111 0.938776
4 ASN ARG LEU ILE LEU THR GLY 0.549451 0.823529
5 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.539326 0.88
6 ALA ARG 9AT 0.533333 0.877551
7 ALA ARG THR LYS GLN THR ALA ARG 0.532609 0.826923
8 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.515789 0.733333
9 GLN THR ALA ARG M3L SER 0.514563 0.714286
10 ARG ILE ALA ALA ALA 0.512821 0.891304
11 ALA ILE LEU HIS ARG LEU LEU GLN 0.509091 0.724138
12 ALA ARG LYS ILE ASP ASN LEU ASP 0.504673 0.767857
13 THR ALA ARG M3L SER THR 0.5 0.762712
14 GLU ARG THR ILE PRO ILE THR ARG GLU 0.495413 0.703125
15 VAL ALA PHE ARG SER 0.489796 0.88
16 VAL ARG MET 0.488095 0.784314
17 SER ARG LYS ILE ASP ASN LEU ASP 0.486486 0.821429
18 ILE GLN GLN SER ILE GLU ARG ILE 0.485149 0.901961
19 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.483516 0.86
20 ALA ILE GLU THR ASA 0.482759 0.673077
21 ACE GLN THR ALA ARG PRK SER THR 0.481132 0.833333
22 ALA ALA LEU THR ARG ALA 0.473684 0.88
23 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.47191 0.86
24 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.463415 0.87234
25 ACE ALA ARG THR LYS GLN 0.463158 0.843137
26 GLU THR VAL ARG PHE GLN SER ASP 0.461538 0.8
27 ALA GLN ASP ILE TYR ARG ALA SER TYR 0.459677 0.766667
28 ALA ARG THR LYS GLN THR ALA ARG LYS 0.457143 0.811321
29 ALA MET ARG VAL 0.454545 0.803922
30 LYS ILE LEU HIS ARG LEU LEU GLN ASP SER 0.453846 0.754098
31 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.451923 0.803571
32 ARG ARG LEU ILE PHE NH2 0.45098 0.823529
33 ACE GLN THR ALA ARG KCR SER THR 0.45045 0.814815
34 ALA ARG THR M3L GLN THR ALA ARG LYS 0.45 0.709677
35 GLY ARG GLY ASP SER PRO 0.446809 0.84
36 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.445783 0.791667
37 ARG ARG ARG ARG ARG ARG ARG ARG 0.445783 0.791667
38 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.445545 0.698413
39 ALA ARG THR ALY GLN THR ALA 0.445545 0.781818
40 PHQ ILE ALA ARG SER 0.445455 0.638889
41 ARG ILE MET GLU NH2 0.443299 0.826923
42 THR ILE MET MET GLN ARG GLY 0.442308 0.789474
43 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.441176 0.698413
44 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.440367 0.77193
45 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.436893 0.721311
46 ARG ARG GLY ILE NH2 0.436782 0.857143
47 ARG ARG ALA ALA 0.435294 0.854167
48 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.432692 0.785714
49 ALA ARG THR MLY GLN THR ALA ARG LYS 0.432692 0.733333
50 ARG ARG ARG GLU THR GLN VAL 0.428571 0.796296
51 ALA ARG TPO LYS 0.42268 0.711864
52 ACE GLY VAL NLE ARG ILE NH2 0.42268 0.857143
53 ARG GLU ARG SER PRO THR ARG 0.421569 0.68254
54 VAL ALA ARG SER 0.420455 0.916667
55 SER GLU ILE GLU PHE ALA ARG LEU 0.420168 0.851852
56 ALA THR ARG ASN PHE SER GLY 0.419643 0.785714
57 ALA TYR ARG 0.419355 0.773585
58 SER ARG ILE ARG ILE ARG GLY TYR VAL ARG 0.418803 0.754098
59 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.417582 0.77551
60 ALA ARG THR MLY GLN 0.415842 0.721311
61 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.414894 0.816327
62 ARG ILE PRO SER TYR ARG TYR ARG TYR 0.414634 0.647887
63 LYS ILE LEU HIS ARG LEU LEU GLN ASP 0.414062 0.704918
64 SER SER ILE GLU PHE ALA ARG LEU 0.409836 0.836364
65 ARG ALA ARG 0.409639 0.808511
66 ARG SER ARG 0.409639 0.84
67 ACE GLN THR ALA ARG BTK SER THR 0.409091 0.833333
68 THR ARG ARG GLU THR GLN LEU 0.407767 0.814815
69 ARG GLY ASP ILE ASN ASN ASN VAL 0.407407 0.781818
70 ALA ASN SER ARG VAL GLN ASP SER ILE ILE 0.40708 0.851852
71 LYS ARG LYS 0.406977 0.795918
72 ALA LYS ALA ILE ALA 0.406593 0.765957
73 GLU ALY ARG 0.40625 0.769231
74 ARG PRO LYS ARG ILE ALA 0.405172 0.693548
75 ASP ARG VAL TYR ILE HIS PRO PHE 0.404762 0.676923
76 ALA THR LYS ILE ASP ASN LEU ASP 0.40367 0.696429
77 ACE THR ARG GLU 0.402439 0.877551
78 DTY ILE ARG LEU LPD 0.401709 0.666667
79 SER GLU LEU GLU ILE LYS ARG TYR 0.401639 0.766667
80 ARG ARG ARG VAL ARG 00S 0.4 0.740741
81 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.4 0.792453
Similar Ligands (3D)
Ligand no: 1; Ligand: ALA ILE ARG SER; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1JQ9; Ligand: PHE LEU SER TYR LYS; 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: 1jq9.bio4) has 33 residues
No: Leader PDB Ligand Sequence Similarity
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