Receptor
PDB id Resolution Class Description Source Keywords
1TJ9 1.1 Å EC: 3.1.1.4 STRUCTURE OF THE COMPLEXED FORMED BETWEEN GROUP II PHOSPHOLI AND A RATIONALLY DESIGNED TETRA PEPTIDE,VAL-ALA-ARG-SER AT R ESOLUTION DABOIA RUSSELLII RUSSELLII PHOSPHOLIPASECOMPLEXVARSCRYSTAL STRUCTURE1.1 RESOLUTIONHYDROLASE
Ref.: STRUCTURE OF THE COMPLEX FORMED BETWEEN GROUP II PHOSPHOLIPASE A2 AND A RATIONALLY DESIGNED TETRA PEPTIDE,VAL-ALA-ARG-SER AT 1.1A RESOLUTION TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACY A:401;
 Invalid;
 none;
 submit data
60.052 C2 H4 O2 CC(=O...
SO4 A:301;
A:302;
A:303;
A:304;
A:305;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
VAL ALA ARG SER B:1;
 Valid;
 none;
 submit data
432.502 n/a O=C([...
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: VAL ALA ARG SER; Similar ligands found: 66
No: Ligand ECFP6 Tc MDL keys Tc
1 VAL ALA ARG SER 1 1
2 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.575342 0.913043
3 VAL ARG SER ARG ARG CYS LEU ARG LEU 0.563218 0.884615
4 ARG ARG ALA ALA 0.56 0.893617
5 VAL ARG SER ARG ARG ABA LEU ARG LEU 0.550562 0.884615
6 VAL ALA PHE ARG SER 0.549451 0.918367
7 GLY ALA ARG ALA HIS SER SER 0.520408 0.737705
8 MET ALA ARG 0.506329 0.823529
9 ARG SER ARG 0.493333 0.877551
10 VAL LEU ARG ASP ASP LEU LEU GLU ALA 0.48913 0.843137
11 ARG ASP ARG ALA ALA LYS LEU 0.488636 0.877551
12 VAL ARG MET 0.481481 0.784314
13 ALA ARG THR M3L GLN THR ALA ARG 0.47 0.714286
14 GLU ALA GLN THR ARG LEU 0.47 0.882353
15 LYS ARG LYS 0.468354 0.833333
16 ALA ARG 9AT 0.466667 0.877551
17 ALA GLN PHE SER ALA SER ALA SER ARG 0.465347 0.849057
18 ALA ARG 0.463768 0.869565
19 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.460674 0.86
20 PRO SER ARG VAL 0.460674 0.836364
21 LYS ALA ALA ARG M3L SER ALA 0.46 0.737705
22 ARG GLU ALA ALA 0.457831 0.893617
23 VAL LYS VAL VAL ALA LYS LYS TYR ARG ASN 0.451923 0.745763
24 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.45098 0.865385
25 MET ABA LEU ARG MET THR ALA VAL MET 0.449541 0.803571
26 ALA ARG LYS LEU ASP 0.449438 0.843137
27 ACE GLU ALA GLN THR ARG LEU 0.445545 0.865385
28 GLN THR ALA ARG M3L SER 0.438095 0.714286
29 MET CYS LEU ARG MET THR ALA VAL MET 0.4375 0.803571
30 ALA ALA LEU THR ARG ALA 0.43617 0.88
31 ILE GLN GLN SER ILE GLU ARG ILE 0.435644 0.865385
32 ALA ARG M3L SER 0.431818 0.762712
33 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.431818 0.86
34 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.431193 0.714286
35 HIS GLY ALA ALA ARG ALA GLU VAL HIS LEU 0.43 0.895833
36 VAL MET ALA PRO ARG ALA LEU LEU LEU 0.429825 0.651515
37 THR ALA ARG MYK SER THR GLY 0.428571 0.758621
38 SER SER ILE GLU PHE ALA ARG LEU 0.42735 0.836364
39 LYS GLN THR ALA ARG M3L SER THR GLY 0.427184 0.714286
40 SER GLU ILE GLU PHE ALA ARG LEU 0.426087 0.851852
41 MET CYS LEU ARG NLE THR ALA VAL MET 0.426087 0.789474
42 ALA ALA ARG KCR SER ALA PRO ALA 0.425 0.703125
43 GLN THR ALA ARG M3L SER THR GLY 0.423423 0.714286
44 ALA ARG THR MLY GLN 0.42268 0.75
45 ARG ARG ARG GLU THR GLN VAL 0.421053 0.865385
46 SER PRO LYS ARG ILE ALA 0.420561 0.725806
47 ALA ILE ARG SER 0.420455 0.916667
48 ALA GLN THR ALA ARG ALY SER THR 0.416667 0.8
49 ASP ALA GLU PHE ARG HIS ASP 0.415094 0.823529
50 ALA ARG TPO LYS 0.414894 0.741379
51 THR ARG ARG GLU THR GLN LEU 0.414141 0.849057
52 ARG GLU ARG SER PRO THR ARG 0.414141 0.709677
53 ALA MET ARG VAL 0.413793 0.803922
54 ASN ARG LEU LEU LEU THR GLY 0.410526 0.849057
55 ACE ALA ARG THR LYS GLN 0.410526 0.843137
56 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.410256 0.714286
57 GLU GLU PHE GLY ARG ALA PHE SER PHE 0.410256 0.8
58 LYS LYS ARG LEU SER VAL GLU 0.408163 0.882353
59 ACE GLN THR ALA ARG PRK SER THR 0.407407 0.8
60 ALA ARG MLZ SER ALA PRO ALA THR 0.40678 0.652174
61 VAL LEU CIR ASP ASP LEU LEU GLU ALA 0.40625 0.769231
62 LYS ARG ARG LYS SEP VAL 0.40625 0.789474
63 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.405405 0.826923
64 ALA ARG THR MLY GLN THR ALA ARG TYR 0.405172 0.671642
65 ALA ARG THR M3L GLN THR ALA ARG LYS 0.4 0.709677
66 GLN ARG SER THR SEP THR 0.4 0.775862
Similar Ligands (3D)
Ligand no: 1; Ligand: VAL ALA 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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