Receptor
PDB id Resolution Class Description Source Keywords
5G3N 1.8 Å EC: 3.1.1.4 DISCOVERY OF A NOVEL SECRETED PHOSPHOLIPASE A2 (SPLA2) INHIB HOMO SAPIENS HYDROLASE SPLA2 SECRETED PHOSPHOLIPASE A2 CARDIOVASCULAR INHIBITOR FRAGMENT
Ref.: DISCOVERY OF AZD2716: A NOVEL SECRETED PHOSPHOLIPAS (SPLA2) INHIBITOR FOR THE TREATMENT OF CORONARY ART DISEASE ACS MED.CHEM.LETT. V. 7 884 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
X28 B:1126;
A:1129;
Valid;
Valid;
none;
none;
ic50 = 0.012 uM
359.418 C23 H21 N O3 c1ccc...
CA B:198;
B:199;
A:199;
A:198;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
FMT A:1128;
B:1125;
Invalid;
Invalid;
none;
none;
submit data
46.025 C H2 O2 C(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5G3N 1.8 Å EC: 3.1.1.4 DISCOVERY OF A NOVEL SECRETED PHOSPHOLIPASE A2 (SPLA2) INHIB HOMO SAPIENS HYDROLASE SPLA2 SECRETED PHOSPHOLIPASE A2 CARDIOVASCULAR INHIBITOR FRAGMENT
Ref.: DISCOVERY OF AZD2716: A NOVEL SECRETED PHOSPHOLIPAS (SPLA2) INHIBITOR FOR THE TREATMENT OF CORONARY ART DISEASE ACS MED.CHEM.LETT. V. 7 884 2016
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 1POE - GEL C20 H45 N O8 P2 CCCCCCCCOC....
2 1DB4 - 8IN C21 H25 N2 O5 P Cc1c(c2cc(....
3 1KQU - BR4 C25 H33 N O3 c1ccc(cc1)....
4 5G3N ic50 = 0.012 uM X28 C23 H21 N O3 c1ccc(cc1)....
5 1KVO ic50 = 0.013 uM OAP C31 H37 N O3 S c1ccc(cc1)....
6 1J1A ic50 = 0.029 uM BHP C31 H37 N O4 c1ccc(cc1)....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 1POE - GEL C20 H45 N O8 P2 CCCCCCCCOC....
2 1DB4 - 8IN C21 H25 N2 O5 P Cc1c(c2cc(....
3 1KQU - BR4 C25 H33 N O3 c1ccc(cc1)....
4 5G3N ic50 = 0.012 uM X28 C23 H21 N O3 c1ccc(cc1)....
5 1KVO ic50 = 0.013 uM OAP C31 H37 N O3 S c1ccc(cc1)....
6 1J1A ic50 = 0.029 uM BHP C31 H37 N O4 c1ccc(cc1)....
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: X28; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 X28 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5G3N; Ligand: X28; Similar sites found: 87
This union binding pocket(no: 1) in the query (biounit: 5g3n.bio2) has 44 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.005218 0.44817 None
2 2GBB CIT 0.004231 0.44369 None
3 5CHR 4NC 0.007374 0.43379 None
4 4UCC ZKW 0.02226 0.43096 None
5 2V57 PRL 0.01171 0.42652 None
6 4DO1 ANN 0.01642 0.41194 None
7 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 0.02397 0.4108 None
8 3WUR O4B 0.02817 0.4083 None
9 3TL1 JRO 0.02155 0.40724 None
10 3HP9 CF1 0.0266 0.40699 None
11 3ZO7 K6H 0.01849 0.40638 None
12 4DNJ ANN 0.01887 0.40565 None
13 4HBM 0Y7 0.01801 0.40291 None
14 2PR5 FMN 0.008541 0.40003 None
15 3E3U NVC 0.009244 0.40906 1.5748
16 1RL4 BRR 0.02193 0.40264 1.5748
17 1R6N 434 0.00518 0.44295 2.3622
18 4XNV BUR 0.02175 0.41083 2.3622
19 3K7S R52 0.01789 0.40305 2.7933
20 2HHP FLC 0.003149 0.48547 3.14961
21 3G58 988 0.009467 0.4166 3.14961
22 3KYQ DPV 0.01608 0.41382 3.14961
23 5A0U CHT 0.01932 0.40541 3.14961
24 5MWE TCE 0.008858 0.42718 3.7037
25 5V4R MGT 0.0005414 0.50432 3.93701
26 5IJJ I6P 0.009174 0.42993 3.93701
27 4QEK GLC 0.005643 0.42907 3.93701
28 1XMY ROL 0.007781 0.42527 3.93701
29 1N6B DMZ 0.007612 0.40921 3.93701
30 1VKF CIT 0.02608 0.40601 3.93701
31 1XM4 PIL 0.01306 0.40579 3.93701
32 3HEE R5P 0.02148 0.4031 3.93701
33 1XMU ROF 0.01315 0.40191 3.93701
34 1VPD TLA 0.04075 0.40074 3.93701
35 1ECM TSA 0.009199 0.42162 4.58716
36 1I0B PEL 0.01333 0.43404 4.72441
37 2QES ADE 0.01448 0.41784 4.72441
38 1XZ3 ICF 0.03609 0.41706 4.72441
39 5CX6 CDP 0.0177 0.41524 4.72441
40 2ATJ BHO 0.01442 0.41369 4.72441
41 2V95 HCY 0.02952 0.4017 4.72441
42 4ZGM 32M 0.0139 0.42448 4.91803
43 1GEG GLC 0.00429 0.47384 5.51181
44 3LE7 ADE 0.00652 0.43944 5.51181
45 3R9V DXC 0.009592 0.42846 5.51181
46 2FP2 TSA 0.003143 0.41894 5.51181
47 4LH7 NMN 0.02781 0.40418 5.51181
48 2V0U FMN 0.007537 0.4024 5.51181
49 4MA7 P2Z 0.04232 0.4023 5.51181
50 4MGA 27L 0.02972 0.40181 5.51181
51 2WKQ FMN 0.008252 0.40068 5.51181
52 3RV5 DXC 0.002046 0.43254 5.61798
53 2VDY HCY 0.007972 0.43328 6.29921
54 4M6T SAM 0.01233 0.42662 6.29921
55 4COL DTP 0.009495 0.40484 6.29921
56 3SQP 3J8 0.02136 0.41291 7.08661
57 2CYB TYR 0.02964 0.40234 7.08661
58 3EJW PAV 0.02323 0.40137 7.08661
59 2G3F IZC 0.0305 0.40069 7.08661
60 5TVI O8N 0.02526 0.41202 7.6087
61 4V3I ASP LEU THR ARG PRO 0.009714 0.43059 7.87402
62 3SHZ 5CO 0.01574 0.40578 7.87402
63 1UCD U5P 0.03126 0.40002 7.87402
64 2FDW D3G 0.009841 0.42015 8.66142
65 2HFK E4H 0.01606 0.41386 8.66142
66 4A38 BZS 0.02287 0.40406 8.66142
67 2DHC DCE 0.02263 0.40397 8.66142
68 5VE5 GSH 0.02176 0.40526 9.44882
69 2ALG DAO 0.02905 0.40062 9.78261
70 2VWA PTY 0.01839 0.41236 9.90099
71 4IA6 EIC 0.002095 0.46154 10.2362
72 4K90 MLA 0.009576 0.40985 10.2362
73 5DYO FLU 0.02262 0.40564 10.2362
74 4DR9 BB2 0.01098 0.40558 10.2362
75 1KPG 16A 0.008103 0.40442 10.2362
76 4URX FK1 0.01851 0.40309 10.2362
77 2IDO TMP 0.02991 0.40209 10.2362
78 1KPH 10A 0.008362 0.40043 10.2362
79 1MT1 AG2 0.01429 0.42063 10.6195
80 1N13 AG2 0.02748 0.40441 10.6195
81 2QQC AG2 0.02567 0.4055 10.7143
82 2GCG DGY 0.02249 0.4016 11.0236
83 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 0.0119 0.42671 13.3858
84 5UGW GSH 0.003436 0.42686 14.1732
85 1JQY A32 0.02689 0.40224 16.5049
86 5OCA 9QZ 0.002874 0.45428 16.5354
87 3KU0 ADE 0.004281 0.45156 17.3228
Pocket No.: 2; Query (leader) PDB : 5G3N; Ligand: X28; Similar sites found: 10
This union binding pocket(no: 2) in the query (biounit: 5g3n.bio1) has 44 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2O1C PPV 0.005747 0.40473 None
2 4V2O CLQ 0.02146 0.40311 None
3 4EVQ PHB 0.01826 0.40261 None
4 4PYW ACE THR THR ALA ILE NH2 0.002808 0.40254 2.3622
5 5KAX RHQ 0.02298 0.40579 3.14961
6 5I8F ML1 0.01798 0.40294 5.51181
7 3O01 DXC 0.00588 0.42991 6.29921
8 3AQT RCO 0.0317 0.4001 7.08661
9 5TVI MYR 0.004935 0.41427 7.6087
10 4DS8 A8S 0.01213 0.40355 10.2362
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