Receptor
PDB id Resolution Class Description Source Keywords
5jao 2.06 Å EC: 3.1.1.47 EXPLOITATION OF A NOVEL BINDING POCKET IN HUMAN LIPOPROTEIN- PHOSPHOLIPASE A2 (LP-PLA2) DISCOVERED THROUGH X-F RAGMENT SCREENING HOMO SAPIENS PHOSPHOLIPASE LIPID METABOLISM HYDROLASE
Ref.: EXPLOITATION OF A NOVEL BINDING POCKET IN HUMAN LIPOPROTEIN-ASSOCIATED PHOSPHOLIPASE A2 (LP-PLA2) D THROUGH X-RAY FRAGMENT SCREENING. J.MED.CHEM. V. 59 5356 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:502;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
CA A:501;
 Part of Protein;
 none;
 submit data
40.078 Ca [Ca+2...
6HX A:504;
 Valid;
 none;
 submit data
217.694 C13 H12 Cl N Cc1cc...
DMS A:503;
 Invalid;
 none;
 submit data
78.133 C2 H6 O S CS(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5LP1 1.91 Å EC: 3.1.1.47 CRYSTAL STRUCTURE OF HUMAN LIPOPROTEIN-ASSOCIATED PHOSPHOLIP COMPLEX WITH A [1.1.1]BICYCLOPENTANE-CONTAINING INHIBITOR AR ESOLUTION. HOMO SAPIENS PLASMA PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE SECRETED ALPHA/BETA-HYDROLASE-FOLD LDL-BOUND; LIPOPROTEIN ASSOCIATEPHOSPHOLIPASE A2 LP-PLA2 GROUP VIIA PLA2 GLYCOPROTEIN HLIPID DEGRADATION POLYMORPHISM SECRETED HYDROLASE-HYDROLINHIBITOR COMPLEX
Ref.: INVESTIGATION OF A BICYCLO[1.1.1]PENTANE AS A PHENY REPLACEMENT WITHIN AN LPPLA2 INHIBITOR. ACS MED CHEM LETT V. 8 43 2017
Members (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5YE8 ic50 ~ 1 mM 8U3 C7 H7 F2 N O2 S CS(=O)(=O)....
2 5JAH - 6HQ C6 H10 N2 O2 CC1(C(=O)N....
3 5JAP ic50 = 0.23 uM 6HZ C19 H19 N O Cc1ccccc1c....
4 5LZ4 Kd = 2 uM 7BW C15 H17 F N2 O2 CC1(CC(=O)....
5 5JAL Kd = 980 uM 6HO C11 H10 F N O c1cc(cc(c1....
6 5YE9 ic50 = 355 nM 8U6 C25 H19 N3 O4 S CC(=O)Nc1c....
7 5JAN - 6HP C10 H16 N2 O3 CC(C)COC1=....
8 5JAS ic50 = 1.7 uM 6HW C17 H16 N2 S Cc1ccccc1c....
9 5LZ9 ic50 = 0.12 uM 7BR C19 H23 F N2 O4 S CC1(CCS(=O....
10 5LZ2 ic50 ~ 1 mM 7BX C10 H10 N2 O2 S c1cc(cc(c1....
11 5YE7 ic50 = 3431 nM 8U0 C24 H20 N2 O4 S CC(=O)Nc1c....
12 5JAT ic50 = 0.23 uM 6HR C20 H22 N2 O S Cc1ccccc1c....
13 5LZ8 ic50 = 0.98 uM 7BP C17 H21 F N2 O2 CC(C)(C)[C....
14 5JAU ic50 = 0.0014 uM 6HU C23 H30 N4 O3 Cc1ccccc1c....
15 5LZ7 Kd = 0.53 uM 7BK C20 H19 F N2 O2 C[C@@]1(CC....
16 5YEA ic50 = 5 nM 8U9 C21 H12 Cl F3 N2 O5 S c1cc(ccc1C....
17 5LYY ic50 = 14 uM 7BJ C16 H19 F N2 O3 c1cc(ccc1O....
18 5LP1 ic50 = 0.398 nM 71H C35 H38 F4 N4 O2 S CCN(CC)CCN....
19 5JAR ic50 = 2 uM 6HV C18 H15 N O S Cc1ccccc1c....
20 5LZ5 Kd = 0.45 uM 7K4 C20 H19 F N2 O2 C[C@]1(CC(....
21 5I8P Kd = 0.000000064 M VQ7 C23 H19 Cl F5 N3 O5 S CN1C(=CC(=....
22 5JAD Kd = 3.4 mM FB2 C6 H7 N O2 S c1ccc(cc1)....
23 5JAO - 6HX C13 H12 Cl N Cc1ccc(cc1....
70% Homology Family (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5YE8 ic50 ~ 1 mM 8U3 C7 H7 F2 N O2 S CS(=O)(=O)....
2 5JAH - 6HQ C6 H10 N2 O2 CC1(C(=O)N....
3 5JAP ic50 = 0.23 uM 6HZ C19 H19 N O Cc1ccccc1c....
4 5LZ4 Kd = 2 uM 7BW C15 H17 F N2 O2 CC1(CC(=O)....
5 5JAL Kd = 980 uM 6HO C11 H10 F N O c1cc(cc(c1....
6 5YE9 ic50 = 355 nM 8U6 C25 H19 N3 O4 S CC(=O)Nc1c....
7 5JAN - 6HP C10 H16 N2 O3 CC(C)COC1=....
8 5JAS ic50 = 1.7 uM 6HW C17 H16 N2 S Cc1ccccc1c....
9 5LZ9 ic50 = 0.12 uM 7BR C19 H23 F N2 O4 S CC1(CCS(=O....
10 5LZ2 ic50 ~ 1 mM 7BX C10 H10 N2 O2 S c1cc(cc(c1....
11 5YE7 ic50 = 3431 nM 8U0 C24 H20 N2 O4 S CC(=O)Nc1c....
12 5JAT ic50 = 0.23 uM 6HR C20 H22 N2 O S Cc1ccccc1c....
13 5LZ8 ic50 = 0.98 uM 7BP C17 H21 F N2 O2 CC(C)(C)[C....
14 5JAU ic50 = 0.0014 uM 6HU C23 H30 N4 O3 Cc1ccccc1c....
15 5LZ7 Kd = 0.53 uM 7BK C20 H19 F N2 O2 C[C@@]1(CC....
16 5YEA ic50 = 5 nM 8U9 C21 H12 Cl F3 N2 O5 S c1cc(ccc1C....
17 5LYY ic50 = 14 uM 7BJ C16 H19 F N2 O3 c1cc(ccc1O....
18 5LP1 ic50 = 0.398 nM 71H C35 H38 F4 N4 O2 S CCN(CC)CCN....
19 5JAR ic50 = 2 uM 6HV C18 H15 N O S Cc1ccccc1c....
20 5LZ5 Kd = 0.45 uM 7K4 C20 H19 F N2 O2 C[C@]1(CC(....
21 5I8P Kd = 0.000000064 M VQ7 C23 H19 Cl F5 N3 O5 S CN1C(=CC(=....
22 5JAD Kd = 3.4 mM FB2 C6 H7 N O2 S c1ccc(cc1)....
23 5JAO - 6HX C13 H12 Cl N Cc1ccc(cc1....
50% Homology Family (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5YE8 ic50 ~ 1 mM 8U3 C7 H7 F2 N O2 S CS(=O)(=O)....
2 5JAH - 6HQ C6 H10 N2 O2 CC1(C(=O)N....
3 5JAP ic50 = 0.23 uM 6HZ C19 H19 N O Cc1ccccc1c....
4 5LZ4 Kd = 2 uM 7BW C15 H17 F N2 O2 CC1(CC(=O)....
5 5JAL Kd = 980 uM 6HO C11 H10 F N O c1cc(cc(c1....
6 5YE9 ic50 = 355 nM 8U6 C25 H19 N3 O4 S CC(=O)Nc1c....
7 5JAN - 6HP C10 H16 N2 O3 CC(C)COC1=....
8 5JAS ic50 = 1.7 uM 6HW C17 H16 N2 S Cc1ccccc1c....
9 5LZ9 ic50 = 0.12 uM 7BR C19 H23 F N2 O4 S CC1(CCS(=O....
10 5LZ2 ic50 ~ 1 mM 7BX C10 H10 N2 O2 S c1cc(cc(c1....
11 5YE7 ic50 = 3431 nM 8U0 C24 H20 N2 O4 S CC(=O)Nc1c....
12 5JAT ic50 = 0.23 uM 6HR C20 H22 N2 O S Cc1ccccc1c....
13 5LZ8 ic50 = 0.98 uM 7BP C17 H21 F N2 O2 CC(C)(C)[C....
14 5JAU ic50 = 0.0014 uM 6HU C23 H30 N4 O3 Cc1ccccc1c....
15 5LZ7 Kd = 0.53 uM 7BK C20 H19 F N2 O2 C[C@@]1(CC....
16 5YEA ic50 = 5 nM 8U9 C21 H12 Cl F3 N2 O5 S c1cc(ccc1C....
17 5LYY ic50 = 14 uM 7BJ C16 H19 F N2 O3 c1cc(ccc1O....
18 5LP1 ic50 = 0.398 nM 71H C35 H38 F4 N4 O2 S CCN(CC)CCN....
19 5JAR ic50 = 2 uM 6HV C18 H15 N O S Cc1ccccc1c....
20 5LZ5 Kd = 0.45 uM 7K4 C20 H19 F N2 O2 C[C@]1(CC(....
21 5I8P Kd = 0.000000064 M VQ7 C23 H19 Cl F5 N3 O5 S CN1C(=CC(=....
22 5JAD Kd = 3.4 mM FB2 C6 H7 N O2 S c1ccc(cc1)....
23 5JAO - 6HX C13 H12 Cl N Cc1ccc(cc1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 6HX; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 6HX 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 6HX; Similar ligands found: 242
No: Ligand Similarity coefficient
1 BP3 0.9491
2 BPY 0.9409
3 B2Y 0.9405
4 977 0.9389
5 JRB 0.9380
6 TI7 0.9371
7 XDK 0.9362
8 SV4 0.9353
9 TT4 0.9340
10 AUV 0.9338
11 S2T 0.9328
12 L13 0.9311
13 W29 0.9297
14 BP6 0.9295
15 WOE 0.9279
16 0QW 0.9265
17 89J 0.9260
18 6J9 0.9252
19 B2T 0.9239
20 1WC 0.9232
21 DC5 0.9231
22 X6P 0.9230
23 S0G 0.9224
24 B4O 0.9210
25 46P 0.9202
26 M5E 0.9192
27 49O 0.9182
28 OBP 0.9173
29 EAJ 0.9164
30 K80 0.9152
31 HNL 0.9148
32 2JM 0.9145
33 AVA 0.9138
34 MIL 0.9135
35 X48 0.9135
36 T2D 0.9124
37 2GD 0.9111
38 WVV 0.9103
39 A4T 0.9101
40 F16 0.9099
41 CTN 0.9092
42 MPK 0.9083
43 BY5 0.9076
44 2TU 0.9059
45 MEX 0.9059
46 2F6 0.9057
47 BPS 0.9043
48 F69 0.9043
49 HNH 0.9042
50 7Q1 0.9038
51 NCT 0.9037
52 6HO 0.9030
53 DNB 0.9026
54 JF6 0.9017
55 A4N 0.9010
56 A9P 0.9008
57 H7S 0.9007
58 URI 0.8997
59 C2M 0.8994
60 79W 0.8989
61 GVG 0.8984
62 N2Z 0.8981
63 HNK 0.8976
64 K48 0.8975
65 1ER 0.8975
66 7QS 0.8970
67 BNL 0.8961
68 5UD 0.8960
69 AOT 0.8950
70 BCK 0.8948
71 FWD 0.8944
72 CUT 0.8940
73 CC5 0.8935
74 M4B 0.8933
75 IWD 0.8933
76 A4Q 0.8932
77 42R 0.8931
78 5AE 0.8930
79 TRP 0.8926
80 S3C 0.8919
81 AED 0.8907
82 78U 0.8905
83 GL7 0.8902
84 N8Z 0.8898
85 CH8 0.8898
86 F5F 0.8898
87 L5D 0.8893
88 R9G 0.8890
89 SAF 0.8890
90 92G 0.8886
91 3VW 0.8878
92 50C 0.8874
93 9W5 0.8865
94 A9K 0.8860
95 PYU 0.8860
96 MMS 0.8860
97 3RP 0.8856
98 DAH 0.8855
99 3IL 0.8855
100 54F 0.8855
101 GLS 0.8847
102 KF5 0.8845
103 HVJ 0.8840
104 GL2 0.8839
105 KWB 0.8838
106 AMR 0.8835
107 DKZ 0.8835
108 8CB 0.8832
109 A9O 0.8832
110 Q4G 0.8832
111 0OL 0.8823
112 1FF 0.8823
113 LNR 0.8821
114 DKX 0.8821
115 52C 0.8818
116 OX2 0.8814
117 GFE 0.8814
118 CJB 0.8810
119 TYU 0.8809
120 N3W 0.8809
121 BZQ 0.8804
122 6W6 0.8801
123 J27 0.8790
124 TCC 0.8788
125 FPL 0.8787
126 AMQ 0.8785
127 G14 0.8781
128 MIF 0.8781
129 SOR 0.8781
130 MJ5 0.8779
131 6TZ 0.8778
132 S1D 0.8777
133 DTR 0.8776
134 NIY 0.8774
135 22L 0.8773
136 GPU 0.8773
137 2B4 0.8772
138 54E 0.8771
139 DCZ 0.8771
140 1KN 0.8771
141 A6H 0.8770
142 AUT 0.8768
143 GL4 0.8764
144 0OY 0.8761
145 GZQ 0.8761
146 A4B 0.8758
147 9GP 0.8758
148 GPK 0.8755
149 FMQ 0.8752
150 JSX 0.8750
151 TCL 0.8744
152 FB4 0.8744
153 IQQ 0.8740
154 GL5 0.8738
155 5AD 0.8737
156 I5A 0.8736
157 DPN 0.8735
158 CLU 0.8735
159 TZM 0.8730
160 9FH 0.8729
161 VBC 0.8727
162 56D 0.8725
163 KYN 0.8723
164 AVI 0.8723
165 GN6 0.8721
166 4GP 0.8716
167 PHE 0.8716
168 BQ5 0.8712
169 EV2 0.8710
170 6NZ 0.8705
171 IOS 0.8705
172 SQV 0.8704
173 1U7 0.8703
174 BRH 0.8702
175 HIS 0.8700
176 GPQ 0.8700
177 2KU 0.8698
178 THM 0.8698
179 CP7 0.8691
180 X29 0.8687
181 BP7 0.8682
182 6J3 0.8682
183 60Q 0.8681
184 5F5 0.8676
185 DK4 0.8675
186 A8Q 0.8666
187 AM1 0.8665
188 CPZ 0.8664
189 NFA 0.8660
190 4LV 0.8659
191 PFF 0.8656
192 3C4 0.8655
193 PIR 0.8650
194 N1E 0.8650
195 I59 0.8649
196 PW1 0.8649
197 2LT 0.8647
198 6ZX 0.8645
199 K7M 0.8644
200 MZR 0.8643
201 0DN 0.8642
202 TB8 0.8641
203 1CY 0.8638
204 791 0.8634
205 9X5 0.8633
206 HFA 0.8632
207 TIH 0.8632
208 091 0.8627
209 ID8 0.8625
210 LT8 0.8625
211 Z15 0.8625
212 CP6 0.8619
213 Z57 0.8619
214 OMD 0.8617
215 J47 0.8617
216 KDG 0.8608
217 F1X 0.8608
218 Q06 0.8598
219 B86 0.8595
220 NAG 0.8582
221 LTN 0.8577
222 5F8 0.8576
223 MSR 0.8573
224 FUD 0.8573
225 ARJ 0.8573
226 NBG 0.8568
227 9PL 0.8565
228 M6H 0.8565
229 MNP 0.8558
230 HX8 0.8557
231 8GK 0.8556
232 2O6 0.8556
233 AVJ 0.8554
234 TAG 0.8548
235 6XI 0.8543
236 5BT 0.8538
237 PUR 0.8537
238 9H2 0.8534
239 DHY 0.8533
240 CFA 0.8527
241 AZC 0.8519
242 GEO 0.8511
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5LP1; Ligand: 71H; 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: 5lp1.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
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