Receptor
PDB id Resolution Class Description Source Keywords
5B1S 1.58 Å EC: 2.5.1.16 CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI SPERMIDINE SYNTHASE I WITH 2-(2-FLUOROPHENYL)ETHANAMINE TRYPANOSOMA CRUZI STRAIN CL BRENER POLYAMINE SYNTHESIS TRANSFERASE
Ref.: IN SILICO, IN VITRO, X-RAY CRYSTALLOGRAPHY, AND INT STRATEGIES FOR DISCOVERING SPERMIDINE SYNTHASE INHI FOR CHAGAS DISEASE SCI REP V. 7 6666 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
S4M D:501;
A:501;
C:501;
B:501;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
356.444 C14 H24 N6 O3 S C[S@@...
BSX A:502;
D:502;
B:502;
C:502;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
ic50 = 124 uM
139.17 C8 H10 F N c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4YUW 1.97 Å EC: 2.5.1.16 CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI SPERMIDINE SYNTHASE I WITH TRANS-4-METHYLCYCLOHEXYLAMINE TRYPANOSOMA CRUZI (STRAIN CL BRENER) METHYLTRANSFERASE POLYAMINE SYNTHESIS TRANSFERASE
Ref.: STRUCTURAL INSIGHTS INTO THE NOVEL INHIBITION MECHA TRYPANOSOMA CRUZI SPERMIDINE SYNTHASE ACTA CRYSTALLOGR.,SECT.D V. 71 1879 2015
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4YUX Kd = 180 uM 4JT C8 H8 N2 S c1ccc2c(c1....
2 4YV2 - S4M C14 H24 N6 O3 S C[S@@H](CC....
3 4YV1 ic50 = 830 uM 4K2 C15 H16 N2 O2 c1cc2cccnc....
4 5B1S ic50 = 124 uM BSX C8 H10 F N c1ccc(c(c1....
5 4YUZ ic50 = 9.1 uM 4JV C16 H16 N4 O Cc1ccc(cc1....
6 4YUV - S4M C14 H24 N6 O3 S C[S@@H](CC....
7 4YUW ic50 = 1.7 uM 4JU C7 H15 N CC1CCC(CC1....
8 4YV0 ic50 = 530 uM 4JW C16 H15 N O3 CN(c1ccccc....
9 4YUY ic50 = 460 uM 1SQ C9 H8 N2 c1ccc2c(c1....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4YUX Kd = 180 uM 4JT C8 H8 N2 S c1ccc2c(c1....
2 4YV2 - S4M C14 H24 N6 O3 S C[S@@H](CC....
3 4YV1 ic50 = 830 uM 4K2 C15 H16 N2 O2 c1cc2cccnc....
4 5B1S ic50 = 124 uM BSX C8 H10 F N c1ccc(c(c1....
5 4YUZ ic50 = 9.1 uM 4JV C16 H16 N4 O Cc1ccc(cc1....
6 4YUV - S4M C14 H24 N6 O3 S C[S@@H](CC....
7 4YUW ic50 = 1.7 uM 4JU C7 H15 N CC1CCC(CC1....
8 4YV0 ic50 = 530 uM 4JW C16 H15 N O3 CN(c1ccccc....
9 4YUY ic50 = 460 uM 1SQ C9 H8 N2 c1ccc2c(c1....
50% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2PWP - SPD C7 H19 N3 C(CCNCCCN)....
2 2I7C ic50 = 8.5 uM AAT C18 H29 N7 O3 S c1nc(c2c(n....
3 2HTE - MTA C11 H15 N5 O3 S CSC[C@@H]1....
4 4YUX Kd = 180 uM 4JT C8 H8 N2 S c1ccc2c(c1....
5 4YV2 - S4M C14 H24 N6 O3 S C[S@@H](CC....
6 4YV1 ic50 = 830 uM 4K2 C15 H16 N2 O2 c1cc2cccnc....
7 5B1S ic50 = 124 uM BSX C8 H10 F N c1ccc(c(c1....
8 4YUZ ic50 = 9.1 uM 4JV C16 H16 N4 O Cc1ccc(cc1....
9 4YUV - S4M C14 H24 N6 O3 S C[S@@H](CC....
10 4YUW ic50 = 1.7 uM 4JU C7 H15 N CC1CCC(CC1....
11 4YV0 ic50 = 530 uM 4JW C16 H15 N O3 CN(c1ccccc....
12 4YUY ic50 = 460 uM 1SQ C9 H8 N2 c1ccc2c(c1....
13 2O05 - MTA C11 H15 N5 O3 S CSC[C@@H]1....
14 3RW9 ic50 = 5 uM DSH C13 H20 N6 O3 S c1nc(c2c(n....
15 2O0L - S4M C14 H24 N6 O3 S C[S@@H](CC....
16 2O07 - SPD C7 H19 N3 C(CCNCCCN)....
17 2O06 - MTA C11 H15 N5 O3 S CSC[C@@H]1....
18 2PT6 - S4M C14 H24 N6 O3 S C[S@@H](CC....
19 2PT9 ic50 = 35 uM 2MH C7 H15 N CC1CCC(CC1....
20 1JQ3 ic50 = 0.2 uM AAT C18 H29 N7 O3 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: S4M; Similar ligands found: 231
No: Ligand ECFP6 Tc MDL keys Tc
1 S4M 1 1
2 M2T 0.720588 0.844156
3 SAM 0.6875 0.909091
4 SMM 0.662651 0.898734
5 5N5 0.647059 0.789474
6 ADN 0.641791 0.766234
7 XYA 0.641791 0.766234
8 RAB 0.641791 0.766234
9 EP4 0.633803 0.818182
10 A4D 0.614286 0.789474
11 5CD 0.614286 0.753247
12 DSH 0.61039 0.906667
13 MTA 0.594595 0.84
14 S7M 0.586207 0.884615
15 DTA 0.581081 0.759494
16 3DH 0.578947 0.815789
17 5AD 0.565217 0.72
18 LMS 0.564103 0.645161
19 A 0.564103 0.682353
20 AMP 0.564103 0.682353
21 ABM 0.5625 0.72619
22 GEK 0.549451 0.846154
23 A12 0.548781 0.681818
24 AP2 0.548781 0.681818
25 ZAS 0.544304 0.7625
26 A2D 0.54321 0.666667
27 5AS 0.542169 0.680851
28 SRA 0.5375 0.670455
29 6RE 0.5375 0.8
30 GJV 0.536585 0.8125
31 AOC 0.530864 0.746835
32 BA3 0.53012 0.666667
33 MAO 0.53012 0.819277
34 M33 0.529412 0.697674
35 MHZ 0.529412 0.911392
36 AAT 0.52809 0.858974
37 J7C 0.52439 0.7875
38 A3N 0.52439 0.782051
39 ADP 0.52381 0.666667
40 B4P 0.52381 0.666667
41 AP5 0.52381 0.666667
42 5X8 0.523256 0.805195
43 ACP 0.523256 0.670455
44 A7D 0.517647 0.842105
45 AN2 0.517647 0.659091
46 AT4 0.517647 0.662921
47 SON 0.517647 0.681818
48 PRX 0.517241 0.729412
49 APC 0.517241 0.681818
50 AU1 0.511628 0.651685
51 CA0 0.511628 0.651685
52 ADX 0.511628 0.645161
53 RBY 0.511364 0.681818
54 ADV 0.511364 0.681818
55 SA8 0.511364 0.883117
56 50T 0.505747 0.659091
57 ATP 0.505747 0.666667
58 HEJ 0.505747 0.666667
59 SFG 0.505747 0.792208
60 G5A 0.505618 0.680851
61 AR6 0.5 0.666667
62 APR 0.5 0.666667
63 5FA 0.5 0.666667
64 ACQ 0.5 0.670455
65 AQP 0.5 0.666667
66 LAD 0.494845 0.747126
67 KAA 0.494845 0.712766
68 EEM 0.494505 0.860759
69 5AL 0.494505 0.678161
70 AD9 0.494382 0.651685
71 AGS 0.494382 0.655556
72 ADP PO3 0.494382 0.702381
73 SAP 0.494382 0.655556
74 NEC 0.493976 0.74359
75 A3G 0.493976 0.794872
76 3AM 0.493827 0.670588
77 Y3J 0.493333 0.679487
78 7D7 0.493151 0.717949
79 62X 0.489583 0.898734
80 TSB 0.489362 0.642105
81 A5A 0.48913 0.648936
82 SAI 0.488889 0.797468
83 SAH 0.488889 0.831169
84 5SV 0.484211 0.776471
85 ADP VO4 0.483871 0.678161
86 6YZ 0.483871 0.670455
87 VO4 ADP 0.483871 0.678161
88 ANP 0.483516 0.651685
89 T99 0.483516 0.662921
90 GAP 0.483516 0.709302
91 TAT 0.483516 0.662921
92 VMS 0.478723 0.635417
93 52H 0.478723 0.628866
94 54H 0.478723 0.635417
95 A5D 0.477778 0.759494
96 53H 0.473684 0.628866
97 DAL AMP 0.473684 0.697674
98 ADP ALF 0.473118 0.655556
99 ALF ADP 0.473118 0.655556
100 ATF 0.473118 0.644444
101 7MC 0.472222 0.752809
102 XAH 0.470588 0.730337
103 K15 0.469388 0.897436
104 9ZD 0.46875 0.666667
105 9ZA 0.46875 0.666667
106 8QN 0.46875 0.678161
107 SSA 0.468085 0.663158
108 SRP 0.468085 0.701149
109 0UM 0.463918 0.871795
110 4AD 0.463918 0.693182
111 PAJ 0.463918 0.67033
112 LSS 0.463918 0.666667
113 2AM 0.463415 0.662791
114 1ZZ 0.46 0.75
115 TXA 0.46 0.662921
116 A3P 0.45977 0.662791
117 NVA LMS 0.459184 0.694737
118 A22 0.458333 0.659091
119 8X1 0.458333 0.677083
120 MAP 0.458333 0.637363
121 5CA 0.458333 0.663158
122 7MD 0.457143 0.730337
123 A3T 0.455556 0.769231
124 MYR AMP 0.455446 0.770115
125 LEU LMS 0.454545 0.677083
126 9X8 0.454545 0.674157
127 OAD 0.454545 0.670455
128 25A 0.453608 0.666667
129 OOB 0.453608 0.659091
130 7D5 0.451219 0.655172
131 WAQ 0.45 0.724138
132 A3S 0.449438 0.782051
133 NSS 0.44898 0.663158
134 A1R 0.44898 0.744186
135 AMO 0.44898 0.681818
136 A3R 0.44898 0.744186
137 ADQ 0.44898 0.670455
138 DSZ 0.44898 0.645833
139 3AD 0.448718 0.776316
140 OVE 0.447059 0.659091
141 B5Y 0.446602 0.655556
142 BIS 0.445545 0.666667
143 SXZ 0.445545 0.8375
144 9K8 0.445545 0.61
145 3OD 0.445545 0.670455
146 ME8 0.445545 0.770115
147 PTJ 0.445545 0.659341
148 AHX 0.444444 0.677778
149 DLL 0.444444 0.659091
150 00A 0.444444 0.630435
151 ADP BMA 0.44 0.689655
152 3UK 0.44 0.651685
153 A6D 0.44 0.701149
154 TAD 0.439252 0.67033
155 S8M 0.438776 0.8
156 PR8 0.435644 0.758621
157 GSU 0.435644 0.663158
158 B5V 0.435644 0.644444
159 A A 0.435644 0.686047
160 P5A 0.435644 0.723404
161 QQY 0.435294 0.643678
162 ACK 0.435294 0.654762
163 CC5 0.434211 0.763158
164 B5M 0.432692 0.655556
165 YAP 0.432692 0.674157
166 JB6 0.431373 0.704545
167 FYA 0.431373 0.717647
168 NB8 0.431373 0.659341
169 PAP 0.430108 0.655172
170 GA7 0.429907 0.72093
171 YSA 0.428571 0.645833
172 KB1 0.427184 0.780488
173 25L 0.427184 0.659091
174 2BA 0.426966 0.658824
175 A2P 0.426966 0.651163
176 CMP 0.426966 0.666667
177 KH3 0.425926 0.910256
178 26A 0.425 0.759494
179 ARJ 0.425 0.701299
180 AMP DBH 0.424528 0.670455
181 TYR AMP 0.424528 0.693182
182 2VA 0.423913 0.75
183 QQX 0.423529 0.636364
184 9SN 0.423077 0.623656
185 V3L 0.421053 0.666667
186 YLB 0.419643 0.772727
187 FA5 0.419048 0.681818
188 8PZ 0.419048 0.645833
189 ATP A A A 0.419048 0.694118
190 RP1 0.418605 0.647727
191 SP1 0.418605 0.647727
192 YLP 0.418182 0.772727
193 ARG AMP 0.416667 0.722222
194 PPS 0.416667 0.62766
195 AR6 AR6 0.416667 0.686047
196 7D3 0.41573 0.640449
197 NVA 2AD 0.414894 0.822785
198 UP5 0.414414 0.637363
199 D3Y 0.414141 0.7625
200 GTA 0.412844 0.655914
201 MTP 0.4125 0.728395
202 3L1 0.4125 0.792208
203 3D1 0.4125 0.792208
204 4UV 0.411215 0.637363
205 649 0.410714 0.6875
206 OMR 0.410714 0.741573
207 TXE 0.410714 0.666667
208 VRT 0.410526 0.810127
209 SO8 0.410526 0.7625
210 LAQ 0.409091 0.692308
211 AHZ 0.409091 0.711111
212 7C5 0.407407 0.666667
213 G3A 0.407407 0.623656
214 2FA 0.407407 0.719512
215 6MD 0.407407 0.779221
216 YLC 0.40708 0.75
217 4TC 0.40708 0.641304
218 LPA AMP 0.405405 0.711111
219 48N 0.405405 0.677778
220 AYB 0.405172 0.764045
221 BS5 0.405172 0.715789
222 2A5 0.404255 0.689655
223 G5P 0.40367 0.623656
224 4UU 0.40367 0.637363
225 AFH 0.40367 0.652174
226 5F1 0.402439 0.753247
227 4UW 0.401786 0.67033
228 6V0 0.401786 0.641304
229 DQV 0.4 0.659091
230 ATR 0.4 0.643678
231 4YB 0.4 0.649485
Ligand no: 2; Ligand: BSX; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 BSX 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YUW; Ligand: S4M; 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: 4yuw.bio1) has 92 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4YUW; Ligand: 4JU; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 4yuw.bio1) has 91 residues
No: Leader PDB Ligand Sequence Similarity
1 3C6K SPD 36.1842
Pocket No.: 3; Query (leader) PDB : 4YUW; Ligand: 4JU; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4yuw.bio1) has 93 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4YUW; Ligand: S4M; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4yuw.bio1) has 90 residues
No: Leader PDB Ligand Sequence Similarity
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