Receptor
PDB id Resolution Class Description Source Keywords
3F8W 2.3 Å EC: 2.4.2.1 CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI PURINE NUCLEOSIDE PHOSPHORYLASE IN COMPLEX WITH ADENOSINE SCHISTOSOMA MANSONI PURINE NUCLEOSIDE PHOSPHORYLASE SCHISTOSOMA ADENOSINE GLYCOSYLTRANSFERASE TRANSFERASE
Ref.: ADENOSINE BINDING TO LOW-MOLECULAR-WEIGHT PURINE NUCLEOSIDE PHOSPHORYLASE: THE STRUCTURAL BASIS FOR RECOGNITION BASED ON ITS COMPLEX WITH THE ENZYME FROM SCHISTOSOMA MANSONI. ACTA CRYSTALLOGR.,SECT.D V. 66 73 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ADN A:300;
B:301;
C:302;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
267.241 C10 H13 N5 O4 c1nc(...
DMS A:306;
B:305;
C:307;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
78.133 C2 H6 O S CS(=O...
SO4 A:303;
B:304;
C:304;
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
3DJF 2.3 Å EC: 2.4.2.1 CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI PURINE NUCLEOSIDE PHOSPHORYLASE IN A COMPLEX WITH BCX-34 SCHISTOSOMA MANSONI PURINE NUCLEOSIDE PHOSPHORYLASE BCX34 INHIBITOR GLYCOSYLTRANSFERASE TRANSFERASE
Ref.: STRUCTURAL BASIS FOR SELECTIVE INHIBITION OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI: AND STRUCTURAL STUDIES. BIOORG.MED.CHEM. V. 18 1421 2010
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 3FB1 - R1P C5 H11 O8 P C([C@@H]1[....
2 3E9R - ADE C5 H5 N5 c1[nH]c2c(....
3 3E0Q - JFD C4 H4 Br N3 O2 C1(=C(NC(=....
4 3FNQ - HPA C5 H4 N4 O c1[nH]c2c(....
5 3FAZ - NOS C10 H12 N4 O5 c1nc2c(n1[....
6 3IEX - GMP C10 H13 N5 O5 c1nc2c(n1[....
7 3DJF ic50 = 0.8 uM BC3 C12 H11 N5 O c1cc(cnc1)....
8 3F8W - ADN C10 H13 N5 O4 c1nc(c2c(n....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3FB1 - R1P C5 H11 O8 P C([C@@H]1[....
2 3E9R - ADE C5 H5 N5 c1[nH]c2c(....
3 3E0Q - JFD C4 H4 Br N3 O2 C1(=C(NC(=....
4 3FNQ - HPA C5 H4 N4 O c1[nH]c2c(....
5 3FAZ - NOS C10 H12 N4 O5 c1nc2c(n1[....
6 3IEX - GMP C10 H13 N5 O5 c1nc2c(n1[....
7 3DJF ic50 = 0.8 uM BC3 C12 H11 N5 O c1cc(cnc1)....
8 3F8W - ADN C10 H13 N5 O4 c1nc(c2c(n....
50% Homology Family (41)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2ON6 Ki = 172 nM IMH C11 H14 N4 O4 c1c(c2c([n....
2 2A0Y Ki = 900 pM DIH C12 H19 N4 O3 C1[C@@H]([....
3 1RR6 - IMH C11 H14 N4 O4 c1c(c2c([n....
4 2A0X Ki = 950 pM DIH C12 H19 N4 O3 C1[C@@H]([....
5 3GB9 - A2F C5 H4 F N5 c1[nH]c2c(....
6 1RT9 - IMH C11 H14 N4 O4 c1c(c2c([n....
7 5UGF - IM5 C12 H17 N5 O3 c1c(c2c([n....
8 3BGS Ki = 380 pM DIH C12 H19 N4 O3 C1[C@@H]([....
9 1RSZ - DIH C12 H19 N4 O3 C1[C@@H]([....
10 2A0W Ki = 270 pM DIH C12 H19 N4 O3 C1[C@@H]([....
11 1B8O Ki = 23 pM IMH C11 H14 N4 O4 c1c(c2c([n....
12 1A9T - R1P C5 H11 O8 P C([C@@H]1[....
13 1VFN Ki = 2.5 uM HPA C5 H4 N4 O c1[nH]c2c(....
14 2QPL ic50 = 18.9 uM BTY C6 H7 N5 O Cc1cc2n(n1....
15 2AI1 ic50 = 300 nM P1G C12 H16 N5 O8 P c1nc2c(n1[....
16 1B8N Ki = 30 pM IMG C11 H15 N5 O4 c1c(c2c([n....
17 1A9S - NOS C10 H12 N4 O5 c1nc2c(n1[....
18 2AI3 ic50 = 5000 nM P2G C11 H14 N5 O8 P c1nc2c(n1[....
19 1LVU Kd = 4.8 uM 9PP C9 H13 N6 O4 P C[C@@H](Cn....
20 1A9P - 9DI C11 H13 N3 O5 c1c(c2c([n....
21 2AI2 ic50 = 30 nM P1D C13 H16 N3 O8 P c1c(c2c([n....
22 1V48 Ki = 16 nM HA1 C10 H14 F2 N5 O4 P c1nc2c(n1C....
23 1A9Q - HPA C5 H4 N4 O c1[nH]c2c(....
24 3FUC Kd = 190 pM 9D9 9DG n/a n/a
25 1A9R - HPA C5 H4 N4 O c1[nH]c2c(....
26 1LV8 Kd = 3.5 uM 9PP C9 H13 N6 O4 P C[C@@H](Cn....
27 1FXU - GU7 C10 H16 N6 O3 c1nc2c(n1C....
28 5IFK - HPA C5 H4 N4 O c1[nH]c2c(....
29 4EAR - IM5 C12 H17 N5 O3 c1c(c2c([n....
30 5ETJ Kd = 66 pM IM5 C12 H17 N5 O3 c1c(c2c([n....
31 4EB8 - IM5 C12 H17 N5 O3 c1c(c2c([n....
32 2P4S Kd = 0.42 nM DIH C12 H19 N4 O3 C1[C@@H]([....
33 3FB1 - R1P C5 H11 O8 P C([C@@H]1[....
34 3E9R - ADE C5 H5 N5 c1[nH]c2c(....
35 3E0Q - JFD C4 H4 Br N3 O2 C1(=C(NC(=....
36 3FNQ - HPA C5 H4 N4 O c1[nH]c2c(....
37 3FAZ - NOS C10 H12 N4 O5 c1nc2c(n1[....
38 3IEX - GMP C10 H13 N5 O5 c1nc2c(n1[....
39 3DJF ic50 = 0.8 uM BC3 C12 H11 N5 O c1cc(cnc1)....
40 3F8W - ADN C10 H13 N5 O4 c1nc(c2c(n....
41 1VMK - GUN C5 H5 N5 O c1[nH]c2c(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ADN; Similar ligands found: 286
No: Ligand ECFP6 Tc MDL keys Tc
1 XYA 1 1
2 ADN 1 1
3 RAB 1 1
4 5N5 0.811321 0.967742
5 5CD 0.796296 0.920635
6 A4D 0.796296 0.967742
7 MTA 0.758621 0.878788
8 EP4 0.754386 0.852941
9 M2T 0.741379 0.828571
10 DTA 0.741379 0.865672
11 AMP 0.709677 0.842857
12 A 0.709677 0.842857
13 3DH 0.704918 0.878788
14 ZAS 0.68254 0.84058
15 5AD 0.672727 0.854839
16 6RE 0.671875 0.830986
17 SRA 0.671875 0.797297
18 AMP MG 0.661538 0.819444
19 DSH 0.661538 0.842857
20 AOC 0.661538 0.907692
21 7D7 0.660714 0.875
22 A3N 0.651515 0.923077
23 A2D 0.651515 0.84507
24 ABM 0.651515 0.819444
25 J7C 0.651515 0.842857
26 ADP 0.647059 0.84507
27 S4M 0.641791 0.766234
28 GJV 0.641791 0.819444
29 3AM 0.640625 0.828571
30 AN2 0.637681 0.833333
31 A12 0.632353 0.810811
32 AP2 0.632353 0.810811
33 BA3 0.632353 0.84507
34 MAO 0.632353 0.75641
35 Y3J 0.627119 0.828125
36 AP5 0.623188 0.84507
37 5AS 0.623188 0.714286
38 B4P 0.623188 0.84507
39 ATP 0.619718 0.84507
40 5X8 0.619718 0.865672
41 SON 0.614286 0.786667
42 A7D 0.614286 0.909091
43 APC 0.611111 0.810811
44 AQP 0.611111 0.84507
45 5FA 0.611111 0.84507
46 2FA 0.606557 0.924242
47 26A 0.606557 0.893939
48 M33 0.605634 0.833333
49 CA0 0.605634 0.821918
50 AU1 0.605634 0.821918
51 MHZ 0.605634 0.75641
52 ADP MG 0.605634 0.808219
53 ADX 0.605634 0.759494
54 AGS 0.60274 0.8
55 AD9 0.60274 0.821918
56 SAP 0.60274 0.8
57 2AM 0.6 0.842857
58 SFG 0.597222 0.850746
59 50T 0.597222 0.833333
60 BEF ADP 0.597222 0.786667
61 ACP 0.597222 0.821918
62 ADP BEF 0.597222 0.786667
63 MTP 0.590164 0.852941
64 APR 0.589041 0.84507
65 PRX 0.589041 0.797297
66 AR6 0.589041 0.84507
67 A3G 0.588235 0.938462
68 TAT 0.586667 0.810811
69 ACQ 0.586667 0.821918
70 A3P 0.585714 0.816901
71 RBY 0.581081 0.810811
72 ADV 0.581081 0.810811
73 SA8 0.581081 0.794521
74 ADP PO3 0.581081 0.842857
75 A5D 0.581081 0.865672
76 1DA 0.580645 1
77 6MD 0.580645 0.952381
78 ADQ 0.575 0.847222
79 OVE 0.573529 0.808219
80 SAH 0.573333 0.84058
81 SAI 0.573333 0.828571
82 ATP MG 0.573333 0.808219
83 G5A 0.573333 0.714286
84 A22 0.56962 0.833333
85 GAP 0.565789 0.821918
86 ANP 0.565789 0.821918
87 SAM 0.565789 0.773333
88 NEC 0.565217 0.876923
89 3AD 0.564516 0.951613
90 25A 0.5625 0.819444
91 7D5 0.560606 0.780822
92 AAT 0.558442 0.819444
93 5AL 0.558442 0.808219
94 EEM 0.558442 0.773333
95 ATF 0.551282 0.810811
96 ADP ALF 0.551282 0.776316
97 A5A 0.551282 0.719512
98 ALF ADP 0.551282 0.776316
99 CC5 0.55 0.935484
100 A3S 0.547945 0.953125
101 VO4 ADP 0.544304 0.808219
102 ADP VO4 0.544304 0.808219
103 SSA 0.544304 0.73494
104 SMM 0.544304 0.74359
105 ANP MG 0.544304 0.776316
106 S7M 0.544304 0.773333
107 SRP 0.544304 0.810811
108 QQX 0.544118 0.756757
109 S8M 0.54321 0.805556
110 ADP BMA 0.542169 0.847222
111 A2P 0.541667 0.802817
112 3D1 0.539683 0.907692
113 3L1 0.539683 0.907692
114 PAP 0.539474 0.830986
115 52H 0.5375 0.694118
116 54H 0.5375 0.702381
117 VMS 0.5375 0.702381
118 LSS 0.536585 0.678161
119 ACK 0.536232 0.811594
120 QQY 0.536232 0.767123
121 A3T 0.533333 0.968254
122 TSB 0.530864 0.731707
123 MAP 0.530864 0.8
124 53H 0.530864 0.694118
125 DAL AMP 0.530864 0.808219
126 5CA 0.530864 0.73494
127 GEK 0.52439 0.805556
128 8QN 0.52439 0.808219
129 OOB 0.52439 0.808219
130 5SV 0.52439 0.75641
131 OAD 0.52381 0.821918
132 25L 0.523256 0.833333
133 PPS 0.518987 0.7375
134 DSZ 0.518072 0.714286
135 4AD 0.518072 0.8
136 NSS 0.518072 0.714286
137 0UM 0.518072 0.808219
138 A1R 0.518072 0.813333
139 AMO 0.518072 0.810811
140 PAJ 0.518072 0.792208
141 A A 0.517647 0.819444
142 6CR 0.515152 0.910448
143 RP1 0.514286 0.77027
144 SP1 0.514286 0.77027
145 2VA 0.513158 0.938462
146 62X 0.511905 0.74359
147 00A 0.511905 0.766234
148 NVA LMS 0.511905 0.678161
149 DLL 0.511905 0.808219
150 AHX 0.511905 0.802632
151 3OD 0.511628 0.821918
152 ME8 0.511628 0.728395
153 PTJ 0.511628 0.75641
154 7D3 0.506849 0.783784
155 V3L 0.506329 0.819444
156 K15 0.505882 0.763158
157 3UK 0.505882 0.797297
158 LEU LMS 0.505882 0.678161
159 A6D 0.505882 0.763158
160 GSU 0.5 0.694118
161 2BA 0.5 0.814286
162 KAA 0.5 0.689655
163 PR8 0.5 0.759494
164 AD3 0.5 1
165 P5A 0.5 0.681818
166 CMP 0.5 0.826087
167 NVA 2AD 0.5 0.867647
168 ATR 0.5 0.816901
169 5F1 0.5 0.80597
170 LAD 0.5 0.769231
171 WAQ 0.5 0.766234
172 ATP A A A 0.494382 0.830986
173 FYA 0.494253 0.808219
174 BIS 0.494253 0.789474
175 SXZ 0.494253 0.773333
176 NB8 0.494253 0.779221
177 TXA 0.494253 0.810811
178 JB6 0.494253 0.766234
179 1ZZ 0.494253 0.728395
180 SO8 0.493671 0.924242
181 VRT 0.493671 0.897059
182 IVH 0.493333 0.835616
183 KB1 0.488636 0.783784
184 MYR AMP 0.488636 0.728395
185 2A5 0.487179 0.797297
186 NOC 0.484375 0.903226
187 4UV 0.483516 0.776316
188 9SN 0.483146 0.75641
189 A2R 0.481928 0.833333
190 7D4 0.480519 0.783784
191 FA5 0.477778 0.786667
192 YAP 0.477778 0.776316
193 D3Y 0.47619 0.924242
194 AFH 0.473118 0.792208
195 AR6 AR6 0.473118 0.819444
196 YSA 0.472527 0.694118
197 XAH 0.472527 0.75
198 TYR AMP 0.472527 0.786667
199 TBN 0.46875 0.983607
200 3BH 0.46875 0.953125
201 AMP DBH 0.467391 0.821918
202 101 0.465753 0.780822
203 LAQ 0.463158 0.728395
204 TO1 0.462687 0.952381
205 7C5 0.462366 0.819444
206 G3A 0.462366 0.779221
207 UPA 0.459184 0.813333
208 LPA AMP 0.458333 0.728395
209 4UU 0.457447 0.776316
210 7MD 0.457447 0.772152
211 G5P 0.457447 0.779221
212 A A A 0.454545 0.808219
213 5ID 0.454545 0.923077
214 GTA 0.452632 0.75
215 TAD 0.452632 0.769231
216 4YB 0.452632 0.678161
217 KH3 0.452632 0.776316
218 3NZ 0.449438 0.884058
219 TYM 0.44898 0.786667
220 OMR 0.44898 0.740741
221 WSA 0.44898 0.702381
222 AHZ 0.447917 0.728395
223 ARG AMP 0.447917 0.740741
224 139 0.445545 0.782051
225 48N 0.443299 0.779221
226 YLP 0.443299 0.731707
227 ARJ 0.441176 0.857143
228 AFX 0.441176 0.768116
229 AV2 0.440476 0.77027
230 D5M 0.44 0.756757
231 DA 0.44 0.756757
232 5J9 0.43956 0.773333
233 TXD 0.438776 0.789474
234 NAX 0.438776 0.759494
235 6V0 0.438776 0.779221
236 UP5 0.438776 0.8
237 NXX 0.438776 0.810811
238 DND 0.438776 0.810811
239 NAI 0.438776 0.789474
240 4UW 0.438776 0.746835
241 PO4 PO4 A A A A PO4 0.438202 0.802817
242 NA7 0.438202 0.810811
243 MZR 0.4375 0.859375
244 V1N 0.43617 0.819444
245 HO4 0.434783 0.952381
246 649 0.434343 0.662921
247 AF3 ADP 3PG 0.434343 0.746835
248 TXE 0.434343 0.789474
249 ALF ADP 3PG 0.434343 0.746835
250 LA8 ALF 3PG 0.434343 0.746835
251 IMO 0.434211 0.777778
252 3AT 0.433735 0.819444
253 G A A A 0.432692 0.779221
254 YLB 0.43 0.731707
255 YLC 0.43 0.75
256 AP0 0.43 0.779221
257 7MC 0.43 0.753086
258 4TC 0.43 0.779221
259 SGV 0.428571 0.967742
260 BS5 0.427184 0.674157
261 A4P 0.425743 0.73494
262 IOT 0.421569 0.722892
263 DAT 0.419753 0.76
264 COD 0.419048 0.72619
265 YLA 0.417476 0.731707
266 ADJ 0.417476 0.740741
267 T5A 0.417476 0.731707
268 AS 0.415584 0.717949
269 J1D 0.415094 0.625
270 0XU 0.414634 0.823529
271 CNA 0.413462 0.810811
272 AYB 0.413462 0.722892
273 103 0.413333 0.716216
274 A U 0.411765 0.8
275 GMP 0.410959 0.882353
276 NAD IBO 0.409524 0.776316
277 GGZ 0.409091 0.7125
278 ITT 0.407407 0.791667
279 BTX 0.40566 0.710843
280 NAD 0.40566 0.808219
281 4TA 0.40566 0.719512
282 SFB 0.401961 0.709302
283 U A G G 0.401869 0.766234
284 BT5 0.401869 0.702381
285 DZD 0.401869 0.769231
286 DTP 0.4 0.76
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DJF; Ligand: BC3; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3djf.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3DJF; Ligand: BC3; Similar sites found: 59
This union binding pocket(no: 2) in the query (biounit: 3djf.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4Q3F TLA 0.008129 0.42809 None
2 2WPB ZZI 0.01795 0.4145 1.74216
3 5AIP 4HP 0.0273 0.40724 2.05479
4 1Q8A HCS 0.01803 0.41566 2.09059
5 4IMG NGF 0.006893 0.40415 2.09059
6 4V15 PLP 0.01677 0.40376 2.09059
7 1TZJ A3B 0.0245 0.4081 2.43902
8 4BWL MN9 0.02441 0.40782 2.43902
9 5JJU AMP 0.0119 0.41096 2.78746
10 2Q3M MLA 0.01136 0.40732 2.78746
11 1MAI I3P 0.006529 0.43067 3.05344
12 5U5G 7VD 0.01969 0.41239 3.13589
13 3BJE URA 0.00001892 0.40141 3.48432
14 5L2R MLA 0.01957 0.4113 3.83275
15 4WA2 SIA GAL NAG 0.03319 0.40168 3.83275
16 3P0F BAU 0.00273 0.433 4.18118
17 5TVF PUT 0.03067 0.41065 4.21053
18 5CSS G3P 0.009811 0.42349 4.42478
19 4YMJ 4EJ 0.02993 0.40293 4.52962
20 5LPB ADP 0.02324 0.40055 4.52962
21 1EOC 4NC 0.02377 0.40006 5.26316
22 3FGZ BEF 0.02111 0.40389 5.46875
23 3KYF 5GP 5GP 0.004997 0.43358 5.62771
24 2CYB TYR 0.02457 0.40385 5.92335
25 4IP7 FLC 0.0287 0.40382 6.27178
26 2ZZV LAC 0.03371 0.40063 6.27178
27 2GN3 MAN 0.02679 0.40063 6.34921
28 4BMX ADE 0.00004508 0.46112 6.3745
29 4QAR ADE 0.000002327 0.58124 6.46766
30 4WKB TDI 0.00005235 0.49041 6.55738
31 3RZ3 U94 0.01301 0.40535 6.55738
32 1R1Q ACE ARG GLU PTR VAL ASN VAL 0.02638 0.40808 7
33 1TUV VK3 0.01224 0.41838 7.01754
34 3G5K BB2 0.01343 0.40117 7.65027
35 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 0.00008528 0.54747 8.36237
36 1RL4 BRR 0.03066 0.40231 8.51064
37 1U4J MAN 0.01303 0.42298 9.32203
38 3LGS ADE 0.00004369 0.50403 9.3633
39 3LGS SAH 0.00004369 0.50403 9.3633
40 1JE1 GMP 0.0002066 0.47196 9.74576
41 4IV9 TSR 0.03505 0.40632 9.7561
42 3EUF BAU 0.001421 0.45057 10.1045
43 3B9Q MLI 0.008002 0.41791 10.1045
44 2OG2 MLI 0.005825 0.41045 10.1045
45 1OFS SUC 0.02311 0.40859 10.4167
46 2XCM ADP 0.01654 0.40042 10.8108
47 1JG3 VAL TYR PRO IAS HIS ALA 0.01976 0.40405 11.0638
48 1U1F 183 0.003052 0.43427 11.7188
49 4TXJ THM 0.00009659 0.48124 11.8467
50 4YJK URA 0.000194 0.51827 12.6984
51 1ZOS MTM 0.000009547 0.54566 13.0435
52 5KOH HCA 0.01401 0.42683 14.2857
53 3BL6 FMC 0.0000184 0.47424 20
54 5A7C 5D4 0.02016 0.41256 30.0885
55 1ODJ GMP 0.000006389 0.56066 31.9149
56 5F7J ADE 0.0000000309 0.63429 33.4375
57 4GLJ RHB 0.00001635 0.51713 33.7979
58 1K27 MTM 0.00000002521 0.63809 36.7491
59 2A8Y MTA 0.00000003504 0.63194 44.0741
Pocket No.: 3; Query (leader) PDB : 3DJF; Ligand: BC3; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3djf.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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