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Receptor
PDB id Resolution Class Description Source Keywords
3BJE 1.44 Å EC: 2.4.2.- CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI NUCLEOSIDE PHOSPHORY URIDINE PHOSPHORYLASE ACTIVITY TRYPANOSOMA BRUCEI NUCLEOSIDE PHOSPHORYLASE URIDINE PHOSPHORYLASE STRUCTURAL MEDICAL STRUCTURAL GENOMICS OF PATHOGENIC PROTOZOA CONSORTIMSGPP TRYPANOSOMA BRUCEI SLEEPING SICKNESS GLYCOSYLTRANTRANSFERASE
Ref.: THE CRYSTAL STRUCTURE AND ACTIVITY OF A PUTATIVE TRYPANOSOMAL NUCLEOSIDE PHOSPHORYLASE REVEAL IT TO HOMODIMERIC URIDINE PHOSPHORYLASE J.MOL.BIOL. V. 396 1244 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA B:402;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
R1P A:401;
B:401;
Valid;
Valid;
none;
none;
submit data
230.11 C5 H11 O8 P C([C@...
URA A:501;
B:501;
Valid;
Valid;
none;
none;
submit data
112.087 C4 H4 N2 O2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3BJE 1.44 Å EC: 2.4.2.- CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI NUCLEOSIDE PHOSPHORY URIDINE PHOSPHORYLASE ACTIVITY TRYPANOSOMA BRUCEI NUCLEOSIDE PHOSPHORYLASE URIDINE PHOSPHORYLASE STRUCTURAL MEDICAL STRUCTURAL GENOMICS OF PATHOGENIC PROTOZOA CONSORTIMSGPP TRYPANOSOMA BRUCEI SLEEPING SICKNESS GLYCOSYLTRANTRANSFERASE
Ref.: THE CRYSTAL STRUCTURE AND ACTIVITY OF A PUTATIVE TRYPANOSOMAL NUCLEOSIDE PHOSPHORYLASE REVEAL IT TO HOMODIMERIC URIDINE PHOSPHORYLASE J.MOL.BIOL. V. 396 1244 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 3BJE - R1P C5 H11 O8 P C([C@@H]1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 3BJE - R1P C5 H11 O8 P C([C@@H]1[....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 3BJE - R1P C5 H11 O8 P C([C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: R1P; Similar ligands found: 25
No: Ligand ECFP6 Tc MDL keys Tc
1 R1P 1 1
2 M1P 0.852941 0.904762
3 XGP 0.852941 0.904762
4 G1P 0.852941 0.904762
5 GL1 0.852941 0.904762
6 RI2 0.609756 0.926829
7 GFP 0.571429 0.826087
8 GP1 0.571429 0.76
9 NG1 0.48 0.690909
10 GN1 0.48 0.690909
11 ALX 0.465116 0.904762
12 BNX 0.465116 0.904762
13 TRE 0.45 0.622222
14 T6P 0.44 0.844444
15 AMG 0.439024 0.6
16 GYP 0.439024 0.6
17 MBG 0.439024 0.6
18 MMA 0.439024 0.6
19 G16 0.4375 0.840909
20 YO5 0.418605 0.8
21 GPM 0.418605 0.8
22 MVP 0.418182 0.808511
23 PRP 0.411765 0.951219
24 PPC 0.411765 0.886364
25 GMB 0.403846 0.840909
Ligand no: 2; Ligand: URA; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 URA 1 1
2 TUL 0.5 0.725
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3BJE; Ligand: R1P; Similar sites found with APoc: 91
This union binding pocket(no: 1) in the query (biounit: 3bje.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 5KVS 6XR 1.7192
2 5KVS NAP 1.7192
3 4I8P NAD 1.7192
4 5N2I NAP 1.72414
5 2Y6Q I7T 2.00573
6 2Y6Q FAD 2.00573
7 3VCY UD1 2.00573
8 2RL1 UD1 2.00573
9 4A0M NAD 2.00573
10 2PS1 PRP 2.21239
11 5GSN FAD 2.29226
12 3MJY FMN 2.31214
13 3MJY IJZ 2.31214
14 3JSX CC2 2.5641
15 3JSX FAD 2.5641
16 1PVN MZP 2.5788
17 4IXH IMP 2.5788
18 1ZEM NAD 2.67176
19 4BMX ADE 2.78884
20 4OXI GAP 2.86533
21 2FAH GDP 2.86533
22 2XVF FAD 2.86533
23 4I3V NAD 2.86533
24 4FFS BIG 2.92887
25 3BP1 GUN 3.10345
26 5I60 67W 3.15186
27 2ZRU FMN 3.15186
28 1X7D NAD 3.15186
29 5EVY FAD 3.15186
30 4WKB TDI 3.27869
31 2VHJ ADP 3.32326
32 5VEG FMN 3.37079
33 1QMG APX 3.4384
34 6GAS FAD 3.62538
35 3FPZ AHZ 3.68098
36 3W5N RAM 3.72493
37 5EXW 7DT 3.72493
38 4D57 ARG AMP 3.72493
39 1RC0 KT5 3.82775
40 5XFV FMN 3.89222
41 4WOP CTP 4
42 3GD4 FAD 4.01146
43 2IU8 PLM 4.01146
44 2W5P CL8 4.02685
45 2QE0 NAP 4.29799
46 1V25 ANP 4.58453
47 1S16 ANP 4.58453
48 1TLL FMN 4.58453
49 1ZOS MTM 4.78261
50 5X30 HCS 4.87106
51 4PIO SAH 4.95356
52 2IZ1 ATR 5.15759
53 2FKA BEF 5.42636
54 5ZZ6 ADP 5.76923
55 5ZZ6 NAD 5.76923
56 3BL6 FMC 6.08696
57 5WS9 AMP 6.30372
58 1U2Z SAH 6.30372
59 2Q1W NAD 6.30631
60 3KPB SAM 6.55738
61 5WXU FLC 6.59026
62 1E96 GTP 6.77083
63 1LSZ NDG NAG NAG NAG 6.80272
64 2DXU BT5 6.80851
65 1T3D CYS 7.61246
66 4XU6 TDA 8.09524
67 6GAR FAD 8.30946
68 3LGS SAH 10.4869
69 3LGS ADE 10.4869
70 1FIQ FAD 10.5023
71 6AYR BIG 10.5042
72 6HT0 GQ8 10.9677
73 4JWJ SAH 11.3861
74 1WG8 SAM 11.9298
75 1NW4 IMH 12.6812
76 5O4J SAH 13.8686
77 5O4J 9KH 13.8686
78 3NRZ FAD 14.0244
79 3CPJ GDP 16.1435
80 3U40 ADN 17.3554
81 1JE1 GMP 18.6441
82 1A69 FMB 21.8487
83 3QPB R1P 22.3404
84 1VHW ADN 23.7154
85 4DA6 GA2 23.7154
86 6F4W FMC 24.0343
87 2AC7 ADN 26.383
88 3KVY R2B 30.4207
89 3EUF BAU 30.4878
90 4TXJ THM 31.7568
91 1U1F 183 46.0938
Pocket No.: 2; Query (leader) PDB : 3BJE; Ligand: URA; Similar sites found with APoc: 300
This union binding pocket(no: 2) in the query (biounit: 3bje.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 5YSI NCA None
2 1GT4 UNA None
3 3DFR NDP None
4 3DFR MTX None
5 2QTR NXX 1.0582
6 1KYV RBF 1.25786
7 4R2M ANP 1.26582
8 4I9A NCN 1.38889
9 1GPM AMP 1.43266
10 6GNF ADP 1.43266
11 3HUN ZZ7 1.43266
12 4ZUL UN1 1.43266
13 5GM1 SAH 1.6835
14 1KY8 NAP 1.7192
15 3A16 PXO 1.7192
16 4K91 SIN 1.7341
17 5GLN XYP XYP XYP 1.74419
18 5GLN XYS 1.74419
19 3OV6 MK0 1.76322
20 1WXI AMP 1.81818
21 4OR7 NAP 1.81818
22 2PA4 UPG 1.85759
23 3VC1 SAH 1.92308
24 2C78 PUL 2.00573
25 5U3F 7TS 2.00573
26 1KEW NAD 2.00573
27 5YAP NAI 2.00573
28 5YAP 8S0 2.00573
29 3SHR CMP 2.00669
30 1AOE NDP 2.08333
31 1AOE GW3 2.08333
32 6MPT C30 2.0979
33 1GAD NAD 2.12121
34 5UC1 486 2.25225
35 5XDT MB3 2.27273
36 1JGT CMA 2.29226
37 1JGT APC 2.29226
38 4ITH RCM 2.29226
39 3ZF8 GDP 2.29508
40 5HWV MBN 2.30769
41 5N5S NAP 2.3301
42 2DKN NAI 2.35294
43 5EJL C2E 2.41935
44 3AB3 GDP 2.43902
45 3JSX CC2 2.5641
46 3JSX FAD 2.5641
47 5JY4 ISC 2.5788
48 5EEH SAH 2.5788
49 5EEH P9P 2.5788
50 5JXZ ISC 2.5788
51 5JXZ ISJ 2.5788
52 3UZO PLP 2.5788
53 3JUK UPG 2.5788
54 3UZO GLU 2.5788
55 3SSO SAH 2.5788
56 4UUG PXG 2.71084
57 3MB5 SAM 2.7451
58 1C9K 5GP 2.77778
59 4BMX ADE 2.78884
60 3FIU AMP 2.81124
61 1NHZ 486 2.85714
62 2YQS UD1 2.86533
63 5YJS SAL 2.86533
64 3HGM ATP 2.86533
65 2OJW ADP 2.86533
66 4I3V NAD 2.86533
67 3ABA FLI 2.86533
68 3VC3 C6P 2.90698
69 3CQD ATP 2.91262
70 4FFS BIG 2.92887
71 4QAR ADE 2.98507
72 4L2I NAD 3.04183
73 4L2I FAD 3.04183
74 1E3W NAD 3.06513
75 1E6W NAD 3.07692
76 1OG1 TAD 3.09735
77 5F7J ADE 3.125
78 6A46 DCM 3.125
79 5TBS ADE 3.13589
80 1WOR RED 3.15186
81 5X8G S0N 3.15186
82 2E7Z MGD 3.15186
83 1XDS SAM 3.15186
84 3DLA NXX 3.15186
85 6FRN FMN 3.15186
86 5O1I 9GH 3.19635
87 2CWH NDP 3.207
88 2CWH PYC 3.207
89 1U1B PAX 3.22581
90 2VDV SAM 3.25203
91 2ZFU SAH 3.25581
92 4WKB TDI 3.27869
93 1HDR NAD 3.27869
94 1K4M NAD 3.28639
95 4RFM 3P6 3.38346
96 2X6T NAP 3.4384
97 1EFY BZC 3.4384
98 4EI7 GDP 3.4384
99 3CBG SAH 3.44828
100 1U7T TDT 3.44828
101 1U7T NAD 3.44828
102 3DJF BC3 3.48432
103 1FND FAD 3.50318
104 1FND A2P 3.50318
105 4CE5 PDG 3.6036
106 1L3I SAH 3.64583
107 3T4L ZEA 3.7037
108 2XIQ MLC 3.72493
109 1K3T BRZ 3.72493
110 1Y8Q ATP 3.72493
111 3ZIU LSS 3.72493
112 1O97 FAD 3.78788
113 1O97 AMP 3.78788
114 1EQ2 NAP 3.87097
115 3BXF 13P 3.92157
116 3BXF FBP 3.92157
117 4M7V RAR 4
118 4M7V NAP 4
119 2P4S DIH 4.01146
120 5LD5 NAD 4.01146
121 6BQC LOP 4.01146
122 1VKO NAD 4.01146
123 1ELI PYC 4.01146
124 1QAW TRP 4.05405
125 2A8Y MTA 4.07407
126 1C3X 8IG 4.13534
127 2ZMF CMP 4.2328
128 5M3E APR 4.24242
129 1VKF CIT 4.25532
130 5C5H 4YB 4.29799
131 2J8Z NAP 4.29799
132 1FEC FAD 4.29799
133 1E1O LYS 4.29799
134 4R5Z PMP 4.29799
135 4R5Z SIN 4.29799
136 5KVA SAM 4.31655
137 2WSB NAD 4.33071
138 4UTU LRY 4.36681
139 4UTW RFW 4.36681
140 4WKC BIG 4.4898
141 4MDH NAD 4.49102
142 5MDH NAD 4.5045
143 3HVJ 705 4.52489
144 3DLG GWE 4.58453
145 2QZS GLC 4.58453
146 2QZS 250 4.58453
147 2QZS ADP 4.58453
148 1K27 MTM 4.59364
149 4CQM NAP 4.5977
150 3ZZS TRP 4.61538
151 2XG5 EC2 4.62428
152 2XG5 EC5 4.62428
153 3DAA PDD 4.69314
154 3IX9 NDP 4.73684
155 1H5R G1P 4.77816
156 1ZOS MTM 4.78261
157 5K3W PLP 4.79233
158 3O9Z NAD 4.80769
159 3O9Z AKG 4.80769
160 1T57 FMN 4.85437
161 3L4S NAD 4.87106
162 3L4S 3PG 4.87106
163 5IUW IAC 4.87106
164 5IUW NAD 4.87106
165 5ZCE MTT 4.87106
166 3VKC FPQ 4.8951
167 3TAY MN0 4.90798
168 2EQA AMP 5.15759
169 5FUB SAH 5.15759
170 2OEG UPG 5.15759
171 6GNO XDI 5.18518
172 3ESS 18N 5.21739
173 1G2O IMH 5.22388
174 5YAK FMN 5.30303
175 2VYN NAD 5.38922
176 5LHT TIH 5.44218
177 4GCZ FMN 5.44413
178 2X65 M1P 5.44413
179 5DYO FLU 5.66038
180 2YI0 YI0 5.67686
181 4R3U 3KK 5.6962
182 4R3U 3HC 5.6962
183 4N9I PCG 5.71429
184 1CT9 AMP 5.73066
185 5F7N NAG GAL FUC FUC A2G 5.83333
186 5F7Y GLC GAL NAG GAL FUC A2G 5.83333
187 1JR8 FAD 5.98291
188 1B8O IMH 5.98592
189 2XXP DSL 6.01719
190 4ZH7 FUC GAL NAG GAL FUC 6.01719
191 4O9S 2RY 6.04651
192 3BL6 FMC 6.08696
193 4KQ6 DLZ 6.14525
194 4XSH NAI 6.14525
195 5ETJ IM5 6.17284
196 5DJU FMN 6.2069
197 2W9S NDP 6.21118
198 4RT1 C2E 6.25
199 2A5F NAD 6.28571
200 5N0L ILE 6.28931
201 1JV1 UD1 6.30372
202 2VPY MGD 6.30372
203 2V68 CAP 6.30372
204 2V67 CAP 6.30372
205 2V6A CAP 6.30372
206 1IR2 CAP 6.30372
207 1UZH CAP 6.30372
208 2BCG GDP 6.31068
209 4Y85 499 6.3253
210 1HDG NAD 6.3253
211 3G89 SAM 6.4257
212 1IYE PGU 6.47249
213 3QWB NDP 6.58683
214 4PNE SAH 6.62252
215 1BHX ASP PHE GLU GLU ILE 6.66667
216 2PZ8 APC 6.69014
217 3B82 NAD 6.76329
218 5AHW CMP 6.80272
219 5MY8 RXZ 6.87679
220 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 6.87679
221 2JAH NDP 6.88259
222 2JAP NDP 6.88259
223 2A0W DIH 6.92042
224 5EWK P34 7
225 3LF0 ATP 7.01754
226 5IFK HPA 7.05128
227 1REQ DCA 7.16332
228 4R84 CSF 7.16332
229 1O94 AMP 7.44986
230 1RJW ETF 7.44986
231 1E5Q SHR 7.73639
232 4L50 D8X 7.89474
233 5OCG 9R5 7.93651
234 1OQC FAD 8
235 1G8K MGD 8.02292
236 2WN6 NDP 8.02292
237 6ACS CIT 8.13953
238 1XNG ATP 8.20895
239 4OAS 2SW 8.33333
240 5ZW3 SAH 8.44444
241 4UYE 9F9 8.47458
242 4PAB THG 8.59599
243 6FA4 D1W 8.67052
244 3VPH NAD 8.70968
245 4YC0 5OF 8.78661
246 4LOO SB4 8.88252
247 5LLT DND 8.92019
248 2CYE COA 9.02256
249 2RDE C2E 9.16335
250 2Z6D FMN 9.23077
251 1WAP TRP 9.33333
252 1RV1 IMZ 9.41177
253 5W75 SUC 9.74212
254 1T90 NAD 10.0287
255 5X62 SAH 10.0287
256 3KYG 5GP 5GP 10.1322
257 5LOG SAH 10.3004
258 4EES FMN 10.4348
259 3LGS SAH 10.4869
260 3LGS ADE 10.4869
261 6AYR BIG 10.5042
262 3ZZQ TRP 10.7692
263 1VMK GUN 11.1913
264 5UKL SIX 11.4613
265 2J9D AMP 11.7647
266 4GLJ RHB 12.1212
267 5UFN SAH 12.1849
268 4B2Z P5S 12.3209
269 2JHP SAH 12.3209
270 4BTI 7R9 12.5
271 1NW4 IMH 12.6812
272 1UZD CAP 12.6866
273 1WDD CAP 14.0625
274 4EMV 0R9 14.1593
275 3G6K POP 14.3266
276 3G6K FAD 14.3266
277 1D1G NDP 15.4762
278 4YMH SAH 15.8333
279 5N5D SAM 15.9292
280 6G9I CXX 16.0714
281 3U40 ADN 17.3554
282 5OM2 DXT 17.5
283 1JE1 GMP 18.6441
284 2PR5 FMN 20.4545
285 4R38 RBF 20.7143
286 4EHU ANP 21.3768
287 1A69 FMB 21.8487
288 3QPB URA 22.3404
289 4DA6 GA2 23.7154
290 1VHW ADN 23.7154
291 5N9Z CAP 23.741
292 6F4W FMC 24.0343
293 2AC7 ADN 26.383
294 3KVY URA 30.4207
295 3KVY R2B 30.4207
296 3EUF BAU 30.4878
297 4TXJ THM 31.7568
298 3P0F BAU 35.0168
299 4YJK URA 40.873
300 1U1F 183 46.0938
Pocket No.: 3; Query (leader) PDB : 3BJE; Ligand: URA; Similar sites found with APoc: 51
This union binding pocket(no: 3) in the query (biounit: 3bje.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 6AM8 PLT 1.14613
2 1PJS SAH 1.43266
3 2Y6Q I7T 2.00573
4 4GV4 MEJ 2.00573
5 3EFV NAD 2.1645
6 1O9J NAD 2.29226
7 4IPH 1FJ 2.43902
8 4J7H TLO 2.5788
9 3C6K MTA 2.62467
10 3C6K SPD 2.62467
11 3GCZ SAM 3.15186
12 5A5W GUO 3.16206
13 2EW5 Y12 3.8674
14 3EEL 53T 3.96476
15 6MJF SAH 4.01146
16 2JG1 ANP 4.24242
17 4ZGS NAD 4.29799
18 1IY8 NAD 4.49438
19 6GEW SFG 4.58453
20 6GEW SAH 4.58453
21 1RBL CAP 4.58716
22 1KQF MGD 4.60829
23 1I8T FAD 4.87106
24 3QV1 NAD 4.87805
25 3WG6 NDP 4.88599
26 1KYZ SAH 5.15759
27 4B7P 9UN 5.65217
28 3QFS NAP 5.73066
29 3QFS FAD 5.73066
30 3HQP OXL 5.73066
31 3HDY FAD 6.01719
32 3HDY GDU 6.01719
33 5DJT FMN 6.2069
34 4CNG SAH 6.27451
35 3P7N FMN 6.30372
36 2VDH CAP 6.30372
37 1WDK NAD 6.30372
38 5W4W 9WG 6.34441
39 3CV6 NAP 6.50155
40 3CV6 HXS 6.50155
41 2DXU BT5 6.80851
42 1FK8 NAD 7.00389
43 2XYQ SAH 8.19672
44 1CER NAD 9.96979
45 4KCT PYR 12.0344
46 5CFT 51G 12.4324
47 4WUJ FMN 16.3265
48 3IS2 FAD 17.5325
49 3D72 FAD 18.7919
50 2Z6C FMN 25.5814
51 4M38 SAH 28.5714
Pocket No.: 4; Query (leader) PDB : 3BJE; Ligand: R1P; Similar sites found with APoc: 19
This union binding pocket(no: 4) in the query (biounit: 3bje.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 5BRT FAD 1.43266
2 3ITJ FAD 2.29226
3 2IVD FAD 2.5788
4 2QA1 FAD 2.5788
5 1X7D ORN 3.15186
6 1J0D 5PA 3.22581
7 3PT9 SAH 4.29799
8 5JO1 6LM 4.47761
9 4WKC BIG 4.4898
10 5MDH NAD 4.5045
11 4UP3 FAD 4.77707
12 4YKG FAD 5.15759
13 1SOW NAD 5.18293
14 1Q1R FAD 6.01719
15 3Q9T FAY 6.30372
16 4BC5 5FX 7.16332
17 4DQ2 BTX 8.53659
18 5Y6Q FAD 9.87654
19 2CUL FAD 13.7931
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