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Receptor
PDB id Resolution Class Description Source Keywords
4RL4 2.2 Å EC: 3.5.4.25 CRYSTAL STRUCTURE OF GTP CYCLOHYDROLASE II FROM HELICOBACTER 26695 HELICOBACTER PYLORI ALPHA/BETA FOLD HYDROLASE DARP RIBOFLAVIN
Ref.: STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF GTP CYCLOHYDROLASE II FROM HELICOBACTER PYLORI REVEALS DEPENDENT CATALYTIC ACTIVITY. J.STRUCT.BIOL. V. 192 100 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PPV A:201;
B:201;
Valid;
Valid;
none;
none;
submit data
177.975 H4 O7 P2 OP(=O...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4RL4 2.2 Å EC: 3.5.4.25 CRYSTAL STRUCTURE OF GTP CYCLOHYDROLASE II FROM HELICOBACTER 26695 HELICOBACTER PYLORI ALPHA/BETA FOLD HYDROLASE DARP RIBOFLAVIN
Ref.: STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF GTP CYCLOHYDROLASE II FROM HELICOBACTER PYLORI REVEALS DEPENDENT CATALYTIC ACTIVITY. J.STRUCT.BIOL. V. 192 100 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4RL4 - PPV H4 O7 P2 OP(=O)(O)O....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4RL4 - PPV H4 O7 P2 OP(=O)(O)O....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4RL4 - PPV H4 O7 P2 OP(=O)(O)O....
2 2BZ1 - TAU C2 H7 N O3 S C(CS(=O)(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PPV; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 PPV 1 1
2 PIS 0.642857 0.84
3 3PO 0.6 1
4 6YW 0.529412 1
5 PPK 0.473684 0.7
6 POP 0.466667 0.909091
7 XPO 0.411765 0.833333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RL4; Ligand: PPV; Similar sites found with APoc: 347
This union binding pocket(no: 1) in the query (biounit: 4rl4.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 2BOI MFU None
2 1SS4 GSH None
3 2W9S NDP 1.24224
4 1QAN SAH 1.41509
5 1F3L SAH 1.41509
6 3LCC SAH 1.41509
7 4H6Q FAD 1.41509
8 4H6Q TFB 1.41509
9 5O4J 9KH 1.82482
10 5O4J SAH 1.82482
11 5O4J PJL 1.82482
12 6DEN TP9 1.88679
13 6DEN G8A 1.88679
14 6DEN FAD 1.88679
15 3OCZ SRA 1.88679
16 1CDO NAD 1.88679
17 5TO8 7FM 1.88679
18 1G79 FMN 1.88679
19 1G79 PLP 1.88679
20 5T96 79J 1.88679
21 4NBU NAI 2
22 2F1K NAP 2.15054
23 1E3I CXF 2.35849
24 4PNE SAH 2.35849
25 1I1N SAH 2.35849
26 4CE5 PDG 2.35849
27 5GM1 SAH 2.35849
28 4HMT FMN 2.35849
29 4HMT NNV 2.35849
30 3LL9 ADP 2.35849
31 2C94 TSF 2.5
32 4K47 WMP 2.60417
33 1YQD NAP 2.83019
34 4O8A FAD 2.83019
35 2ZJ3 G6P 2.83019
36 2V0C ANZ 2.83019
37 2E7Z MGD 2.83019
38 1DLJ NAI 2.83019
39 1DLJ UGA 2.83019
40 1V8B NAD 2.83019
41 2Q16 ITT 2.83019
42 1Y8Q ATP 2.83019
43 1GZ4 ATP 2.83019
44 4M73 M72 2.83019
45 4M73 SAH 2.83019
46 3WGT FAD 2.83019
47 3WGT QSC 2.83019
48 2YX1 SFG 2.83019
49 2O2C G6Q 2.83019
50 5WKC FAD 2.83019
51 5BW4 SAM 2.83019
52 1T9M FMN 2.83019
53 2H21 SAM 2.83019
54 3BLI ACO 2.83019
55 6F9Q NAD 2.83019
56 4YAG NAI 2.83019
57 5AHO TLA 2.83019
58 1EQ2 NAP 2.83019
59 1T9D FAD 2.83019
60 3H2B SAH 2.95567
61 2AJH MET 3.06122
62 1DR1 NAP 3.1746
63 1DR1 HBI 3.1746
64 1G55 SAH 3.30189
65 4QED NAP 3.30189
66 2FK8 SAM 3.30189
67 5KF6 FAD 3.30189
68 5KF6 TFB 3.30189
69 5ZW3 SAH 3.30189
70 5FFF NAP 3.30189
71 5FEU NAP 3.30189
72 1AE1 NAP 3.30189
73 1H9A NAP 3.30189
74 3PT9 SAH 3.30189
75 1Q19 APC 3.30189
76 3FUU ADN 3.30189
77 5FFF 5XC 3.30189
78 1PJS NAD 3.30189
79 1ELI PYC 3.30189
80 4YGF AZM 3.30189
81 4KM2 ATR 3.35196
82 3EWP APR 3.38983
83 1KPH SAH 3.77358
84 1KPG SAH 3.77358
85 1ZQ9 SAM 3.77358
86 5T67 JHZ 3.77358
87 5T67 SAH 3.77358
88 1N2X SAM 3.77358
89 3H7U NAP 3.77358
90 1SAY PYR 3.77358
91 2IVF MD1 3.77358
92 4X60 SFG 3.77358
93 4X60 3XV 3.77358
94 2QGI UDP 3.77358
95 5I34 IMP 3.77358
96 1KOJ PAN 3.77358
97 4KRI SAH 3.77358
98 3RSR N5P 3.77358
99 2AE2 NAP 3.77358
100 2AE2 PTO 3.77358
101 2X6T NAP 3.77358
102 3GD4 NAD 3.77358
103 3GD4 FAD 3.77358
104 3LL5 ADP 3.77358
105 3LL5 IPE 3.77358
106 3LL5 ATP 3.77358
107 1ZUW DGL 3.77358
108 2BL9 CP6 3.78151
109 2BL9 NDP 3.78151
110 5ZZ6 ADP 3.84615
111 5ZZ6 NAD 3.84615
112 1TPY SAH 4.24528
113 1L1E SAH 4.24528
114 2FZW NAD 4.24528
115 1EFV AMP 4.24528
116 1EFV FAD 4.24528
117 1NJR XYL 4.24528
118 5JH2 A2P 4.24528
119 1OBB NAD 4.24528
120 3WCZ NAP 4.24528
121 1BXG NAD 4.24528
122 5DM1 5D7 4.24528
123 5DM1 SAH 4.24528
124 1VBJ NAP 4.24528
125 1DMR PGD 4.24528
126 4RVG TYD 4.24528
127 5MGZ SAH 4.24528
128 6AMI TRP 4.24528
129 1EU1 MGD 4.24528
130 6ARJ SAH 4.24528
131 6ARJ BW4 4.24528
132 1C1X NAD 4.24528
133 1ZXM ANP 4.24528
134 2NAD NAD 4.24528
135 5WGR FAD 4.24528
136 3B20 NAD 4.24528
137 3IA4 NDP 4.32099
138 3HAZ FAD 4.71698
139 2JHF NAD 4.71698
140 5TOW NAI 4.71698
141 5TOW ADN 4.71698
142 1KOL NAD 4.71698
143 5JCM ISD 4.71698
144 5JCM FAD 4.71698
145 5JCM NAD 4.71698
146 5KOK SAH 4.71698
147 5A04 NDP 4.71698
148 1H6C NDP 4.71698
149 5A04 BGC 4.71698
150 2P69 PLP 4.71698
151 4KCT FDP 4.71698
152 5KOK S9T 4.71698
153 1KQF MGD 4.71698
154 5D2H AKG 4.71698
155 1RYD NDP 4.71698
156 2GSD NAD 4.71698
157 6ECT SAM 4.71698
158 2VT3 ATP 4.71698
159 3GFB NAD 4.71698
160 4JWF SAH 4.71698
161 1RC0 KT5 4.78469
162 1D1T NAD 5.18868
163 6F3N ADN 5.18868
164 6F3N NAD 5.18868
165 5HRA DAS 5.18868
166 6F3M NAD 5.18868
167 1V5F TPP 5.18868
168 1V5F FAD 5.18868
169 5AZ1 NDP 5.18868
170 3CAQ NDP 5.18868
171 1MOQ GLP 5.18868
172 1R18 SAH 5.18868
173 4RPL FAD 5.18868
174 4RPL 3UC 5.18868
175 3VC1 GST 5.18868
176 3VC1 SAH 5.18868
177 2G37 FAD 5.18868
178 5A3B APR 5.18868
179 1P0F NAP 5.18868
180 2QTZ FAD 5.18868
181 2QTZ NAP 5.18868
182 3GEG NAD 5.18868
183 2VVT I24 5.18868
184 1VL8 NAP 5.18868
185 4IVN BMX 5.18868
186 2Q28 ADP 5.18868
187 4IWN GEK 5.18868
188 3WB0 FEG 5.42169
189 2WR9 MAN MAN 5.46875
190 4RQU NAD 5.66038
191 1TIW FAD 5.66038
192 1TIW TFB 5.66038
193 5AGR A52 5.66038
194 6B92 SAH 5.66038
195 2GMH FAD 5.66038
196 4X7R NTO 5.66038
197 4X7R 3YW 5.66038
198 4X7R UDP 5.66038
199 4UTG ANP 5.66038
200 2VPY MGD 5.66038
201 3KRB NAP 5.66038
202 1LDN NAD 5.66038
203 6GFK SAH 5.66038
204 3G89 SAM 5.66038
205 4AMV F6R 5.66038
206 2DFV NAD 5.66038
207 3VPH NAD 5.66038
208 3VPH OXM 5.66038
209 6FDF SAH 5.66038
210 4B7X NAP 5.66038
211 5K9B FMN 6.11111
212 1U3U BNF 6.13208
213 1U3U NAD 6.13208
214 4RDI ATP 6.13208
215 2NYA MGD 6.13208
216 4D79 ATP 6.13208
217 2IV2 MGD 6.13208
218 1QK3 5GP 6.13208
219 3KJS NAP 6.13208
220 3GF4 FAD 6.13208
221 4HKP TKW 6.13208
222 3HQP FDP 6.13208
223 1VP5 NAP 6.13208
224 3Q9N COA 6.38298
225 3NDJ SAH 6.60377
226 3NDJ JHZ 6.60377
227 1FRB ZST 6.60377
228 3CBG SAH 6.60377
229 4PIO SAH 6.60377
230 4PIO AVI 6.60377
231 1ZGD NAP 6.60377
232 1TMO 2MD 6.60377
233 2NXE SAM 6.60377
234 5XNC MTA 6.60377
235 5G09 6DF 6.60377
236 5Z49 RUB 6.69456
237 2VHW NAI 7.07547
238 1MUU NAD 7.07547
239 1MV8 NAD 7.07547
240 3B1Q NOS 7.07547
241 3NJ4 NAD 7.07547
242 2RGJ FAD 7.07547
243 3C6K SPD 7.07547
244 3C6K MTA 7.07547
245 1WK8 VMS 7.2165
246 5FA8 SAM 7.45342
247 4EDF UPG 7.54717
248 5FOM A2H 7.54717
249 5BJX UDP 7.54717
250 5BJX NAD 7.54717
251 3OND ADN 7.54717
252 3OND NAD 7.54717
253 2IXB A2G 7.54717
254 2IXB NAD 7.54717
255 1YBH FAD 7.54717
256 4KIB SAH 7.54717
257 2GZM DGL 7.54717
258 4EA7 JB2 7.54717
259 4EA7 COA 7.54717
260 1G60 SAM 7.54717
261 3IX9 NDP 7.89474
262 1WG8 SAM 8.01887
263 2WFG ZZB 8.01887
264 5ZCM NDP DTT 8.01887
265 1O97 FAD 8.01887
266 1O97 AMP 8.01887
267 1KYQ NAD 8.01887
268 1K4M NAD 8.01887
269 1X87 NAD 8.01887
270 4QTU SAM 8.14815
271 1D1G NDP 8.33333
272 2POC BG6 8.49057
273 4YCA NDP 8.49057
274 4Y30 SAH 8.49057
275 4Y30 49L 8.49057
276 1Z3C SA8 8.49057
277 5WP4 SAH 8.49057
278 4L2I FAD 8.49057
279 1LSS NAD 8.57143
280 4IJR NDP 8.96226
281 1R27 MGD 8.96226
282 4EIL NDP 8.96226
283 3WG6 NDP 8.96226
284 6GKV SAH 8.96226
285 2JFZ 003 9.01961
286 2JFZ DGL 9.01961
287 3A1C ACP 9.40767
288 4UUG PXG 9.43396
289 2DT5 NAD 9.47867
290 5APG EEM 9.72973
291 1L3I SAH 9.90566
292 2ZJ1 ARJ 9.90566
293 2ZJ1 NAD 9.90566
294 5M67 NAD 9.90566
295 5M67 ADE 9.90566
296 5M67 3D1 9.90566
297 1EKO I84 9.90566
298 3NRR NAP 9.90566
299 3NRR D16 9.90566
300 6ECU SAH 9.90566
301 3D36 ADP 9.90566
302 4N02 FNR 9.90566
303 2EV9 SKM 10.2662
304 2EV9 NAP 10.2662
305 5M42 FMN 10.3774
306 2YGM GLA NAG GAL FUC 10.3774
307 1U1I NAD 10.3774
308 3GDH SAH 10.8491
309 1ZQ5 E04 10.8491
310 1ZQ5 NAP 10.8491
311 1XCL SAH 11.0638
312 3EGI ADP 11.165
313 4NMC FAD 11.3208
314 4NMC 2OP 11.3208
315 1GA8 UPF 11.3208
316 1GA8 DEL 11.3208
317 1G8K MGD 11.3208
318 4M7V NAP 11.4286
319 4D5G FAD 11.7925
320 4D5G TPP 11.7925
321 1I8T FAD 11.7925
322 4ZVV GN0 12.2642
323 4ZVV NAD 12.2642
324 2H29 DND 12.6984
325 4EMI FAD 12.7358
326 4EMI NAD 12.7358
327 4EMJ FAD 12.7358
328 1P1C SAH 13.0653
329 1UWK NAD 13.2075
330 1UWK URO 13.2075
331 3WDM ADN 13.2075
332 1H2B NAJ 14.1509
333 2QTR NXX 14.2857
334 4YDD MD1 14.6226
335 4YDD MGD 14.6226
336 3RYC GDP 14.6853
337 1LTH NAD 16.5094
338 3L9W AMP 16.9811
339 3L9W GSH 16.9811
340 4KGD TDP 17.9245
341 4KGD FAD 17.9245
342 2Q4W FAD 18.8679
343 2ASF CIT 18.9781
344 3T7S SAM 20.283
345 3DMH GMP 20.7547
346 3DMH SAM 20.7547
347 1L5Y BEF 30.9677
Pocket No.: 2; Query (leader) PDB : 4RL4; Ligand: PPV; Similar sites found with APoc: 19
This union binding pocket(no: 2) in the query (biounit: 4rl4.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 4X8O AP5 None
2 6B2M COA 2.83019
3 3CU0 GAL GAL SO4 2.83019
4 1QPR PPC 2.83019
5 2XXP DSL 3.77358
6 3ZF8 GDP 4.24528
7 2C5S AMP 4.24528
8 4NDO ATP 4.24528
9 5MM0 GDD 6.13208
10 6H3O FAD 6.60377
11 5A0R ACE GLU VAL ASN PRO 7.07071
12 5VZ0 ADP 7.07547
13 4GIM PSU 7.07547
14 4M1U MBG A2G 7.07547
15 2APC UDM 7.54717
16 5GUD 2IT 8.49057
17 5GUD NDP 8.49057
18 2ZAT NAP 9.43396
19 2I8T GDD 9.58084
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