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: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 PPV 1 1
2 PIS 0.642857 0.84
3 3PO 0.6 1
4 PPK 0.473684 0.7
5 POP 0.466667 0.909091
6 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: 240
This union binding pocket(no: 1) in the query (biounit: 4rl4.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SS4 GSH 0.002877 0.40229 None
2 2W9S NDP 0.02083 0.42783 1.24224
3 1QAN SAH 0.003454 0.44191 1.41509
4 1F3L SAH 0.006695 0.43804 1.41509
5 3LCC SAH 0.007474 0.42634 1.41509
6 4H6Q FAD 0.01924 0.42039 1.41509
7 4H6Q TFB 0.0224 0.42039 1.41509
8 4G74 FAD 0.04274 0.41308 1.41509
9 5O4J 9KH 0.02829 0.4041 1.82482
10 5O4J SAH 0.02829 0.4041 1.82482
11 5O4J PJL 0.03455 0.40224 1.82482
12 1CDO NAD 0.01508 0.41561 1.88679
13 5TO8 7FM 0.0462 0.41278 1.88679
14 5T96 79J 0.01603 0.40348 1.88679
15 2V3B FAD 0.01348 0.43188 2.35849
16 2V3A FAD 0.02254 0.42925 2.35849
17 4PNE SAH 0.01143 0.42721 2.35849
18 1I1N SAH 0.01143 0.42701 2.35849
19 4CE5 PDG 0.01397 0.42168 2.35849
20 5GM1 SAH 0.01528 0.41854 2.35849
21 4HMT NNV 0.02581 0.41079 2.35849
22 4HMT FMN 0.0245 0.41079 2.35849
23 2C94 TSF 0.02887 0.40548 2.5
24 4K47 WMP 0.004873 0.43157 2.60417
25 2Q16 ITT 0.0007622 0.49627 2.83019
26 4O8A FAD 0.004497 0.4667 2.83019
27 2V0C ANZ 0.00267 0.45452 2.83019
28 2E7Z MGD 0.0111 0.44768 2.83019
29 1V8B NAD 0.0136 0.44098 2.83019
30 1Y8Q ATP 0.004074 0.43204 2.83019
31 1T9M FMN 0.01219 0.42126 2.83019
32 4M73 SAH 0.0206 0.41594 2.83019
33 3WGT QSC 0.04491 0.41542 2.83019
34 3WGT FAD 0.04374 0.41542 2.83019
35 2YX1 SFG 0.01427 0.41429 2.83019
36 2O2C G6Q 0.01523 0.41422 2.83019
37 5BW4 SAM 0.01608 0.41112 2.83019
38 2H21 SAM 0.03217 0.40916 2.83019
39 4YAG NAI 0.04723 0.40801 2.83019
40 5AHO TLA 0.01192 0.40477 2.83019
41 1EQ2 NAP 0.04121 0.40315 2.83019
42 3H2B SAH 0.02262 0.40108 2.95567
43 2AJH MET 0.0009463 0.46717 3.06122
44 1DR1 HBI 0.03242 0.42384 3.1746
45 1DR1 NAP 0.03242 0.42384 3.1746
46 1G55 SAH 0.002375 0.46213 3.30189
47 4QED NAP 0.004048 0.4602 3.30189
48 2FK8 SAM 0.003752 0.45402 3.30189
49 5KF6 TFB 0.008253 0.4451 3.30189
50 5KF6 FAD 0.008253 0.4451 3.30189
51 1PJS NAD 0.008251 0.43939 3.30189
52 1AE1 NAP 0.03297 0.41131 3.30189
53 3PT9 SAH 0.01081 0.41066 3.30189
54 3FUU ADN 0.01007 0.40996 3.30189
55 1ELI PYC 0.03985 0.40142 3.30189
56 4YGF AZM 0.02672 0.40121 3.30189
57 4KM2 ATR 0.0427 0.42437 3.35196
58 3EWP APR 0.02101 0.40406 3.38983
59 1KPH SAH 0.0023 0.47219 3.77358
60 1KPG SAH 0.004965 0.45926 3.77358
61 1ZQ9 SAM 0.001806 0.44977 3.77358
62 5T67 JHZ 0.01805 0.44657 3.77358
63 5T67 SAH 0.01544 0.44645 3.77358
64 1N2X SAM 0.006123 0.43774 3.77358
65 3H7U NAP 0.01127 0.43686 3.77358
66 2IVF MD1 0.01259 0.43276 3.77358
67 2QGI UDP 0.007062 0.42087 3.77358
68 5I34 IMP 0.01482 0.42059 3.77358
69 4KRI SAH 0.01375 0.41753 3.77358
70 2AE2 PTO 0.04204 0.41099 3.77358
71 2AE2 NAP 0.04204 0.41099 3.77358
72 2X6T NAP 0.02474 0.4104 3.77358
73 3LL5 ADP 0.02451 0.40484 3.77358
74 3LL5 IPE 0.02451 0.40484 3.77358
75 3LL5 ATP 0.01834 0.40471 3.77358
76 1ZUW DGL 0.009123 0.40452 3.77358
77 2BL9 CP6 0.03983 0.41975 3.78151
78 2BL9 NDP 0.03983 0.41975 3.78151
79 1TPY SAH 0.00235 0.47022 4.24528
80 1L1E SAH 0.002358 0.46872 4.24528
81 2FZW NAD 0.008085 0.45555 4.24528
82 1EFV FAD 0.01589 0.44188 4.24528
83 1EFV AMP 0.01589 0.44188 4.24528
84 5JH2 A2P 0.003717 0.43893 4.24528
85 1OBB NAD 0.008051 0.43753 4.24528
86 3WCZ NAP 0.01332 0.434 4.24528
87 5DM1 5D7 0.01994 0.42869 4.24528
88 5DM1 SAH 0.01924 0.42869 4.24528
89 1VBJ NAP 0.01578 0.42803 4.24528
90 1DMR PGD 0.03559 0.4269 4.24528
91 4RVG TYD 0.03766 0.42435 4.24528
92 5MGZ SAH 0.009401 0.42262 4.24528
93 5K8V 6RE 0.03454 0.4138 4.24528
94 2NAD NAD 0.03922 0.40363 4.24528
95 5WGR FAD 0.04596 0.40111 4.24528
96 3W7T BMA 0.03931 0.4004 4.24528
97 3IA4 NDP 0.03276 0.42279 4.32099
98 3A0T ADP 0.02523 0.40746 4.60526
99 2JHF NAD 0.02528 0.45948 4.71698
100 4K28 NAD 0.006767 0.44428 4.71698
101 5JCM FAD 0.04135 0.43169 4.71698
102 5JCM NAD 0.0422 0.43169 4.71698
103 5JCM ISD 0.0422 0.43169 4.71698
104 5KOK SAH 0.01077 0.42981 4.71698
105 5A04 BGC 0.04894 0.42552 4.71698
106 5A04 NDP 0.04386 0.42552 4.71698
107 5T0B SIA GAL NAG 0.01705 0.41972 4.71698
108 5KOK S9T 0.03654 0.41444 4.71698
109 1KQF MGD 0.01715 0.41232 4.71698
110 5D2H AKG 0.01356 0.4121 4.71698
111 2VT3 ATP 0.01593 0.40375 4.71698
112 4JWF SAH 0.04791 0.40206 4.71698
113 1RC0 KT5 0.01454 0.42544 4.78469
114 5HRA DAS 0.004245 0.439 5.18868
115 1D1T NAD 0.01113 0.43158 5.18868
116 5AZ1 NDP 0.01582 0.43124 5.18868
117 3CAQ NDP 0.02458 0.42935 5.18868
118 1R18 SAH 0.006514 0.42841 5.18868
119 4RPL FAD 0.03179 0.42304 5.18868
120 3VC1 SAH 0.02836 0.42175 5.18868
121 3VC1 GST 0.02836 0.42175 5.18868
122 2G37 FAD 0.01045 0.4205 5.18868
123 5A3B APR 0.0219 0.41787 5.18868
124 1P0F NAP 0.02857 0.41493 5.18868
125 2QTZ FAD 0.01891 0.41264 5.18868
126 4WZ8 3W7 0.02508 0.41188 5.18868
127 2QTZ NAP 0.04966 0.40996 5.18868
128 4IVN BMX 0.01608 0.40111 5.18868
129 4IWN GEK 0.04138 0.40025 5.18868
130 3WB0 FEG 0.001408 0.48247 5.42169
131 2WR9 MAN MAN 0.004949 0.42746 5.46875
132 4RQU NAD 0.002772 0.47621 5.66038
133 1TIW FAD 0.006949 0.4627 5.66038
134 1TIW TFB 0.006949 0.4627 5.66038
135 5AGR A52 0.002191 0.46024 5.66038
136 2GMH FAD 0.02084 0.42902 5.66038
137 4X7R NTO 0.02544 0.4287 5.66038
138 3VPH OXM 0.01934 0.42725 5.66038
139 4X7R 3YW 0.01405 0.42594 5.66038
140 4X7R UDP 0.01842 0.42507 5.66038
141 4AMV F6R 0.01174 0.42375 5.66038
142 3KRB NAP 0.01801 0.42363 5.66038
143 3G89 SAM 0.00762 0.42102 5.66038
144 2DFV NAD 0.02172 0.41422 5.66038
145 4B7X NAP 0.03558 0.40141 5.66038
146 5K9B FMN 0.01616 0.40092 6.11111
147 1U3U NAD 0.008637 0.45618 6.13208
148 1U3U BNF 0.008637 0.45618 6.13208
149 4RDI ATP 0.003988 0.43423 6.13208
150 2NYA MGD 0.02075 0.43001 6.13208
151 4D79 ATP 0.006526 0.42773 6.13208
152 2IV2 MGD 0.02083 0.42476 6.13208
153 3KJS NAP 0.04805 0.40796 6.13208
154 3GF4 FAD 0.04822 0.40724 6.13208
155 4HKP TKW 0.01645 0.40614 6.13208
156 3HQP FDP 0.0167 0.40308 6.13208
157 1VP5 NAP 0.04264 0.40079 6.13208
158 3Q9N COA 0.01564 0.41257 6.38298
159 3NDJ JHZ 0.02664 0.43832 6.60377
160 3NDJ SAH 0.02664 0.43832 6.60377
161 1FRB ZST 0.01968 0.4377 6.60377
162 4PIO AVI 0.01141 0.43405 6.60377
163 4PIO SAH 0.01191 0.43405 6.60377
164 1ZGD NAP 0.02692 0.40818 6.60377
165 1TMO 2MD 0.03271 0.40773 6.60377
166 2NXE SAM 0.02044 0.40684 6.60377
167 2VHW NAI 0.00391 0.47542 7.07547
168 1MUU NAD 0.005541 0.45196 7.07547
169 1MV8 NAD 0.005614 0.44985 7.07547
170 3B1Q NOS 0.01307 0.44983 7.07547
171 2RGJ FAD 0.02648 0.41666 7.07547
172 3C6K MTA 0.02278 0.40439 7.07547
173 3C6K SPD 0.02278 0.40439 7.07547
174 1WK8 VMS 0.003023 0.44549 7.2165
175 5FA8 SAM 0.00185 0.46533 7.45342
176 3OND ADN 0.02333 0.43511 7.54717
177 3OND NAD 0.02333 0.43511 7.54717
178 4KIB SAH 0.01104 0.41539 7.54717
179 2GZM DGL 0.008342 0.40746 7.54717
180 1G60 SAM 0.02591 0.40736 7.54717
181 3IX9 NDP 0.03615 0.41354 7.89474
182 1WG8 SAM 0.001352 0.47832 8.01887
183 2WFG ZZB 0.0021 0.4714 8.01887
184 1O97 AMP 0.04523 0.42109 8.01887
185 1O97 FAD 0.04523 0.42109 8.01887
186 1KYQ NAD 0.01401 0.42101 8.01887
187 1X87 NAD 0.01672 0.40998 8.01887
188 1K4M NAD 0.0284 0.40899 8.01887
189 4QTU SAM 0.01032 0.41114 8.14815
190 2POC BG6 0.003853 0.44529 8.49057
191 4Y2H SAH 0.02151 0.42235 8.49057
192 1Z3C SA8 0.01538 0.42073 8.49057
193 4Y2H 49K 0.0284 0.41532 8.49057
194 1LSS NAD 0.001595 0.47255 8.57143
195 4IJR NDP 0.003081 0.47757 8.96226
196 1R27 MGD 0.01355 0.43999 8.96226
197 4EIL NDP 0.01775 0.42831 8.96226
198 3WG6 NDP 0.02141 0.41889 8.96226
199 2JFZ 003 0.047 0.41138 9.01961
200 3A1C ACP 0.01131 0.41536 9.40767
201 4UUG PXG 0.02688 0.40833 9.43396
202 5APG EEM 0.005532 0.44218 9.72973
203 1L3I SAH 0.004974 0.43832 9.90566
204 2ZJ1 ARJ 0.02578 0.43433 9.90566
205 5M67 3D1 0.02696 0.43079 9.90566
206 2ZJ1 NAD 0.03155 0.43052 9.90566
207 5M67 NAD 0.02926 0.42773 9.90566
208 5M67 ADE 0.02902 0.42754 9.90566
209 1EKO I84 0.03006 0.42508 9.90566
210 3NRR NAP 0.04332 0.42185 9.90566
211 3NRR D16 0.04899 0.42181 9.90566
212 2EV9 SKM 0.03199 0.41889 10.2662
213 2EV9 NAP 0.03199 0.41889 10.2662
214 5M42 FMN 0.01143 0.41356 10.3774
215 1ZQ5 NAP 0.04335 0.41932 10.8491
216 1ZQ5 E04 0.04335 0.41932 10.8491
217 1XCL SAH 0.02022 0.40592 11.0638
218 3EGI ADP 0.001707 0.44361 11.165
219 4NMC FAD 0.004651 0.47261 11.3208
220 4NMC 2OP 0.01558 0.42907 11.3208
221 4M7V NAP 0.04802 0.41069 11.4286
222 1I8T FAD 0.0212 0.41709 11.7925
223 2H29 DND 0.01391 0.42721 12.6984
224 4EMI FAD 0.008694 0.45012 12.7358
225 4EMI NAD 0.01573 0.45012 12.7358
226 4EMJ FAD 0.01534 0.42962 12.7358
227 1QSR ACO 0.01971 0.40126 12.963
228 1P1C SAH 0.01072 0.41356 13.0653
229 1UWK NAD 0.01238 0.42698 13.2075
230 1UWK URO 0.01238 0.42698 13.2075
231 2QTR NXX 0.02211 0.41919 14.2857
232 4YDD MGD 0.02484 0.43546 14.6226
233 4YDD MD1 0.02484 0.43546 14.6226
234 3RYC GDP 0.04235 0.40472 14.6853
235 3L9W AMP 0.02326 0.41055 16.9811
236 3L9W GSH 0.02131 0.40957 16.9811
237 2Q4W FAD 0.03562 0.41345 18.8679
238 3T7S SAM 0.01205 0.41629 20.283
239 3DMH SAM 0.006606 0.43079 20.7547
240 3DMH GMP 0.009486 0.43079 20.7547
Pocket No.: 2; Query (leader) PDB : 4RL4; Ligand: PPV; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4rl4.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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