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Receptor
PDB id Resolution Class Description Source Keywords
1VBH 2.3 Å EC: 2.7.9.1 PYRUVATE PHOSPHATE DIKINASE WITH BOUND MG-PEP FROM MAIZE ZEA MAYS TRANSFERASE MAIZE RIKEN STRUCTURAL GENOMICS/PROTEOMICS INIRSGI STRUCTURAL GENOMICS
Ref.: CRYSTAL STRUCTURES OF PYRUVATE PHOSPHATE DIKINASE F REVEALED AN ALTERNATIVE CONFORMATION IN THE SWIVELI MOTION BIOCHEMISTRY V. 44 1136 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:2000;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
PEP A:3000;
 Valid;
 none;
 submit data
168.042 C3 H5 O6 P C=C(C...
SO4 A:3001;
 Invalid;
 none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1VBH 2.3 Å EC: 2.7.9.1 PYRUVATE PHOSPHATE DIKINASE WITH BOUND MG-PEP FROM MAIZE ZEA MAYS TRANSFERASE MAIZE RIKEN STRUCTURAL GENOMICS/PROTEOMICS INIRSGI STRUCTURAL GENOMICS
Ref.: CRYSTAL STRUCTURES OF PYRUVATE PHOSPHATE DIKINASE F REVEALED AN ALTERNATIVE CONFORMATION IN THE SWIVELI MOTION BIOCHEMISTRY V. 44 1136 2005
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1VBH - PEP C3 H5 O6 P C=C(C(=O)O....
70% 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 1KC7 Ki = 3 uM PPR C3 H5 O6 P C(C(=O)C(=....
2 1VBH - PEP C3 H5 O6 P C=C(C(=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 1KC7 Ki = 3 uM PPR C3 H5 O6 P C(C(=O)C(=....
2 1VBH - PEP C3 H5 O6 P C=C(C(=O)O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PEP; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 PEP 1 1
2 UVW 0.44 0.709677
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1VBH; Ligand: PEP; Similar sites found with APoc: 283
This union binding pocket(no: 1) in the query (biounit: 1vbh.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 2J3M PRI 1.04895
2 2J3M ATP 1.04895
3 3RWP ABQ 1.28617
4 6F5W KG1 1.35501
5 4PNI KQQ 1.42602
6 2PUL ACP 1.51134
7 5V2J UDP 1.55902
8 4REL KMP 1.56951
9 4L9I 8PR 1.5873
10 2Z48 A2G 1.62037
11 2Z49 AMG 1.62037
12 3CV2 OXL 1.69173
13 4S28 AIR 1.73611
14 4S28 SAH 1.73611
15 4QTB 38Z 1.84211
16 2VHW NAI 1.85676
17 3FQ8 PMP 1.87354
18 5WS9 ATP 1.89474
19 5WS9 OXL 1.89474
20 1QPB PYM 1.95382
21 1Y57 MPZ 1.99115
22 4KQW NAP 2
23 4KCT PYR 2.00401
24 1Z6K OAA 2.04778
25 1P7T PYR 2.05198
26 2VCH UDP 2.08333
27 1PA9 CSN 2.11268
28 5OC1 FAD 2.12389
29 4N70 2HX 2.13415
30 4P53 NAI 2.14286
31 1Z6T ADP 2.19966
32 1T8U UAP SGN IDS SGN 2.20588
33 1T8U A3P 2.20588
34 5A0U CHT 2.26415
35 2B9H ADP 2.26629
36 3C0G 3AM 2.2792
37 4PJ3 ANP 2.28311
38 2CNE DFJ 2.30263
39 5NTD BES 2.30326
40 1NY5 ADP 2.32558
41 5CEO 50D 2.33333
42 3GD4 NAD 2.34834
43 1D8C GLV 2.35131
44 1RPN NDP 2.38806
45 4ZLA BES 2.39044
46 4XWM CBI 2.49633
47 5WRI A3P 2.5
48 5GWT NAD 2.51799
49 5WC2 ADP 2.5463
50 4OHY ANP 2.5522
51 2VUT NAD 2.55682
52 4IP7 FLC 2.57827
53 1Q19 SSC 2.58449
54 5WRJ A3P 2.64026
55 5XFV FMN 2.69461
56 3DZD ADP 2.71739
57 3EYA TDP 2.73224
58 5VKT NAP 2.76243
59 1BG2 ADP 2.76923
60 5AAV GW5 2.77778
61 1X1R GDP 2.80899
62 3LRE ADP 2.8169
63 3MGB PAP 2.82132
64 5FAW CHT 2.82209
65 4W93 3L9 2.82258
66 2QZS GLC 2.8866
67 2QZS 250 2.8866
68 2QZS ADP 2.8866
69 2IXB NAD 2.92793
70 1IZC PYR 2.94985
71 5X1M DHB 2.95359
72 5X1M THG 2.95359
73 3NEM AMO 2.96804
74 2V7O DRN 2.97619
75 3IHG FAD 2.99065
76 5MW4 5JU 2.99401
77 3KRB NAP 2.99401
78 2VK4 TPP 3.01954
79 6CQF F97 3.0303
80 4PVV HO4 3.08642
81 4YZN 4K5 3.13589
82 3G5D 1N1 3.14685
83 5TPR NAD 3.15315
84 3TWO NDP 3.16092
85 4B0T ADP 3.24544
86 1SQ5 ADP 3.24675
87 3BZ3 YAM 3.26087
88 4XF6 ADP 3.2967
89 4XF6 LIP 3.2967
90 4XF6 INS 3.2967
91 5KBF CMP 3.32226
92 3SHR CMP 3.34448
93 2HGS GSH 3.37553
94 3C6K SPD 3.41207
95 3C6K MTA 3.41207
96 2V5K OXM 3.48432
97 1VM6 NAD 3.50877
98 2WSI FAD 3.59477
99 1CX4 CMP 3.60656
100 4GCZ FMN 3.63636
101 1MZC BNE 3.66492
102 1MZC FPP 3.66492
103 1VHT BA3 3.66972
104 5AZ1 NDP 3.68272
105 5JNW 6LJ 3.77358
106 2BO4 FLC 3.77834
107 5U6C 7YS 3.80952
108 1VKJ A3P 3.85965
109 1J49 NAD 3.9039
110 4B5W PYR 3.90625
111 4ZS4 ATP 3.90879
112 2AWN ADP 3.93701
113 1RHC F42 ACN 3.93939
114 6HOY AR6 3.97351
115 6HOY TSN 3.97351
116 4JR7 GNP 4.01069
117 1Q20 PLO 4.01338
118 1Q20 A3P 4.01338
119 4FL3 ANP 4.09449
120 1YQD NAP 4.09836
121 5XET ME8 4.15879
122 3ZRR PXG 4.16667
123 5X20 NAD 4.16667
124 3B8I OXL 4.18118
125 1PIG AGL GLC HMC AGL GLC BGC 4.23387
126 5NKB 8ZT 4.24837
127 2PVN P63 4.26136
128 2NCD ADP 4.28571
129 2V68 CAP 4.28571
130 2V67 CAP 4.28571
131 1IR2 CAP 4.28571
132 1KQN NAD 4.30108
133 3PDT ADP 4.36364
134 3LXN MI1 4.40252
135 4L9Z COA 4.42478
136 4L9Z OXL 4.42478
137 4WOP CTP 4.44444
138 1UZD CAP 4.47761
139 2WQN ADP 4.51613
140 4IZY 1J2 4.60705
141 4JK3 NAD 4.6332
142 4GJ3 0XP 4.63576
143 1XJD STU 4.63768
144 3IID APR 4.73934
145 2GU8 796 4.74777
146 3IHZ FK5 4.7619
147 4Y0X ADP 4.8
148 2J4K U5P 4.86726
149 2D4V NAD 4.8951
150 2NPX NAD 4.9217
151 4UXL 5P8 4.96894
152 5C03 AGS 4.97076
153 1EE0 CAA 4.97512
154 3RG9 NDP 5
155 2Y6Q FAD 5.02513
156 3PLS ANP 5.03356
157 5M7P ADP 5.06608
158 4MO2 FDA 5.16304
159 4MO2 FAD 5.16304
160 1U0J ADP 5.24345
161 6C6O ENG 5.26316
162 5UIU 8CG 5.26316
163 2C9O ADP 5.26316
164 3NTY NAP 5.26316
165 3D91 REM 5.27859
166 5TA6 79D 5.30726
167 2GWH A3P 5.36913
168 4A4X JUP 5.37634
169 4G9E C4L 5.37634
170 5FLJ QUE 5.37634
171 1AQU A3P 5.38721
172 4XGU ADP 5.42453
173 2V6A CAP 5.47368
174 5XKT GNP 5.5
175 1JQN DCO 5.54926
176 1C9K 5GP 5.55556
177 5EFQ ADP 5.59701
178 4B7X NAP 5.65476
179 5A89 FMN 5.76923
180 4M26 SIN 5.76923
181 4M26 ZZU 5.76923
182 5UR1 YY9 5.78778
183 4IZC 1GZ 5.81818
184 5H81 NAP 5.9126
185 4LRJ ANP 5.91716
186 1OX5 1PR 5.94595
187 3WV8 ATP 5.9633
188 2QFY AKG 6.08899
189 3LXK MI1 6.11621
190 3UIM ANP 6.13497
191 1J0D 5PA 6.15836
192 4GC1 MAN MAN 6.15942
193 4OFG PCG 6.25
194 4NST ADP 6.26781
195 5WX3 COA 6.31313
196 1SAY PYR 6.37119
197 1KJ1 MAN 6.42202
198 3EKK GS2 6.51466
199 1T3Q FAD 6.54762
200 5IH9 6BF 6.56716
201 5O4J 9KH 6.56934
202 5O4J SAH 6.56934
203 5O4J PJL 6.56934
204 2QEN ADP 6.57143
205 4YJK URA 6.74603
206 2G50 PYR 6.79245
207 3A76 SPD 6.81818
208 1J99 AND 6.82594
209 5TUF FAD 6.84597
210 4E93 GUI 6.89655
211 1ZGS XMM 6.93512
212 5VZ0 2BA 7.07763
213 4NG2 OHN 7.07965
214 2X34 UQ8 7.18232
215 2EXX NAP 7.18954
216 3UWV 2PG 7.27969
217 2VVG ADP 7.42857
218 3Q9T FAY 7.45234
219 2VWT PYR 7.49064
220 2ZEJ GDP 7.6087
221 1JIL 485 7.61905
222 3TA2 AKG 7.62712
223 1U1J MET 7.71242
224 1D2N ANP 7.72059
225 5G5G MCN 7.86026
226 5F5N NAD 7.95848
227 3HQP OXL 8.01603
228 6A1G 9OL 8.05556
229 1RKX NAD 8.12325
230 1Z6Z NAP 8.15603
231 4DDY DN6 8.36502
232 1JG3 ADN 8.51064
233 1N1D C2G 8.52713
234 4Q9M FPP 8.53659
235 5BV6 35G 8.55263
236 1GXU 2HP 8.79121
237 5UUO GSH 8.87372
238 2BR6 HSL 9.12698
239 3NJ4 AFX 9.1954
240 5N87 N66 9.26518
241 1E6E FAD 9.375
242 1ZDU P3A 9.38776
243 3E9I XAH 9.53347
244 3ZCB ATP 9.67742
245 4XYM A12 10
246 1NE6 SP1 10.2473
247 4TWP AXI 10.3321
248 2Z5F A3P 10.4027
249 5DK4 ATP 10.6383
250 5DK4 5BX 10.6383
251 2F59 INI 10.828
252 1ZCB GDP 11.0497
253 5OJI ISN 11.1538
254 1FKB RAP 11.215
255 4UTG ANP 11.2717
256 2PID YSA 11.7978
257 4LHW GNP 12.069
258 3U7S 017 12.1212
259 3CX8 GSP 12.426
260 1WVG APR 12.5348
261 1Z0S ATP 12.9496
262 5K2M ADP 13.2075
263 4C2W ANP 13.4615
264 2PX8 SAH 13.7546
265 5GLN XYP XYP XYP 13.9535
266 4OH4 ANP 14.2857
267 1LOR BMP 14.4737
268 4LIK CIT 14.7959
269 4IJR NDP 15.407
270 1ZY5 ANP 15.5116
271 1BZY IMU 15.6682
272 2WW4 ADP 16.2544
273 4B5P ACO 16.5
274 5DEY 59T 16.835
275 1GP2 GDP 16.9014
276 4L80 OXL 17.2414
277 6C0T EE4 17.2911
278 2KIN ADP 18.0672
279 5EYK 5U5 20.339
280 3V8S 0HD 20.9756
281 2FLI DX5 22.7273
282 2Y65 ADP 40
283 2XZ9 PYR 46.6049
284 1K3A ACP 50
Pocket No.: 2; Query (leader) PDB : 1VBH; Ligand: PEP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1vbh.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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