Receptor
PDB id Resolution Class Description Source Keywords
2F6U 1.55 Å EC: 2.5.1.42 CRYSTAL STRUCTURE OF (S)-3-O-GERANYLGERANYLGLYCERYL PHOSPHATE SYNTHASE COMPLEXED WITH CITRATE ARCHAEOGLOBUS FULGIDUS NON-CANONICAL TIM-BARREL; PRENYLTRANSFERASE; ARCHAEAL LIPID SYNTHESIS; DIMER
Ref.: THE CRYSTAL STRUCTURE OF (S)-3-O-GERANYLGERANYLGLYCERYL PHOSPHATE SYNTHASE REVEALS AN ANCIENT FOLD FOR AN ANCIENT ENZYME J.BIOL.CHEM. V. 281 6070 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CIT A:3001;
B:3002;
Valid;
Valid;
none;
none;
submit data
192.124 C6 H8 O7 C(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2F6U 1.55 Å EC: 2.5.1.42 CRYSTAL STRUCTURE OF (S)-3-O-GERANYLGERANYLGLYCERYL PHOSPHATE SYNTHASE COMPLEXED WITH CITRATE ARCHAEOGLOBUS FULGIDUS NON-CANONICAL TIM-BARREL; PRENYLTRANSFERASE; ARCHAEAL LIPID SYNTHESIS; DIMER
Ref.: THE CRYSTAL STRUCTURE OF (S)-3-O-GERANYLGERANYLGLYCERYL PHOSPHATE SYNTHASE REVEALS AN ANCIENT FOLD FOR AN ANCIENT ENZYME J.BIOL.CHEM. V. 281 6070 2006
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2F6U - CIT C6 H8 O7 C(C(=O)O)C....
2 2F6X - 1GP C3 H9 O6 P C([C@@H](C....
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 2F6U - CIT C6 H8 O7 C(C(=O)O)C....
2 2F6X - 1GP C3 H9 O6 P C([C@@H](C....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2F6U - CIT C6 H8 O7 C(C(=O)O)C....
2 2F6X - 1GP C3 H9 O6 P C([C@@H](C....
3 4NAE - 1GP C3 H9 O6 P C([C@@H](C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CIT; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 CIT 1 1
2 HCA 0.576923 0.884615
3 MAH 0.44 0.807692
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2F6U; Ligand: CIT; Similar sites found: 248
This union binding pocket(no: 1) in the query (biounit: 2f6u.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4I9A NCN 0.001956 0.45485 1.28205
2 1UUO BRF 0.01912 0.44268 1.28205
3 1UUO ORO 0.01807 0.44268 1.28205
4 3K56 IS3 0.00949 0.416 1.28205
5 3TTZ 07N 0.01183 0.40899 1.51515
6 1L3I SAH 0.03152 0.4058 1.5625
7 3UWV 2PG 0.00002985 0.55406 1.7094
8 5U5G NAP 0.03648 0.4049 1.7094
9 1Q5H DUD 0.005163 0.43553 2.04082
10 4EWN 0VR 0.0001131 0.51477 2.13675
11 4YMZ 13P 0.00008794 0.49217 2.13675
12 3OIX FMN 0.002372 0.46017 2.13675
13 1I0Z NAI 0.03812 0.40504 2.13675
14 1T32 OHH 0.01067 0.41555 2.23214
15 1GZF NAD 0.02514 0.40376 2.36967
16 1GZF ADP 0.02165 0.40193 2.36967
17 1NJJ ORX 0.01222 0.41998 2.5641
18 1V1A ADP 0.01113 0.41663 2.5641
19 5H56 TYD 0.03131 0.40846 2.5641
20 5H56 ADP 0.03131 0.40846 2.5641
21 1M5W DXP 0.01103 0.40294 2.5641
22 1XUJ BOZ 0.04837 0.41627 2.69058
23 1YF4 CYS TYR PHE GLN ASN CYS PRO ARG GLY NH2 0.02328 0.41535 2.69058
24 1HDR NAD 0.01079 0.45227 2.99145
25 2E5V FAD 0.02062 0.43414 2.99145
26 5L2Z 70C 0.0144 0.43237 2.99145
27 1SQA UI1 0.02348 0.41979 2.99145
28 2NVA PL2 0.01701 0.41864 2.99145
29 1N1G BCP 0.02978 0.41627 2.99145
30 4OLT GCS GCS GCS GCS GCS GCS 0.03418 0.40874 2.99145
31 2A92 NAI 0.03779 0.40749 2.99145
32 4I4B 1CV 0.04843 0.40368 2.99145
33 3UBM COA 0.02953 0.40318 2.99145
34 1SOW NAD 0.04601 0.40282 2.99145
35 3EXS 5RP 0.0003121 0.48441 3.16742
36 5GM9 CBK 0.04315 0.40213 3.28639
37 4N65 FMN 0.007285 0.44218 3.30189
38 4N65 AQN 0.02478 0.41001 3.30189
39 4R81 FMN 0.01445 0.41451 3.39806
40 1SW0 PGA 0.00002696 0.54001 3.4188
41 2QCD U5P 0.0001412 0.51723 3.4188
42 3MI2 PFU 0.001159 0.50537 3.4188
43 4HKP TKW 0.0003282 0.5027 3.4188
44 4HKP 16B 0.0003984 0.49205 3.4188
45 1EIX BMQ 0.0008547 0.47301 3.4188
46 2RDT FMN 0.00261 0.46129 3.4188
47 2RDT 2RD 0.003568 0.46129 3.4188
48 1TB3 FMN 0.006269 0.44696 3.4188
49 3HF3 FMN 0.007464 0.43271 3.4188
50 4PLG NAI 0.03681 0.41317 3.4188
51 4D86 ADP 0.01852 0.40898 3.4188
52 2RGO FAD 0.04867 0.40646 3.4188
53 2Z9C FMN 0.01797 0.40965 3.5
54 2QTR NXX 0.03506 0.40815 3.7037
55 1OFD FMN 0.001501 0.48649 3.84615
56 2HSA FMN 0.001077 0.4861 3.84615
57 3KRU FMN 0.002264 0.47313 3.84615
58 1OFD AKG 0.006708 0.44911 3.84615
59 3WG6 NDP 0.01727 0.42227 3.84615
60 1AFS NAP 0.01927 0.42097 3.84615
61 2HW1 ANP 0.01996 0.40896 3.84615
62 1JG3 ADN 0.02437 0.4011 3.84615
63 3N7O N7O 0.02397 0.41078 3.9823
64 3L9R L9Q 0.03499 0.41038 4.08163
65 2YPI PGA 0.00005165 0.52284 4.2735
66 1UJP CIT 0.00003019 0.46185 4.2735
67 5X8G S0N 0.02381 0.43298 4.2735
68 2VJM COA 0.02175 0.413 4.2735
69 5GXU FMN 0.01786 0.40803 4.2735
70 1E3W NAD 0.04122 0.4032 4.2735
71 1UTJ ABN 0.02598 0.40303 4.2735
72 4IXH IMP 0.0003751 0.50165 4.70085
73 3CQD ATP 0.01239 0.43908 4.70085
74 1QPR PPC 0.007123 0.43206 4.70085
75 2NPX NAD 0.03696 0.42763 4.70085
76 2C0U FAD NBT 0.02494 0.42247 4.70085
77 1BWV CAP 0.01455 0.41259 4.70085
78 1GV0 NAD 0.03389 0.4078 4.70085
79 2XZ9 PYR 0.007334 0.40356 4.70085
80 1Q6O LG6 0.0003684 0.48903 5.09259
81 1AL8 DHP 0.005007 0.45215 5.12821
82 1AL8 FMN 0.003387 0.45215 5.12821
83 2Q3R FMN 0.003849 0.44395 5.12821
84 1F76 FMN 0.00917 0.43273 5.12821
85 1TUF AZ1 0.0111 0.42692 5.12821
86 1H74 ILE 0.02954 0.40858 5.12821
87 1VL0 NAI 0.03055 0.4052 5.12821
88 2PX8 SAH 0.02497 0.40056 5.12821
89 3B82 NAD 0.02325 0.40863 5.31401
90 3BW2 FMN 0.00004124 0.56267 5.55556
91 4JIQ 1L5 0.007153 0.43838 5.55556
92 4JIQ FMN 0.007153 0.43838 5.55556
93 1ZFJ IMP 0.006717 0.43158 5.55556
94 1RHC F42 ACN 0.02809 0.41218 5.55556
95 1GUZ NAD 0.03371 0.40674 5.55556
96 5THZ SAH 0.02964 0.40308 5.55556
97 4R38 RBF 0.02293 0.40419 5.71429
98 2TPS TPS 0.007982 0.43589 5.72687
99 1DJL NAP 0.02084 0.42259 5.7971
100 1L5Y BEF 0.0003055 0.41121 5.80645
101 5J6Y BGC 0.006023 0.41329 5.85106
102 5J6Y GLC 0.006023 0.41329 5.85106
103 2UUU PL3 0.01136 0.45408 5.98291
104 2UUU FAD 0.01136 0.45408 5.98291
105 1PS9 FMN 0.002953 0.45351 5.98291
106 4QNW FMN 0.003148 0.45028 5.98291
107 1NZY BCA 0.005998 0.44528 5.98291
108 2ZRU FMN 0.009293 0.44483 5.98291
109 3AXK NDP 0.007987 0.4219 5.98291
110 1WDD CAP 0.01166 0.41931 5.98291
111 1RBL CAP 0.01416 0.4183 5.98291
112 1LDM NAD 0.02536 0.41457 5.98291
113 4LUT DCS 0.0179 0.40614 5.98291
114 4JAL SAH 0.01361 0.41406 5.98802
115 1PNO NAP 0.02094 0.41903 6.11111
116 3EWP APR 0.02082 0.4126 6.21469
117 5A5W GUO 0.00001204 0.60528 6.32411
118 4C0X FMN 0.02718 0.40922 6.40394
119 4CW5 FMN 0.001127 0.46912 6.41026
120 1GTE FMN 0.003562 0.46508 6.41026
121 4IGH 1EA 0.01799 0.44871 6.41026
122 4IGH ORO 0.01799 0.44871 6.41026
123 4IGH FMN 0.01799 0.44871 6.41026
124 2VD9 EPC 0.00624 0.42937 6.41026
125 2VD9 IN5 0.006055 0.42796 6.41026
126 1QO8 FAD 0.04481 0.41282 6.41026
127 1D4O NAP 0.01443 0.42378 6.52174
128 3QH2 3NM 0.0004736 0.46925 6.78733
129 1JCM 137 0.003244 0.44375 6.83761
130 1O97 AMP 0.025 0.43606 6.83761
131 2B4G FMN 0.01711 0.41988 6.83761
132 9LDT NAD 0.02441 0.41663 6.83761
133 3PNL ADP 0.01794 0.41297 6.83761
134 9LDB NAD 0.03093 0.41109 6.83761
135 4DQ2 BTX 0.032 0.40795 6.83761
136 4JK3 NAD 0.02992 0.407 6.83761
137 1H2B NAJ 0.04676 0.40349 6.83761
138 3GFS FMN 0.01277 0.40733 6.89655
139 2V67 CAP 0.0113 0.42174 7.14286
140 2V63 CAP 0.01135 0.42164 7.14286
141 2V6A CAP 0.01077 0.42107 7.14286
142 2VDH CAP 0.01432 0.41643 7.14286
143 1PQ7 ARG 0.01807 0.404 7.14286
144 3B0P FMN 0.00005353 0.53107 7.26496
145 1PVN MZP 0.0006225 0.51195 7.26496
146 1VYP FMN 0.004258 0.45017 7.26496
147 1VYP TNF 0.003975 0.45017 7.26496
148 2OOR TXP 0.01486 0.42445 7.26496
149 3ATY FMN 0.01395 0.42172 7.26496
150 1NM5 NAD 0.04479 0.41956 7.26496
151 3KFC 61X 0.03868 0.40693 7.26496
152 2H29 DND 0.02722 0.41521 7.40741
153 1UZD CAP 0.01064 0.42308 7.46269
154 1TRD PGH 0.00001746 0.54936 7.69231
155 2Q8Z NUP 0.001476 0.47084 7.69231
156 3C3N FMN 0.009636 0.4429 7.69231
157 3G6K POP 0.03208 0.41243 7.69231
158 3G6K FAD 0.02762 0.41138 7.69231
159 4JD3 COA 0.04797 0.41116 7.69231
160 4JD3 PLM 0.04958 0.41116 7.69231
161 4A62 ANP 0.02723 0.40197 7.69231
162 3OVR 5SP 0.001537 0.46814 7.89474
163 2Z6J FMN 0.00009403 0.54203 8.11966
164 2Z6I FMN 0.00005841 0.54133 8.11966
165 4AF0 IMP 0.0008372 0.48174 8.11966
166 3CV6 HXS 0.008301 0.45059 8.11966
167 3CV6 NAP 0.007956 0.45059 8.11966
168 1OYB HBA 0.006113 0.44343 8.11966
169 1OYB FMN 0.004988 0.44343 8.11966
170 1KBI PYR 0.009457 0.43346 8.11966
171 3ZEU AGS 0.01489 0.41554 8.11966
172 3ZEU ADP 0.01332 0.41454 8.11966
173 3O03 NAP 0.03435 0.40381 8.11966
174 1UZH CAP 0.01585 0.41414 8.19672
175 1IAU ACE ILE GLU PRO ASJ 0.01406 0.40951 8.37004
176 4PTZ FMN 0.02112 0.40247 8.37696
177 1ME8 RVP 0.0008536 0.50094 8.54701
178 2BLE 5GP 0.002474 0.46556 8.54701
179 1P4C FMN 0.005229 0.45244 8.54701
180 1EP2 FMN 0.005878 0.44574 8.54701
181 1EP2 ORO 0.008142 0.44574 8.54701
182 1AJ8 COA 0.02298 0.4006 8.54701
183 2FLI DX5 0.001061 0.47454 8.63636
184 5EYW PGA 0.00007331 0.4955 8.97436
185 1Z48 FMN 0.003126 0.4424 8.97436
186 1Z41 FMN 0.004252 0.43568 8.97436
187 5DXV NAP 0.01766 0.41332 8.97436
188 4XP7 FNR 0.01735 0.40868 8.97436
189 3TAO PGH 0.000008389 0.56168 9.40171
190 1IR1 CAP 0.01356 0.41594 9.40171
191 3LL5 IPE 0.02921 0.4157 9.40171
192 1VKF CIT 0.001611 0.42274 9.57447
193 4BI7 PGA 0.00011 0.50344 9.82906
194 1DQX BMP 0.000426 0.49486 9.82906
195 3MJY IJZ 0.0026 0.46992 9.82906
196 3MJY FMN 0.0026 0.46992 9.82906
197 1DBT U5P 0.001253 0.46678 9.82906
198 4L2H AR6 AR6 0.02173 0.4205 9.82906
199 4EZD SEY 0.003149 0.40485 9.82906
200 1W8S FBP 0.01957 0.40022 9.82906
201 2C6Q NDP 0.003475 0.47427 10.2564
202 2C6Q IMP 0.001452 0.47294 10.2564
203 1KBJ FMN 0.006378 0.44099 10.2564
204 5AYV NAP 0.01106 0.42547 10.2564
205 2OEM 1AE 0.01647 0.40182 10.2564
206 1RYD GLC 0.003635 0.40689 10.6838
207 3KDN CAP 0.004222 0.4733 11.1111
208 3H0L ADP 0.007376 0.4142 11.1111
209 3NYQ MCA 0.04151 0.40526 11.1111
210 3NYQ AMP 0.04341 0.40526 11.1111
211 1OX5 1PR 0.0008502 0.48998 11.5385
212 4B0T ADP 0.01841 0.4154 11.5385
213 2EC9 24X 0.02201 0.41133 11.6667
214 1X1Z BMP 0.002228 0.48961 11.9658
215 2Q3O FMN 0.002893 0.45397 11.9658
216 2GOU FMN 0.01879 0.42502 11.9658
217 3RO7 TDR 0.04419 0.42377 11.9658
218 1KZN CBN 0.01645 0.40986 12.1951
219 5CSS G3P 0.0006569 0.46554 12.3894
220 1ICP FMN 0.0008635 0.49117 12.3932
221 3B9O FMN 0.02224 0.40133 12.3932
222 1LFD GNP 0.03454 0.40101 12.6437
223 4UTU LRY 0.0000778 0.52014 12.6638
224 4UTW RFW 0.00007589 0.45074 12.6638
225 2Y88 2ER 0.00002178 0.58552 12.8205
226 4R84 CSF 0.02047 0.40317 12.8205
227 2FXV 5GP 0.02102 0.41091 12.8866
228 2BTM PGA 0.00006364 0.51504 13.2479
229 4M5P FMN 0.005356 0.43843 13.2479
230 2OO0 PLP 0.007305 0.42385 13.2479
231 2NLI LAC 0.03016 0.4081 13.2479
232 2NLI FMN 0.02498 0.40698 13.2479
233 5TCI MLI 0.00002115 0.48634 14.1026
234 4Q4K FMN 0.00002443 0.56723 14.5299
235 2GAG FOA 0.04313 0.41615 14.9573
236 1OVD FMN 0.001331 0.49051 15.3846
237 1OVD ORO 0.001331 0.49051 15.3846
238 1QDS PGA 0.00002531 0.53808 16.2393
239 1LBF 137 0.000476 0.5016 18.3761
240 3W9Z FMN 0.002881 0.44842 19.2308
241 3LF0 ATP 0.02986 0.40143 19.2982
242 4ORM FMN 0.005395 0.47801 19.6581
243 4ORM 2V6 0.005395 0.47801 19.6581
244 4ORM ORO 0.005395 0.47801 19.6581
245 1LYX PGA 0.00000365 0.5864 20.0855
246 4J56 FAD 0.02688 0.42689 20.1754
247 3VKC FPQ 0.0001122 0.52458 33.2168
248 4JEJ 1GP 0.00000003649 0.68212 42.3077
Pocket No.: 2; Query (leader) PDB : 2F6U; Ligand: CIT; 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: 2f6u.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback