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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;
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192.124 C6 H8 O7 C(C(=...
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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 4 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: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 CIT 1 1
2 7QD 0.653846 0.958333
3 HCA 0.576923 0.884615
4 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 with APoc: 355
This union binding pocket(no: 1) in the query (biounit: 2f6u.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 4I9A NCN 1.28205
2 1UUO FMN 1.28205
3 1UUO ORO 1.28205
4 1UUO BRF 1.28205
5 3K56 IS3 1.28205
6 3TTZ 07N 1.51515
7 1L3I SAH 1.5625
8 3UWV 2PG 1.7094
9 5AE2 FAD 1.7094
10 5AE2 FYC 1.7094
11 5EJL C2E 1.7094
12 5U5G NAP 1.7094
13 4FK7 P34 1.74672
14 4IF4 BEF 1.92308
15 1Q5H DUD 2.04082
16 4EWN 0VR 2.13675
17 4YMZ 13P 2.13675
18 2GJN FMN 2.13675
19 2GJN NIS 2.13675
20 3OIX FMN 2.13675
21 5OCS FMN 2.13675
22 6CEP NAD 2.13675
23 1E5D FMN 2.13675
24 1T32 OHH 2.23214
25 1GZF NAD 2.36967
26 1GZF ADP 2.36967
27 4Z0G 5GP 2.5641
28 1M5W DXP 2.5641
29 5GVR LMR 2.5641
30 1V1A ADP 2.5641
31 1NJJ ORX 2.5641
32 3L9W FMN 2.5641
33 2ZIF SAM 2.5641
34 1YF4 CYS TYR PHE GLN ASN CYS PRO ARG GLY NH2 2.69058
35 5KQG 6VX 2.80899
36 5VM6 9EG 2.91971
37 2E5V FAD 2.99145
38 5L2Z 70C 2.99145
39 1SQA UI1 2.99145
40 2NVA PL2 2.99145
41 1N1G BCP 2.99145
42 1VFS DCS 2.99145
43 1HDR NAD 2.99145
44 2A92 NAI 2.99145
45 4OLT GCS GCS GCS GCS GCS GCS 2.99145
46 6AYU F6P 2.99145
47 4PJT 2YQ 2.99145
48 4I4B 1CV 2.99145
49 3UBM COA 2.99145
50 3KJS NAP 2.99145
51 1SOW NAD 2.99145
52 3EXS 5RP 3.16742
53 5GM9 CBK 3.28639
54 4N65 FMN 3.30189
55 4N65 AQN 3.30189
56 4R81 FMN 3.39806
57 1SW0 PGA 3.4188
58 2QCD U5P 3.4188
59 3MI2 PFU 3.4188
60 4HKP TKW 3.4188
61 4HKP 16B 3.4188
62 1EIX BMQ 3.4188
63 2RDT 2RD 3.4188
64 2RDT FMN 3.4188
65 3HF3 FMN 3.4188
66 1KC7 PPR 3.4188
67 1TB3 FMN 3.4188
68 3GDN MXN 3.4188
69 6ASY ATP 3.4188
70 4PLG NAI 3.4188
71 4PLG OXM 3.4188
72 5VSM 5AD 3.4188
73 6C0T EE4 3.4188
74 4D86 ADP 3.4188
75 2RGO FAD 3.4188
76 5VSM MET 3.4188
77 1VKJ A3P 3.4188
78 4V15 PLP 3.4188
79 4TXI FAD 3.4188
80 1HYH NAD 3.4188
81 5HS2 CTP 3.44828
82 1T5B FMN 3.48259
83 2Z9C DTC 3.5
84 2Z9C FMN 3.5
85 2QTR NXX 3.7037
86 1OFD FMN 3.84615
87 2HSA FMN 3.84615
88 3KRU FMN 3.84615
89 1OFD AKG 3.84615
90 5BSH PRO 3.84615
91 3WG6 NDP 3.84615
92 2HW1 ANP 3.84615
93 3NC9 TR3 3.84615
94 2JK0 ASP 3.84615
95 1JG3 ADN 3.84615
96 2FKA BEF 3.87597
97 3FGZ BEF 3.90625
98 3N7O N7O 3.9823
99 3L9R L9Q 4.08163
100 3F4F UMP 4.19162
101 1K4M NAD 4.22535
102 1UJP CIT 4.2735
103 2YPI PGA 4.2735
104 6DVH FMN 4.2735
105 5X8G S0N 4.2735
106 4CNG SAH 4.2735
107 6BKA FMN 4.2735
108 2VJM COA 4.2735
109 5GXU FMN 4.2735
110 1E3W NAD 4.2735
111 4IXH IMP 4.70085
112 3CQD ATP 4.70085
113 1QPR PPC 4.70085
114 2NPX NAD 4.70085
115 2C0U FAD NBT 4.70085
116 1BWV CAP 4.70085
117 1GV0 NAD 4.70085
118 2XZ9 PYR 4.70085
119 4PXL NAD 4.70085
120 1Q6O LG6 5.09259
121 1AL8 FMN 5.12821
122 1AL8 DHP 5.12821
123 2Q3R FMN 5.12821
124 1F76 FMN 5.12821
125 1TUF AZ1 5.12821
126 4D57 ARG AMP 5.12821
127 1H74 ILE 5.12821
128 2AWN ADP 5.12821
129 1VL0 NAI 5.12821
130 1NIU DCS 5.12821
131 2PX8 SAH 5.12821
132 3B82 NAD 5.31401
133 3BW2 FMN 5.55556
134 6AM8 TRP 5.55556
135 4JIQ 1L5 5.55556
136 4JIQ FMN 5.55556
137 1ZFJ IMP 5.55556
138 5U97 PIT 5.55556
139 6ACS CIT 5.55556
140 5O96 SAM 5.55556
141 1RHC F42 ACN 5.55556
142 1RM6 FAD 5.55556
143 1GUZ NAD 5.55556
144 5THZ SAH 5.55556
145 1OZH HE3 5.55556
146 4R38 RBF 5.71429
147 2TPS TPS 5.72687
148 1DJL NAP 5.7971
149 1L5Y BEF 5.80645
150 5J6Y BGC 5.85106
151 5J6Y GLC 5.85106
152 5YSI NCA 5.92105
153 2UUU PL3 5.98291
154 1PS9 FMN 5.98291
155 2UUU FAD 5.98291
156 4QNW FMN 5.98291
157 3AXK NDP 5.98291
158 2ZRU FMN 5.98291
159 1WDD CAP 5.98291
160 1RBL CAP 5.98291
161 1LDM NAD 5.98291
162 1NZY BCA 5.98291
163 4LUT DCS 5.98291
164 1JXZ BCA 5.98291
165 4JAL SAH 5.98802
166 3MAX LLX 5.99455
167 1B1C FMN 6.07735
168 1PNO NAP 6.11111
169 3EWP APR 6.21469
170 5A5W GUO 6.32411
171 4C0X FMN 6.40394
172 1CX9 NHP 6.41026
173 4CW5 FMN 6.41026
174 1GTE FMN 6.41026
175 1GTE IUR 6.41026
176 4IGH 1EA 6.41026
177 4IGH ORO 6.41026
178 4IGH FMN 6.41026
179 2VD9 IN5 6.41026
180 1LQA NDP 6.41026
181 1QO8 FAD 6.41026
182 2VD9 EPC 6.41026
183 5N9Z CAP 6.47482
184 5OYA CAP 6.47482
185 1D4O NAP 6.52174
186 2BYS LOB 6.60793
187 3QH2 3NM 6.78733
188 5XFV FMN 6.83761
189 4WZH FMN 6.83761
190 1JCM 137 6.83761
191 1O97 AMP 6.83761
192 1O97 FAD 6.83761
193 9LDB NAD 6.83761
194 3PNL ADP 6.83761
195 5A04 BGC 6.83761
196 5A04 NDP 6.83761
197 4DQ2 BTX 6.83761
198 4QIJ 1HA 6.83761
199 4JK3 NAD 6.83761
200 9LDT NAD 6.83761
201 1H2B NAJ 6.83761
202 4E1Z 0MX 6.83761
203 3GFS FMN 6.89655
204 2V67 CAP 7.14286
205 2V63 CAP 7.14286
206 2V6A CAP 7.14286
207 2VDH CAP 7.14286
208 2V68 CAP 7.14286
209 1IR2 CAP 7.14286
210 1GK8 CAP 7.14286
211 1PQ7 ARG 7.14286
212 5FAH 5VT 7.14286
213 5AHN IMP 7.15746
214 3B0P FMN 7.26496
215 1PVN MZP 7.26496
216 5J5R IMP 7.26496
217 5J5R 6G1 7.26496
218 1VYP FMN 7.26496
219 1VYP TNF 7.26496
220 2OOR TXP 7.26496
221 3ATY FMN 7.26496
222 1NM5 NAD 7.26496
223 5ODQ 9SB 7.26496
224 3KFC 61X 7.26496
225 2H29 DND 7.40741
226 1UZD CAP 7.46269
227 1TRD PGH 7.69231
228 4Z87 5GP 7.69231
229 2Q8Z NUP 7.69231
230 3C3N FMN 7.69231
231 3WGT QSC 7.69231
232 1O94 AMP 7.69231
233 3G6K POP 7.69231
234 3G6K FAD 7.69231
235 4JD3 PLM 7.69231
236 4JD3 COA 7.69231
237 5GQX GLC GLC GLC GLC GLC GLC GLC 7.69231
238 4A62 ANP 7.69231
239 1IGW PYR 7.69231
240 3OVR 5SP 7.89474
241 2Z6J FMN 8.11966
242 2Z6I FMN 8.11966
243 4AF0 IMP 8.11966
244 3CV6 HXS 8.11966
245 3CV6 NAP 8.11966
246 1OYB FMN 8.11966
247 1OYB HBA 8.11966
248 1KBI PYR 8.11966
249 1KBI FMN 8.11966
250 5HSA FAS 8.11966
251 3O03 NAP 8.11966
252 1UZH CAP 8.19672
253 1IAU ACE ILE GLU PRO ASJ 8.37004
254 4PTZ FMN 8.37696
255 1ME8 RVP 8.54701
256 2BLE 5GP 8.54701
257 1P4C FMN 8.54701
258 6BFG FMN 8.54701
259 1EP2 ORO 8.54701
260 1EP2 FMN 8.54701
261 5ABH YWN 8.54701
262 1AJ8 COA 8.54701
263 2FLI DX5 8.63636
264 5AHM IMP 8.75
265 5EYW PGA 8.97436
266 1Z41 FMN 8.97436
267 1Z48 FMN 8.97436
268 1Z44 FMN 8.97436
269 5DXV NAP 8.97436
270 4XP7 FNR 8.97436
271 3TAO PGH 9.40171
272 1IR1 CAP 9.40171
273 3LL5 ADP 9.40171
274 3LL5 IPE 9.40171
275 1VKF CIT 9.57447
276 4OOP DUP 9.63855
277 4BI7 PGA 9.82906
278 1DQX BMP 9.82906
279 1DBT U5P 9.82906
280 3MJY IJZ 9.82906
281 3MJY FMN 9.82906
282 4L2H AR6 AR6 9.82906
283 4EZD SEY 9.82906
284 1W8S FBP 9.82906
285 6BHV DQV 9.9631
286 2C6Q NDP 10.2564
287 2C6Q IMP 10.2564
288 1KBJ FMN 10.2564
289 5AYV NAP 10.2564
290 4L8F MTX 10.2564
291 3MKH FAD 10.2564
292 4TMC FMN 10.2564
293 4TMC HBA 10.2564
294 5WAN FMN 10.2564
295 2OEM 1AE 10.2564
296 4X6F 3XU 10.4762
297 1RYD GLC 10.6838
298 5GVH FMN 11.1111
299 6BVE PGA 11.1111
300 3KDN CAP 11.1111
301 3H0L ADP 11.1111
302 1OX5 1PR 11.5385
303 2HIM ASP 11.5385
304 4B0T ADP 11.5385
305 1PFK ADP 11.5385
306 4UTG ANP 11.5385
307 2EC9 24X 11.6667
308 1X1Z BMP 11.9658
309 2Q3O FMN 11.9658
310 2GOU FMN 11.9658
311 4JYD SAH 11.9658
312 1KZN CBN 12.1951
313 5NWD 9C8 12.2449
314 1LOR BMP 12.2807
315 5CSS G3P 12.3894
316 6DZN AE3 12.3894
317 1ICP FMN 12.3932
318 3B9O FMN 12.3932
319 1LFD GNP 12.6437
320 4UTW RFW 12.6638
321 4UTU LRY 12.6638
322 5NGZ 2BG 12.6904
323 2Y88 2ER 12.8205
324 4R84 CSF 12.8205
325 1H8P PC 12.844
326 2FXV 5GP 12.8866
327 2BTM PGA 13.2479
328 4M5P FMN 13.2479
329 2OO0 PLP 13.2479
330 2NLI LAC 13.2479
331 2NLI FMN 13.2479
332 5TCI MLI 14.1026
333 4Q4K FMN 14.5299
334 5ZYN FAD 14.5299
335 2GAG FOA 14.9573
336 2B5W NAP 14.9573
337 1OVD ORO 15.3846
338 1OVD FMN 15.3846
339 3D9F N6C 15.3846
340 3D9F FAD 15.3846
341 1QDS PGA 16.2393
342 3WQD PLP 999 17.9487
343 1LBF 137 18.3761
344 3W9Z FMN 19.2308
345 3LF0 ATP 19.2982
346 4ORM FMN 19.6581
347 4ORM 2V6 19.6581
348 4ORM ORO 19.6581
349 1TV5 FMN 19.6581
350 1LYX PGA 20.0855
351 4J56 FAD 20.1754
352 2ZFZ ARG 24.0506
353 1VBO MAN MAN MAN 29.5302
354 3VKC FPQ 33.2168
355 4JEJ 1GP 42.3077
Pocket No.: 2; Query (leader) PDB : 2F6U; Ligand: CIT; Similar sites found with APoc: 113
This union binding pocket(no: 2) in the query (biounit: 2f6u.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 2JBZ COA None
2 5OJL TXP 1.28205
3 4CNE SAH 1.28205
4 2ZXI FAD 2.13675
5 2GV8 NDP 2.13675
6 5KJW 53C 2.13675
7 5LW0 AR6 2.1645
8 3WXB NDP 2.5641
9 1X87 NAD 2.5641
10 6GAS FAD 2.5641
11 4N02 FNR 2.5641
12 1GZ6 NAI 2.5641
13 3KA2 2NC 2.95567
14 3FSM 2NC 2.95567
15 2WSA 646 2.99145
16 2WSA MYA 2.99145
17 3SSO SAH 2.99145
18 2C91 NAP 2.99145
19 2H8Z FMN 2.99145
20 2H8Z 8CM 2.99145
21 2BP1 NDP 2.99145
22 2QA1 FAD 2.99145
23 4URF NAD 2.99145
24 3VZ3 NAP 2.99145
25 4D8N 0HM 3.13901
26 1RC0 KT5 3.34928
27 1VGR COA 3.4188
28 5EB4 FAD 3.4188
29 6H3O FAD 3.4188
30 4PZ2 NAD 3.4188
31 6EOF ADP 3.4188
32 1WPQ NAD 3.4188
33 1AE1 NAP 3.4188
34 4JCA CIT 3.59281
35 4H2D FMN 3.63636
36 1AFS NAP 3.84615
37 3N39 FMN 3.84615
38 1EFY BZC 3.84615
39 3ESS 18N 3.91304
40 1TLL FMN 4.2735
41 4A59 AMP 4.2735
42 3KVY URA 4.2735
43 4YCA NDP 4.2735
44 3E5H GNP 4.49438
45 5BYK A3P 4.70085
46 5BYK OAQ 4.70085
47 4GJ3 0XP 4.70085
48 1GEE NAD 4.70085
49 1J0D 5PA 4.70085
50 4B5P ACO 5
51 4WZA ACP 5.12821
52 2PLK P3D 5.12821
53 1GVE NAP 5.12821
54 1H74 ADP 5.12821
55 4L2I FAD 5.12821
56 1GVF PGH 5.12821
57 6AIC AMP 5.14019
58 4Y7U 2KH 5.19481
59 6CUZ FEV 5.55556
60 3LXK MI1 5.55556
61 1QSM ACO 5.92105
62 1HGX 5GP 6.01093
63 2W83 GTP 6.06061
64 4LTN NAI 6.09137
65 4LTN FMN 6.09137
66 2GMH FAD 6.41026
67 1P4V GLY 6.41026
68 3QPB URA 6.41026
69 1VHN FMN 6.41026
70 5DOZ NDP 6.83761
71 2WW4 ADP 6.83761
72 1ZIN AP5 6.91244
73 3TN7 NJP 7.00389
74 1GAR U89 7.07547
75 1NM5 NAP 7.26496
76 5G5G FAD 7.26496
77 1WVC CTP 7.26496
78 4JTA NAP 7.26496
79 2VHW NAI 7.26496
80 5FFF NAP 7.26496
81 2R14 FMN 7.69231
82 2R14 TXD 7.69231
83 4TVD BGC 7.69231
84 5T79 NDP 7.69231
85 2VAP GDP 7.96703
86 3ILR SGN IXD 8.11966
87 1AKV FMN 8.16327
88 4J5R A1R 8.21918
89 4C3Y ANB 8.54701
90 5L9O GOP 8.58209
91 1HFE CYS 8.94309
92 1BVY FMN 9.42408
93 3KAP FMN 9.52381
94 5KZD RCJ 9.82906
95 5IUW NAD 10.664
96 1H6C NDP 10.6838
97 4O12 2QG 11.5385
98 5GJO PLP 11.9658
99 5XDT MB3 11.9658
100 5XDT GDP 11.9658
101 1UWK NAD 12.3932
102 1UWK URO 12.3932
103 5LD8 6U5 12.6437
104 4A3U FMN 12.8205
105 4PLT OXM 13.6752
106 4PLT NAI 13.6752
107 2C49 ANP 14.1026
108 1OIV GDP 16.7539
109 1EXB NDP 17.4757
110 1TMT DPN PRO ARG 18.3761
111 1EB1 ZAL PRO MMO 18.3761
112 1BXK NAD 22.6496
113 1H5Q NAP 25.641
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