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Receptor
PDB id Resolution Class Description Source Keywords
6BVE 1.78 Å EC: 5.3.1.1 TRIOSEPHOSPHATE ISOMERASE OF SYNECHOCYSTIS IN COMPLEX WITH 2 PHOSPHOGLYCOLIC ACID SYNECHOCYSTIS SP. (STRAIN PCC 6803 / KORGANISM_TAXID: 1111708 TIM SYNECHOCYSTIS REDOX REGULATION ISOMERASE
Ref.: STRUCTURAL BASIS FOR THE LIMITED RESPONSE TO OXIDAT THIOL-CONJUGATING AGENTS BY TRIOSEPHOSPHATE ISOMERA THE PHOTOSYNTHETIC BACTERIASYNECHOCYSTIS. FRONT MOL BIOSCI V. 5 103 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PGA A:302;
B:302;
Valid;
Valid;
none;
none;
submit data
156.031 C2 H5 O6 P C(C(=...
NA B:301;
A:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6BVE 1.78 Å EC: 5.3.1.1 TRIOSEPHOSPHATE ISOMERASE OF SYNECHOCYSTIS IN COMPLEX WITH 2 PHOSPHOGLYCOLIC ACID SYNECHOCYSTIS SP. (STRAIN PCC 6803 / KORGANISM_TAXID: 1111708 TIM SYNECHOCYSTIS REDOX REGULATION ISOMERASE
Ref.: STRUCTURAL BASIS FOR THE LIMITED RESPONSE TO OXIDAT THIOL-CONJUGATING AGENTS BY TRIOSEPHOSPHATE ISOMERA THE PHOTOSYNTHETIC BACTERIASYNECHOCYSTIS. FRONT MOL BIOSCI V. 5 103 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 6BVE - PGA C2 H5 O6 P C(C(=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 10 families.
1 6BVE - PGA C2 H5 O6 P C(C(=O)O)O....
50% Homology Family (63)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1IIH Ki = 1.3 mM 3PG C3 H7 O7 P C([C@H](C(....
2 2X1T - RES C4 H10 N O8 P C([C@H]([C....
3 5I3K Ki = 12 uM PGA C2 H5 O6 P C(C(=O)O)O....
4 2VEL - PGA C2 H5 O6 P C(C(=O)O)O....
5 5I3I Ki = 2.6 mM PGA C2 H5 O6 P C(C(=O)O)O....
6 2V2C Ki = 0.39 mM PGA C2 H5 O6 P C(C(=O)O)O....
7 2VEN - CIT C6 H8 O7 C(C(=O)O)C....
8 5I3H Ki = 120 uM PGA C2 H5 O6 P C(C(=O)O)O....
9 2X1S - X1S C3 H6 O5 S C(CS(=O)(=....
10 1KV5 Ki = 60 uM PGA C2 H5 O6 P C(C(=O)O)O....
11 4TIM Ki = 6.9 mM 2PG C3 H7 O7 P C([C@H](C(....
12 1TTJ - PGH C2 H6 N O6 P C(C(=O)NO)....
13 6TIM Ki = 0.61 mM G3P C3 H9 O6 P C([C@H](CO....
14 1TRD Ki = 4 uM PGH C2 H6 N O6 P C(C(=O)NO)....
15 2VEK - CIT C6 H8 O7 C(C(=O)O)C....
16 2V2H Ki = 0.17 mM PGA C2 H5 O6 P C(C(=O)O)O....
17 2J27 Ki = 0.3 mM PGA C2 H5 O6 P C(C(=O)O)O....
18 4PC8 - GOA C2 H4 O3 C(C(=O)O)O
19 2X1R - X1R C6 H12 O4 S CCCS(=O)(=....
20 2X2G - 3PG C3 H7 O7 P C([C@H](C(....
21 1TTI - PGA C2 H5 O6 P C(C(=O)O)O....
22 1NF0 - 13P C3 H7 O6 P C(C(=O)COP....
23 7TIM - PGH C2 H6 N O6 P C(C(=O)NO)....
24 2YPI Ki = 15 uM PGA C2 H5 O6 P C(C(=O)O)O....
25 1NEY - 13P C3 H7 O6 P C(C(=O)COP....
26 2BTM - PGA C2 H5 O6 P C(C(=O)O)O....
27 5EYW - PGA C2 H5 O6 P C(C(=O)O)O....
28 4YMZ - 13P C3 H7 O6 P C(C(=O)COP....
29 3UWV - 2PG C3 H7 O7 P C([C@H](C(....
30 3UWW - 3PG C3 H7 O7 P C([C@H](C(....
31 3UWZ - G2H C3 H9 O6 P C(C(CO)OP(....
32 3M9Y - CIT C6 H8 O7 C(C(=O)O)C....
33 3UWU - G3P C3 H9 O6 P C([C@H](CO....
34 1LYX Ki = 0.029 mM PGA C2 H5 O6 P C(C(=O)O)O....
35 1O5X - 3PY C3 H4 O4 C(C(=O)C(=....
36 2VFH - 3PG C3 H7 O7 P C([C@H](C(....
37 1M7O - 3PG C3 H7 O7 P C([C@H](C(....
38 2VFE - 3PG C3 H7 O7 P C([C@H](C(....
39 2VFI Ki = 1.9 mM 3PG C3 H7 O7 P C([C@H](C(....
40 1M7P - G3H C3 H7 O6 P C([C@H](C=....
41 3PVF - PGA C2 H5 O6 P C(C(=O)O)O....
42 2VFG - 3PG C3 H7 O7 P C([C@H](C(....
43 3TAO Kd = 7.28 uM PGH C2 H6 N O6 P C(C(=O)NO)....
44 1SUX - BTS C10 H11 N O3 S3 c1ccc2c(c1....
45 1TPW Ki = 0.5 mM PGH C2 H6 N O6 P C(C(=O)NO)....
46 1SW3 - PGA C2 H5 O6 P C(C(=O)O)O....
47 1TPB - PGH C2 H6 N O6 P C(C(=O)NO)....
48 1SW0 - PGA C2 H5 O6 P C(C(=O)O)O....
49 1TPH - PGH C2 H6 N O6 P C(C(=O)NO)....
50 1TPU - PGH C2 H6 N O6 P C(C(=O)NO)....
51 1TPV - PGH C2 H6 N O6 P C(C(=O)NO)....
52 1SW7 - PGA C2 H5 O6 P C(C(=O)O)O....
53 1TPC - PGH C2 H6 N O6 P C(C(=O)NO)....
54 2VXN - PGA C2 H5 O6 P C(C(=O)O)O....
55 2Y62 - G3P C3 H9 O6 P C([C@H](CO....
56 1AMK Ki = 0.05 mM PGA C2 H5 O6 P C(C(=O)O)O....
57 2Y61 - G3P C3 H9 O6 P C([C@H](CO....
58 1QDS Ki = 0.048 mM PGA C2 H5 O6 P C(C(=O)O)O....
59 1N55 - PGA C2 H5 O6 P C(C(=O)O)O....
60 1IF2 - 129 C3 H8 N O5 P C(CP(=O)(O....
61 6BVE - PGA C2 H5 O6 P C(C(=O)O)O....
62 4BI6 Kd = 113.3 uM PGA C2 H5 O6 P C(C(=O)O)O....
63 4BI7 Kd = 26.4 uM PGA C2 H5 O6 P C(C(=O)O)O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PGA; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 PGA 1 1
2 HPV 0.555556 0.903226
3 13P 0.5 0.818182
4 PGH 0.482759 0.651163
5 3PG 0.433333 0.90625
6 3PP 0.423077 0.866667
7 PAE 0.416667 0.806452
8 EFS 0.416667 0.741935
9 SEP 0.40625 0.710526
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6BVE; Ligand: PGA; Similar sites found with APoc: 266
This union binding pocket(no: 1) in the query (biounit: 6bve.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1QAW TRP None
2 1WN3 HXC None
3 1Q0S SAH 0.816327
4 4NZ6 DGL 1.22449
5 3DZ6 M8E 1.22449
6 4JEJ 1GP 1.22951
7 1JG3 ADN 1.2766
8 3M6P BB2 1.5544
9 1X1Z BMP 1.63265
10 3KDN CAP 1.63265
11 5U61 7WG 1.63265
12 5T79 NDP 1.63265
13 2QEN ADP 1.63265
14 4BUY F37 1.66667
15 1LOR BMP 1.75439
16 4MSG 2C6 1.84332
17 5J5R IMP 2.04082
18 5J5R 6G1 2.04082
19 1DQX BMP 2.04082
20 2AQJ TRP 2.04082
21 2AQJ FAD 2.04082
22 5GSN FAD 2.04082
23 5NWD 9C8 2.09424
24 3QH2 3NM 2.26244
25 3QMN COA 2.32558
26 4Q4K FMN 2.44898
27 5XFV FMN 2.44898
28 4WZH FMN 2.44898
29 4ORM 2V6 2.44898
30 4ORM ORO 2.44898
31 4ORM FMN 2.44898
32 1TV5 FMN 2.44898
33 2C91 NAP 2.44898
34 1FL2 FAD 2.44898
35 3PP0 03Q 2.44898
36 3OJF NDP 2.44898
37 6F9Q NAD 2.44898
38 5OE4 3UK 2.44898
39 4PYW ACE THR THR ALA ILE NH2 2.44898
40 1SFF IK2 2.44898
41 3EXS 5RP 2.71493
42 2HSA FMN 2.85714
43 2Q3O FMN 2.85714
44 2RDT 2RD 2.85714
45 2RDT FMN 2.85714
46 1UJP CIT 2.85714
47 2OO0 PLP 2.85714
48 5OCS FMN 2.85714
49 2OEM 1AE 2.85714
50 4XP7 FNR 2.85714
51 4TMC FMN 2.85714
52 1EIX BMQ 2.85714
53 4I9A NCN 2.85714
54 6ARJ SAH 2.85714
55 1ZFJ IMP 2.85714
56 4TMC HBA 2.85714
57 2R14 FMN 2.85714
58 2R14 TXD 2.85714
59 2CNE DFJ 2.85714
60 5C9P FUC 2.85714
61 4R6W SAH 2.85714
62 2A2C ADP 2.92887
63 2A2C NG1 2.92887
64 3CTL S6P 3.0303
65 2FLI DX5 3.18182
66 2BLE 5GP 3.26531
67 1PVN MZP 3.26531
68 1GVF PGH 3.26531
69 3HF3 FMN 3.26531
70 1F76 FMN 3.26531
71 5VJE GOS 3.26531
72 1TB3 FMN 3.26531
73 6DVH FMN 3.26531
74 3PFD FDA 3.26531
75 1FDJ 13P 3.26531
76 5YRM BGC GLC 3.52113
77 1IR2 CAP 3.57143
78 4EWN 0VR 3.67347
79 5TCI MLI 3.67347
80 3GAY P6T 3.67347
81 6G28 AR6 3.67347
82 1GVE NAP 3.67347
83 2Q8Z NUP 3.67347
84 6GVZ CHO 3.67347
85 4N02 FNR 3.67347
86 5X8G S0N 3.67347
87 3NRZ FAD 3.67347
88 1DL2 NAG NAG BMA 3.67347
89 1AFS NAP 3.67347
90 2BUP ATP 3.67347
91 2BUP ADP 3.67347
92 1UZD CAP 3.73134
93 3BW2 FMN 3.79404
94 3MJY IJZ 4.04624
95 3MJY FMN 4.04624
96 1OFD FMN 4.08163
97 1OFD AKG 4.08163
98 1LBF 137 4.08163
99 1AL8 DHP 4.08163
100 1AL8 FMN 4.08163
101 2QCD U5P 4.08163
102 4HKP TKW 4.08163
103 3MI2 PFU 4.08163
104 4HKP 16B 4.08163
105 1JCM 137 4.08163
106 2WET FAD 4.08163
107 6CI9 NAP 4.08163
108 2WKV COA 4.08163
109 1U7Z PMT 4.08163
110 1C3M MAN MAN 4.08163
111 1UZH CAP 4.09836
112 2Z6I FMN 4.21687
113 1BWV CAP 4.34783
114 5VM6 9EG 4.37956
115 5SVV FMN 4.37956
116 3OVR 5SP 4.38596
117 1OX5 1PR 4.4898
118 2C6Q NDP 4.4898
119 2C6Q IMP 4.4898
120 6AM8 PLT 4.4898
121 3WQD PLP 999 4.4898
122 6CUZ FEV 4.4898
123 1OYB FMN 4.4898
124 1OYB HBA 4.4898
125 3ATY FMN 4.4898
126 4EO3 FMN 4.4898
127 1CZA G6P 4.4898
128 2VHW NAI 4.4898
129 1Q6O LG6 4.62963
130 3G6N MET ALA SER 4.71204
131 5GVH FMN 4.89796
132 4IXH IMP 4.89796
133 2NVA PL2 4.89796
134 2Q3R FMN 4.89796
135 4JIQ 1L5 4.89796
136 4JIQ FMN 4.89796
137 5K0A FAD 4.89796
138 3NT6 FAD 4.89796
139 4L2I FAD 4.89796
140 2Y88 2ER 4.91803
141 1ICP FMN 5.30612
142 2BP1 NDP 5.30612
143 1P4C FMN 5.30612
144 5AHN IMP 5.31697
145 1QKQ MAN 5.6338
146 1NJJ ORX 5.71429
147 3C56 PH4 5.71429
148 1PS9 FMN 5.71429
149 3N9R TD3 5.71429
150 3T6E MQ9 5.71429
151 2V63 CAP 5.71429
152 2VDH CAP 5.71429
153 2V6A CAP 5.71429
154 4AF0 IMP 5.71429
155 2V68 CAP 5.71429
156 2V67 CAP 5.71429
157 3VKC FPQ 5.71429
158 1GK8 CAP 5.71429
159 4CW5 FMN 5.72687
160 1DBT U5P 5.85774
161 2Z6J FMN 6.12245
162 4Z87 5GP 6.12245
163 4Z0G 5GP 6.12245
164 4A22 TD4 6.12245
165 1KBJ FMN 6.12245
166 1KBI PYR 6.12245
167 1KBI FMN 6.12245
168 6BFG FMN 6.12245
169 2WOX NDP 6.12245
170 2WME NAP 6.12245
171 1M5W DXP 6.17284
172 1RBL CAP 6.42202
173 5AHM IMP 6.5
174 1GTE IUR 6.53061
175 1GTE FMN 6.53061
176 1TUF AZ1 6.53061
177 1JQI FAD 6.53061
178 3ITJ CIT 6.53061
179 2PLK P3D 6.53061
180 4NAE 1GP 6.66667
181 4IGH FMN 6.93878
182 4IGH 1EA 6.93878
183 4IGH ORO 6.93878
184 6BKA FMN 6.93878
185 3B0P FMN 6.93878
186 5GJO PLP 6.93878
187 2FJK 13P 6.93878
188 1UWK URO 6.93878
189 1UWK NAD 6.93878
190 3T7V SAM 6.93878
191 4A3U FMN 6.93878
192 3N2S FMN 6.93878
193 3ESS 18N 6.95652
194 1T0S BML 6.97674
195 1IR1 CAP 7.31707
196 5A5W GUO 7.34694
197 3OIX FMN 7.34694
198 1UUO ORO 7.34694
199 1UUO BRF 7.34694
200 1UUO FMN 7.34694
201 2UUU FAD 7.34694
202 1D1Q 4NP 7.45342
203 3AXK NDP 7.75194
204 2GJN NIS 7.7551
205 2GJN FMN 7.7551
206 1WDD CAP 7.8125
207 2O4N TPV 8.08081
208 1Z41 FMN 8.16327
209 1LQA NDP 8.16327
210 1Z44 FMN 8.16327
211 1C3X 8IG 8.16327
212 1Z48 FMN 8.16327
213 2ZRU FMN 8.57143
214 1TDF FAD 8.57143
215 2HQM FAD 8.57143
216 2IHU TP9 8.57143
217 5OYA CAP 8.63309
218 1F5V FMN 8.75
219 6GAS FAD 8.76133
220 3KRU FMN 8.97959
221 4MIB 28M 8.97959
222 5J60 FAD 8.97959
223 3H4L ANP 9.38776
224 4QYS PLR 9.79592
225 1FFU FAD 9.79592
226 1EP2 ORO 10.2041
227 1EP2 FMN 10.2041
228 4QNW FMN 10.2041
229 1DJN FMN 10.2041
230 4UP3 FAD 10.2041
231 3C3N FMN 10.6122
232 1RP0 AHZ 10.6122
233 1HFE CYS 10.6122
234 4C5N ACP 10.6122
235 3W9Z FMN 10.6122
236 5N9Z CAP 10.7914
237 1T3Q FAD 11.0204
238 3QFA FAD 11.0204
239 2DPM SAM 11.0204
240 2F6U CIT 11.1111
241 2HMT NAI 11.1111
242 1ME8 RVP 11.1332
243 1OVD ORO 11.4286
244 1OVD FMN 11.4286
245 1QO8 FAD 11.4286
246 5HJM MTA 11.4286
247 1N62 FAD 11.8367
248 5OOH 9ZZ 12.6214
249 5OOH NAP 12.6214
250 1CX9 NHP 13.0612
251 4YKG FAD 13.4694
252 3EAU PDN 13.8776
253 3EAU NDP 13.8776
254 2GOU FMN 13.8776
255 1EXB NDP 13.8776
256 3ITA AIC 14.6939
257 4JB1 NAP 15.5102
258 4JB1 FAD 15.5102
259 5ODQ FAD 16.3043
260 5ODQ 9SB 16.3043
261 1KY8 NAP 16.7347
262 1VYP TNF 18.3673
263 1VYP FMN 18.3673
264 4JTA NAP 21.6216
265 4UTU LRY 24.0175
266 4UTW RFW 24.0175
Pocket No.: 2; Query (leader) PDB : 6BVE; Ligand: PGA; Similar sites found with APoc: 20
This union binding pocket(no: 2) in the query (biounit: 6bve.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1BKJ FMN 1.66667
2 1GET NAP 2.04082
3 1GET FAD 2.04082
4 5YW5 ADE 2.23464
5 5ZFJ 9BF 2.64317
6 4Y30 SAH 2.85714
7 5YRL GLC GLC 3.52113
8 4B0T ADP 4.89796
9 3EYA TDP 4.89796
10 5ZYN FAD 5.71429
11 2IHT TPP 5.71429
12 4ZRN NAD 6.12245
13 2EW5 Y12 6.62983
14 1F06 2NP 7.7551
15 1F06 NDP 7.7551
16 1O4T OXL 9.02256
17 4QYS PLP SEP 9.79592
18 3CV6 HXS 9.79592
19 5N9X THR 10.2041
20 2GKS ADP 13.8776
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