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Receptor
PDB id Resolution Class Description Source Keywords
4YMZ 1.87 Å EC: 5.3.1.1 DHAP BOUND LEPTOSPIRA INTERROGANS TRIOSEPHOSPHATE ISOMERASE LEPTOSPIRA INTERROGANS SEROVAR ICTEROHAEMORRHAGIAE STR. RGA TIM BARRELS BETA-ALPHA BARRELS ISOMERASE DIHYDROXYACETONEPHOSPHATE GLYCOLYSIS
Ref.: CONNECTING ACTIVE-SITE LOOP CONFORMATIONS AND CATAL TRIOSEPHOSPHATE ISOMERASE: INSIGHTS FROM A RARE VAR RESIDUE 96 IN THE PLASMODIAL ENZYME CHEMBIOCHEM V. 17 620 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO B:305;
B:306;
A:310;
A:307;
B:307;
A:311;
B:308;
A:304;
A:303;
A:308;
A:309;
A:305;
B:303;
A:306;
B:304;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
13P B:301;
A:301;
Valid;
Valid;
none;
none;
submit data
170.058 C3 H7 O6 P C(C(=...
SO4 B:302;
A:302;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4YMZ 1.87 Å EC: 5.3.1.1 DHAP BOUND LEPTOSPIRA INTERROGANS TRIOSEPHOSPHATE ISOMERASE LEPTOSPIRA INTERROGANS SEROVAR ICTEROHAEMORRHAGIAE STR. RGA TIM BARRELS BETA-ALPHA BARRELS ISOMERASE DIHYDROXYACETONEPHOSPHATE GLYCOLYSIS
Ref.: CONNECTING ACTIVE-SITE LOOP CONFORMATIONS AND CATAL TRIOSEPHOSPHATE ISOMERASE: INSIGHTS FROM A RARE VAR RESIDUE 96 IN THE PLASMODIAL ENZYME CHEMBIOCHEM V. 17 620 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 4YMZ - 13P C3 H7 O6 P C(C(=O)COP....
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 4YMZ - 13P C3 H7 O6 P C(C(=O)COP....
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: 13P; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 13P 1 1
2 PGA 0.5 0.818182
3 HPV 0.4375 0.90625
4 PGH 0.424242 0.622222
5 IBS 0.404255 0.815789
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YMZ; Ligand: 13P; Similar sites found with APoc: 297
This union binding pocket(no: 1) in the query (biounit: 4ymz.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1FIW PBZ None
2 1QAW TRP None
3 1WAP TRP None
4 2NVA PL2 1.19522
5 3ESS 18N 1.30435
6 5YRL GLC GLC 1.40845
7 1RC0 KT5 1.43541
8 3OIX FMN 1.59363
9 6BKA FMN 1.59363
10 1DQX BMP 1.59363
11 1F8G NAD 1.59363
12 5DX1 SFG 1.59363
13 5DX8 SFG 1.59363
14 5DWQ SFG 1.59363
15 5DXA SFG 1.59363
16 5DX0 SFG 1.59363
17 3MJY IJZ 1.99203
18 3MJY FMN 1.99203
19 4CW5 FMN 1.99203
20 4C5N ACP 1.99203
21 1WUU ANP 1.99203
22 4MIG G3F 1.99203
23 2DPM SAM 1.99203
24 4C5N PXL 1.99203
25 1RM4 NDP 1.99203
26 2F6U CIT 2.13675
27 3C3N FMN 2.24359
28 2FLI DX5 2.27273
29 2GJN NIS 2.39044
30 2BLE 5GP 2.39044
31 3ATY FMN 2.39044
32 1FL2 FAD 2.39044
33 1VYP TNF 2.39044
34 1VYP FMN 2.39044
35 5GJO PLP 2.39044
36 2GJN FMN 2.39044
37 4USQ FAD 2.39044
38 1NV8 SAM 2.39044
39 3QV1 NAD 2.43902
40 4JEJ 1GP 2.45902
41 1DBT U5P 2.51046
42 2TPS TPS 2.64317
43 1CX9 NHP 2.78884
44 5J5R 6G1 2.78884
45 5J5R IMP 2.78884
46 1PVN MZP 2.78884
47 1ME8 RVP 2.78884
48 3HF3 FMN 2.78884
49 4QNW FMN 2.78884
50 2O07 SPD 2.78884
51 2O07 MTA 2.78884
52 1ZFJ IMP 2.78884
53 2FJK 13P 2.78884
54 4N02 FNR 2.78884
55 5ZYN FAD 2.78884
56 3PFD FDA 2.78884
57 1M5W DXP 2.88066
58 3GDH SAH 2.90456
59 6GVZ CHO 2.95082
60 1OFD FMN 3.18725
61 3KRU FMN 3.18725
62 1OFD AKG 3.18725
63 3W9Z FMN 3.18725
64 1AL8 FMN 3.18725
65 1AL8 DHP 3.18725
66 2PLK P3D 3.18725
67 4TMC FMN 3.18725
68 2Q3R FMN 3.18725
69 4TMC HBA 3.18725
70 1UZD CAP 3.18725
71 3BW2 FMN 3.18725
72 5U61 7WG 3.18725
73 3EAU PDN 3.18725
74 3EAU NDP 3.18725
75 3OJF IMJ 3.18725
76 4UP3 FAD 3.18725
77 1XKQ NDP 3.18725
78 1GY8 NAD 3.27456
79 5WHU SIA 3.3557
80 3TN7 NJP 3.50195
81 1OVD ORO 3.58566
82 1OVD FMN 3.58566
83 1GTE FMN 3.58566
84 1GTE IUR 3.58566
85 1KBJ FMN 3.58566
86 1KBI PYR 3.58566
87 1KBI FMN 3.58566
88 1PS9 FMN 3.58566
89 1T3Q FAD 3.58566
90 4XP7 FNR 3.58566
91 4I9A NCN 3.58566
92 2GOU FMN 3.58566
93 4JIQ 1L5 3.58566
94 4JIQ FMN 3.58566
95 2R14 FMN 3.58566
96 2R14 TXD 3.58566
97 5J60 FAD 3.58566
98 4N14 WR7 3.58566
99 1HXD BTN 3.58566
100 4IXH IMP 3.60111
101 5A5W GUO 3.98406
102 5AHM IMP 3.98406
103 5AHN IMP 3.98406
104 2Q3O FMN 3.98406
105 3C56 PH4 3.98406
106 4QYS PLP SEP 3.98406
107 2Z6I FMN 3.98406
108 1OYB FMN 3.98406
109 1OYB HBA 3.98406
110 3N9R TD3 3.98406
111 2BP1 NDP 3.98406
112 1RX0 FAD 3.98406
113 4QYS PLR 3.98406
114 1CZA G6P 3.98406
115 1OX5 1PR 4.38247
116 2QCD U5P 4.38247
117 4HKP TKW 4.38247
118 2WKV COA 4.38247
119 1N62 FAD 4.38247
120 3NT6 FAD 4.38247
121 4HKP 16B 4.38247
122 3MI2 PFU 4.38247
123 2C91 NAP 4.38247
124 3CTL S6P 4.38247
125 5YF1 8V0 4.38247
126 5YF1 SFG 4.38247
127 1WN3 HXC 4.41176
128 3EWP APR 4.51977
129 3EWR APR 4.7619
130 4EWN 0VR 4.78088
131 4ADC PLP 4.78088
132 6DVH FMN 4.78088
133 1NJJ ORX 4.78088
134 1SFF IK2 4.78088
135 3VKC FPQ 4.78088
136 3A5Z KAA 4.78088
137 5OOH 9ZZ 4.85437
138 5OOH NAP 4.85437
139 1LBF 137 4.8583
140 4NAE 1GP 4.88889
141 1UZH CAP 4.91803
142 2VDH CAP 5
143 2V63 CAP 5
144 2V68 CAP 5
145 2V6A CAP 5
146 2V67 CAP 5
147 1GK8 CAP 5
148 4MSG 2C6 5.06912
149 1Q6O LG6 5.09259
150 1KY8 NAP 5.17928
151 1F76 FMN 5.17928
152 6GAS FAD 5.17928
153 4C3Y FAD 5.17928
154 1GVE NAP 5.17928
155 4AF0 IMP 5.17928
156 2OO0 PLP 5.17928
157 5XFV FMN 5.57769
158 3GAY P6T 5.57769
159 5TCI MLI 5.57769
160 1JCM 137 5.57769
161 1Z41 FMN 5.57769
162 1Z48 FMN 5.57769
163 4Q4K FMN 5.57769
164 1Z44 FMN 5.57769
165 4EI7 GDP 5.57769
166 2Q8Z NUP 5.57769
167 2WET FAD 5.57769
168 1NM5 NAD 5.91133
169 1JG3 ADN 5.95745
170 4WZH FMN 5.9761
171 4ORM ORO 5.9761
172 4ORM FMN 5.9761
173 4ORM 2V6 5.9761
174 1TV5 FMN 5.9761
175 1X1Z BMP 5.9761
176 4MIB 28M 5.9761
177 6CI9 NAP 5.9761
178 1J0D 5PA 5.9761
179 4UTU LRY 6.3745
180 4UTW RFW 6.3745
181 1ICP FMN 6.3745
182 1UJP CIT 6.3745
183 4L2I FAD 6.3745
184 6FK3 PPI 6.3745
185 1AFS NAP 6.3745
186 3IHG FAD 6.3745
187 1LOR BMP 6.57895
188 1PNO NAP 6.66667
189 1GVF PGH 6.77291
190 3KDN CAP 6.77291
191 4XTX 590 6.77291
192 1LQA NDP 6.77291
193 3T6E MQ9 6.77291
194 6GNC FAD 6.77291
195 2NV2 GLN 6.77291
196 2OOR NAD 6.89655
197 4A22 TD4 6.97674
198 3AXK NDP 6.97674
199 1WDD CAP 7.03125
200 4IGH FMN 7.17131
201 4IGH 1EA 7.17131
202 4IGH ORO 7.17131
203 2RDT FMN 7.17131
204 2RDT 2RD 7.17131
205 5HSA FAS 7.17131
206 1TB3 FMN 7.17131
207 4OSP NAP 7.17131
208 6CUZ FEV 7.2165
209 2YIP YIO 7.24638
210 1L3I SAH 7.29167
211 2Z6J FMN 7.56972
212 3B0P FMN 7.56972
213 4A3U FMN 7.56972
214 2CNE DFJ 7.56972
215 1XHL NDP 7.56972
216 3QDL FMN 7.61905
217 3EXS 5RP 7.69231
218 1QKQ MAN 7.74648
219 1EP2 ORO 7.96813
220 1EP2 FMN 7.96813
221 1UUO BRF 7.96813
222 1UUO FMN 7.96813
223 1UUO ORO 7.96813
224 5AE2 FAD 7.96813
225 5X8G S0N 7.96813
226 3NOJ PYR 7.96813
227 2IID PHE 8.23293
228 2IID FAD 8.23293
229 2ZRU FMN 8.36653
230 3WQD PLP 999 8.36653
231 1O94 ADP 8.36653
232 1DJN FMN 8.36653
233 2AJ4 ANP 8.36653
234 4CTA ATP 8.36653
235 2IHU TP9 8.36653
236 2IHT TPP 8.36653
237 5N9Z CAP 8.76494
238 5OYA CAP 8.76494
239 2J8C U10 8.76494
240 3QFA FAD 8.76494
241 2UUU FAD 8.76494
242 2Y88 2ER 9.16335
243 2Q0L FAD 9.16335
244 3OVR 5SP 9.21053
245 3QMN COA 9.30233
246 1C3M MAN MAN 9.52381
247 1NAA 6FA 9.56175
248 5V2J UDP 9.56175
249 5V2J 7WV 9.56175
250 1EXB NDP 9.70874
251 1IR1 CAP 9.7561
252 3H86 AP5 9.89583
253 1BVY FMN 9.94764
254 4Z87 5GP 9.96016
255 4Z0G 5GP 9.96016
256 1QO8 FAD 9.96016
257 4JTA NAP 9.96016
258 6BFG FMN 9.96016
259 3CTY FAD 10.3586
260 3GGO ENO 10.3586
261 3GGO NAI 10.3586
262 5L9G MO0 10.3586
263 1EIX BMQ 11.0204
264 6AM8 PLT 11.1554
265 6AMI TRP 11.1554
266 5VJE GOS 11.1554
267 5GVH FMN 11.1554
268 1T0S BML 11.6279
269 3PNL ADP 11.8483
270 2HSA FMN 12.3506
271 1BWV CAP 12.3506
272 1FDJ 13P 12.3506
273 3QPB URA 12.3506
274 1FDJ 2FP 12.3506
275 2JAH NDP 12.5506
276 3QH2 3NM 12.6697
277 5DDW 5B6 12.749
278 5ZFJ 9BF 12.7753
279 1IR2 CAP 12.8571
280 5SVV FMN 13.1387
281 2C6Q NDP 13.1474
282 2C6Q IMP 13.1474
283 4L1F FAD 13.9442
284 5HJM MTA 14.3426
285 2OEM 1AE 15.1394
286 2HMT NAI 15.2778
287 5J62 FMN 15.5844
288 5N0J FAD 15.9363
289 3AJ4 SEP 16.9643
290 1P4C FMN 17.1315
291 2O4N TPV 17.1717
292 5ODQ FAD 17.3913
293 5ODQ 9SB 17.3913
294 5OCS FMN 19.1235
295 5VM6 9EG 19.708
296 1RBL CAP 24.7706
297 5X62 SAH 27.49
Pocket No.: 2; Query (leader) PDB : 4YMZ; Ligand: 13P; Similar sites found with APoc: 50
This union binding pocket(no: 2) in the query (biounit: 4ymz.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 6ARJ SAH 1.59363
2 4HXY NDP 1.59363
3 2WOE AR6 1.99203
4 2VDF OCT 2.39044
5 1JQI FAD 2.39044
6 3PP0 03Q 2.39044
7 2DXU BT5 2.55319
8 3W8X FAD 2.78884
9 3W8X FTK 2.78884
10 1F5V FMN 2.91667
11 1QMG DMV 3.18725
12 1L7E NAI 3.18725
13 2AQJ TRP 3.58566
14 2AQJ FAD 3.58566
15 2RGO FAD 3.58566
16 5C5H 4YB 3.58566
17 6F7L FAD 3.58566
18 1RP0 AHZ 3.98406
19 3G6N MET ALA SER 4.18848
20 5EJ2 NAD 4.38247
21 2VHW NAI 4.38247
22 1F06 2NP 4.38247
23 1F06 NDP 4.38247
24 4BUY F37 4.58333
25 6G28 AR6 5.17928
26 1HFE CYS 5.17928
27 1DL2 NAG NAG BMA 5.57769
28 4CQM NAP 5.57769
29 1TUF AZ1 6.77291
30 1GQ2 NAP 6.84685
31 3PPM JG1 7.17131
32 4YKG FAD 7.96813
33 1UWK NAD 7.96813
34 1UWK URO 7.96813
35 2GKS ADP 8.36653
36 1FP2 SAH 8.76494
37 5UAO FAD 9.16335
38 1D4D FAD 9.56175
39 1D1Q 4NP 9.93789
40 2A92 NAI 10.3586
41 5X30 HCS 10.757
42 2BZG SAH 11.2069
43 5Y6Q FAD 11.7284
44 2HQM FAD 13.9442
45 2D1S SLU 14.741
46 4YSX FAD 14.7436
47 2VK4 TPP 17.1315
48 5XDT MB3 19.1235
49 5MZY 8EZ 19.5219
50 2X06 NAD 21.1155
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