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 13 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 9 families.
1 4YMZ - 13P C3 H7 O6 P C(C(=O)COP....
50% Homology Family (62)
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 4BI6 Kd = 113.3 uM PGA C2 H5 O6 P C(C(=O)O)O....
62 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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4ymz.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4YMZ; Ligand: 13P; Similar sites found: 144
This union binding pocket(no: 2) in the query (biounit: 4ymz.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3OIX FMN 0.0007806 0.47902 1.59363
2 1DQX BMP 0.004094 0.43924 1.59363
3 4HXY NDP 0.04339 0.40041 1.59363
4 3MJY IJZ 0.0002893 0.51411 1.99203
5 3MJY FMN 0.0002893 0.51411 1.99203
6 4CW5 FMN 0.004389 0.43397 1.99203
7 1WUU ANP 0.01505 0.4125 1.99203
8 2DPM SAM 0.02166 0.4045 1.99203
9 2WOE AR6 0.02392 0.40073 1.99203
10 2F6U CIT 0.00008794 0.49217 2.13675
11 2FLI DX5 0.0004612 0.48664 2.27273
12 5GJO PLP 0.0007529 0.46481 2.39044
13 1FL2 FAD 0.01425 0.43327 2.39044
14 3ATY FMN 0.007601 0.43067 2.39044
15 2VDF OCT 0.006832 0.42552 2.39044
16 1VYP TNF 0.0108 0.42291 2.39044
17 1VYP FMN 0.01154 0.42291 2.39044
18 2GJN FMN 0.00007394 0.40928 2.39044
19 3QV1 NAD 0.02841 0.40281 2.43902
20 4JEJ 1GP 0.008789 0.43806 2.45902
21 2TPS TPS 0.02669 0.40421 2.64317
22 3HF3 FMN 0.002903 0.44671 2.78884
23 3W8X FAD 0.01016 0.44574 2.78884
24 4QNW FMN 0.003623 0.44189 2.78884
25 2FJK 13P 0.00128 0.43714 2.78884
26 2O07 MTA 0.01413 0.42114 2.78884
27 1M5W DXP 0.002384 0.4382 2.88066
28 3KRU FMN 0.001147 0.48298 3.18725
29 3W9Z FMN 0.0008735 0.46866 3.18725
30 2PLK P3D 0.001306 0.46405 3.18725
31 3BW2 FMN 0.01315 0.45201 3.18725
32 2Q3R FMN 0.005336 0.43167 3.18725
33 1UZD CAP 0.006986 0.42761 3.18725
34 5U61 7WG 0.02302 0.41819 3.18725
35 1QMG DMV 0.01203 0.40781 3.18725
36 1L7E NAI 0.02255 0.40658 3.18725
37 1OVD FMN 0.0001858 0.52974 3.58566
38 1OVD ORO 0.0001858 0.52974 3.58566
39 1PS9 FMN 0.004559 0.43865 3.58566
40 4XP7 FNR 0.00557 0.42884 3.58566
41 1T3Q FAD 0.01686 0.42742 3.58566
42 1KBJ FMN 0.03851 0.42079 3.58566
43 2GOU FMN 0.02017 0.4191 3.58566
44 4JIQ FMN 0.01396 0.41867 3.58566
45 4JIQ 1L5 0.01396 0.41867 3.58566
46 2RGO FAD 0.03858 0.40817 3.58566
47 5C5H 4YB 0.02359 0.40698 3.58566
48 4IXH IMP 0.0003471 0.49678 3.60111
49 2Z6I FMN 0.000011 0.57008 3.98406
50 5A5W GUO 0.00005092 0.56345 3.98406
51 2Q3O FMN 0.001518 0.46266 3.98406
52 3C56 PH4 0.001899 0.454 3.98406
53 3N9R TD3 0.001074 0.45205 3.98406
54 2BP1 NDP 0.01874 0.42188 3.98406
55 4QYS PLR 0.003007 0.41128 3.98406
56 3G6N MET ALA SER 0.01162 0.40452 4.18848
57 1OX5 1PR 0.0002422 0.51185 4.38247
58 3CTL S6P 0.0006485 0.4772 4.38247
59 2QCD U5P 0.002713 0.44629 4.38247
60 4HKP TKW 0.004492 0.43898 4.38247
61 3MI2 PFU 0.01769 0.43513 4.38247
62 4HKP 16B 0.004902 0.43159 4.38247
63 2C91 NAP 0.02178 0.41843 4.38247
64 1N62 FAD 0.03094 0.41427 4.38247
65 2VHW NAI 0.04729 0.40245 4.38247
66 1F06 NDP 0.04757 0.40036 4.38247
67 1F06 2NP 0.04757 0.40036 4.38247
68 4BUY F37 0.02018 0.4144 4.58333
69 4EWN 0VR 0.00004784 0.47279 4.78088
70 1NJJ ORX 0.00126 0.46482 4.78088
71 3VKC FPQ 0.0003357 0.40442 4.78088
72 4NAE 1GP 0.00003841 0.47915 4.88889
73 1UZH CAP 0.009908 0.42 4.91803
74 2V63 CAP 0.00843 0.42352 5
75 2VDH CAP 0.008457 0.42345 5
76 2V6A CAP 0.009359 0.4195 5
77 2V67 CAP 0.01142 0.41691 5
78 4MSG 2C6 0.0154 0.42637 5.06912
79 1Q6O LG6 0.03532 0.41023 5.09259
80 2OO0 PLP 0.00182 0.44854 5.17928
81 4C3Y FAD 0.01665 0.4315 5.17928
82 1GVE NAP 0.01313 0.42891 5.17928
83 1F76 FMN 0.009228 0.42787 5.17928
84 4Q4K FMN 0.00001544 0.5692 5.57769
85 2B4G FMN 0.00215 0.4617 5.57769
86 1JCM 137 0.002269 0.44606 5.57769
87 1JG3 ADN 0.01511 0.40731 5.95745
88 4WZH FMN 0.000189 0.51387 5.9761
89 4ORM 2V6 0.011 0.45573 5.9761
90 4ORM FMN 0.011 0.45573 5.9761
91 4ORM ORO 0.011 0.45573 5.9761
92 1X1Z BMP 0.009672 0.44943 5.9761
93 4UTW RFW 0.00001558 0.54956 6.3745
94 4UTU LRY 0.00001552 0.49754 6.3745
95 1ICP FMN 0.004855 0.44643 6.3745
96 3IHG FAD 0.01705 0.42065 6.3745
97 3KDN CAP 0.001505 0.49237 6.77291
98 1TUF AZ1 0.008385 0.4285 6.77291
99 1LQA NDP 0.04336 0.40251 6.77291
100 4A22 TD4 0.004197 0.46361 6.97674
101 3AXK NDP 0.009121 0.41427 6.97674
102 1WDD CAP 0.01148 0.41507 7.03125
103 4IGH ORO 0.005969 0.4712 7.17131
104 4IGH 1EA 0.005969 0.4712 7.17131
105 4IGH FMN 0.005969 0.4712 7.17131
106 1TB3 FMN 0.004489 0.44954 7.17131
107 4OSP NAP 0.03614 0.4012 7.17131
108 3B0P FMN 0.0001345 0.50382 7.56972
109 4A3U FMN 0.01839 0.4065 7.56972
110 3EXS 5RP 0.0000978 0.48625 7.69231
111 1QKQ MAN 0.0035 0.46615 7.74648
112 5X8G S0N 0.03649 0.4186 7.96813
113 1UWK NAD 0.04111 0.41349 7.96813
114 1UWK URO 0.04111 0.41349 7.96813
115 2IID PHE 0.04035 0.41965 8.23293
116 2IID FAD 0.04035 0.41965 8.23293
117 2ZRU FMN 0.001011 0.49097 8.36653
118 1DJN FMN 0.01411 0.41548 8.36653
119 2GKS ADP 0.0152 0.41066 8.36653
120 2IHU TP9 0.03735 0.40699 8.36653
121 2Y88 2ER 0.0002199 0.52455 9.16335
122 5UAO FAD 0.02052 0.42571 9.16335
123 3OVR 5SP 0.0003345 0.49564 9.21053
124 3QMN COA 0.004466 0.43551 9.30233
125 1D4D FAD 0.04477 0.40987 9.56175
126 3H86 AP5 0.03792 0.40459 9.89583
127 2A92 NAI 0.03479 0.4055 10.3586
128 1EIX BMQ 0.007514 0.42045 11.0204
129 1B57 PGH 0.001901 0.44016 11.1554
130 2BZG SAH 0.01872 0.40268 11.2069
131 2HSA FMN 0.00242 0.46202 12.3506
132 3QH2 3NM 0.003181 0.43207 12.6697
133 1IR2 CAP 0.008332 0.42378 12.8571
134 5SVV FMN 0.02084 0.40209 13.1387
135 2C6Q NDP 0.001206 0.49363 13.1474
136 2C6Q IMP 0.0004379 0.49353 13.1474
137 2D1S SLU 0.04006 0.40002 14.741
138 4YSX FAD 0.04306 0.40829 14.7436
139 2OEM 1AE 0.0009496 0.45734 15.1394
140 2VK4 TPP 0.03089 0.40094 17.1315
141 2O4N TPV 0.0198 0.41088 17.1717
142 5XDT MB3 0.03849 0.40424 19.1235
143 5MZY 8EZ 0.0351 0.40064 19.5219
144 1RBL CAP 0.007705 0.42718 24.7706
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