Receptor
PDB id Resolution Class Description Source Keywords
5EYW 1.7 Å EC: 5.3.1.1 CRYSTAL STRUCTURE OF LITOPENAEUS VANNAMEI TRIOSEPHOSPHATE IS COMPLEXED WITH 2-PHOSPHOGLYCOLIC ACID LITOPENAEUS VANNAMEI TIM SHRIMP 2-PHOSPHOGLYCOLIC ACID LOW-THERMAL STABILITY
Ref.: STRUCTURAL INSIGHTS FROM A NOVEL INVERTEBRATE TRIOSEPHOSPHATE ISOMERASE FROM LITOPENAEUS VANNAMEI BIOCHIM.BIOPHYS.ACTA V.1864 1696 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PGA B:301;
A:301;
Valid;
Valid;
none;
none;
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156.031 C2 H5 O6 P C(C(=...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5EYW 1.7 Å EC: 5.3.1.1 CRYSTAL STRUCTURE OF LITOPENAEUS VANNAMEI TRIOSEPHOSPHATE IS COMPLEXED WITH 2-PHOSPHOGLYCOLIC ACID LITOPENAEUS VANNAMEI TIM SHRIMP 2-PHOSPHOGLYCOLIC ACID LOW-THERMAL STABILITY
Ref.: STRUCTURAL INSIGHTS FROM A NOVEL INVERTEBRATE TRIOSEPHOSPHATE ISOMERASE FROM LITOPENAEUS VANNAMEI BIOCHIM.BIOPHYS.ACTA V.1864 1696 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 5EYW - PGA C2 H5 O6 P C(C(=O)O)O....
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 5EYW - PGA C2 H5 O6 P C(C(=O)O)O....
2 1TPW Ki = 0.5 mM PGH C2 H6 N O6 P C(C(=O)NO)....
3 1SW3 - PGA C2 H5 O6 P C(C(=O)O)O....
4 1TPB - PGH C2 H6 N O6 P C(C(=O)NO)....
5 1SW0 - PGA C2 H5 O6 P C(C(=O)O)O....
6 1TPH - PGH C2 H6 N O6 P C(C(=O)NO)....
7 1TPU - PGH C2 H6 N O6 P C(C(=O)NO)....
8 1TPV - PGH C2 H6 N O6 P C(C(=O)NO)....
9 1SW7 - PGA C2 H5 O6 P C(C(=O)O)O....
10 1TPC - PGH C2 H6 N O6 P C(C(=O)NO)....
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: 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 EFS 0.416667 0.741935
8 PAE 0.416667 0.806452
9 SEP 0.40625 0.710526
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5EYW; Ligand: PGA; Similar sites found: 141
This union binding pocket(no: 1) in the query (biounit: 5eyw.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3QMN COA 0.002753 0.44598 None
2 3QH2 3NM 0.004628 0.42411 None
3 1ICP FMN 0.005976 0.44177 2.00803
4 1Q0S SAH 0.01437 0.41658 2.00803
5 2CNE DFJ 0.02587 0.4165 2.00803
6 3ATY FMN 0.01489 0.41579 2.00803
7 5FBN 5WF 0.03482 0.40548 2.00803
8 4ORM FMN 0.01291 0.45183 2.40964
9 4ORM ORO 0.01291 0.45183 2.40964
10 4ORM 2V6 0.01291 0.45183 2.40964
11 4JIQ 1L5 0.02848 0.40276 2.40964
12 4JIQ FMN 0.02848 0.40276 2.40964
13 2GOU FMN 0.04117 0.40268 2.40964
14 4BUY F37 0.01099 0.42809 2.5
15 4MSG 2C6 0.008569 0.43979 2.76498
16 4IXH IMP 0.0001859 0.51045 2.81124
17 4EWN 0VR 0.00003806 0.47629 2.81124
18 4A22 TD4 0.005772 0.4562 2.81124
19 4QYS PLP SEP 0.003153 0.45007 2.81124
20 4QYS PLR 0.002213 0.43961 2.81124
21 2Q3R FMN 0.01059 0.41682 2.81124
22 1VYP FMN 0.01796 0.41306 2.81124
23 1VYP TNF 0.01685 0.41306 2.81124
24 3PFD FDA 0.03951 0.40854 2.81124
25 1XKQ NDP 0.0387 0.40412 2.81124
26 1Z44 FMN 0.002714 0.40362 2.81124
27 1QKQ MAN 0.003452 0.46644 2.8169
28 4J3L AJ5 0.0192 0.4003 2.85714
29 1JG3 ADN 0.01593 0.40618 2.97872
30 2FLI DX5 0.0005813 0.48162 3.18182
31 2Z6I FMN 0.0000114 0.5693 3.21285
32 3KRU FMN 0.001713 0.47391 3.21285
33 2OO0 PLP 0.001081 0.4596 3.21285
34 3BW2 FMN 0.01574 0.44763 3.21285
35 2C91 NAP 0.01428 0.4281 3.21285
36 2BP1 NDP 0.01568 0.42597 3.21285
37 4XP7 FNR 0.009935 0.41638 3.21285
38 2IHU TP9 0.02741 0.41416 3.21285
39 2VHW NAI 0.04932 0.40147 3.21285
40 1YNQ NDP 0.03325 0.4006 3.21285
41 3CTL S6P 0.001094 0.46591 3.4632
42 4WZH FMN 0.0002961 0.50395 3.61446
43 3MJY FMN 0.0004855 0.50241 3.61446
44 3MJY IJZ 0.0004855 0.50241 3.61446
45 5IXJ THR 0.002417 0.46345 3.61446
46 2Q3O FMN 0.001498 0.46295 3.61446
47 1NJJ ORX 0.001524 0.46071 3.61446
48 2B4G FMN 0.002886 0.45516 3.61446
49 2PLK P3D 0.002201 0.45272 3.61446
50 3W9Z FMN 0.002207 0.44875 3.61446
51 1JCM 137 0.002624 0.44296 3.61446
52 3VKC FPQ 0.0005402 0.40013 3.61446
53 1EIX BMQ 0.007583 0.42025 3.67347
54 5A5W GUO 0.00002319 0.5816 4.01606
55 1OVD ORO 0.0004013 0.51212 4.01606
56 1OVD FMN 0.0004013 0.51212 4.01606
57 2OEM 1AE 0.001268 0.45129 4.01606
58 2DVZ GLU 0.01305 0.40001 4.01606
59 1X1Z BMP 0.007143 0.45659 4.36508
60 4CW5 FMN 0.003967 0.43615 4.40529
61 1FL2 FAD 0.01308 0.43527 4.41767
62 2Q8Z NUP 0.01063 0.42173 4.41767
63 1J0D 5PA 0.02913 0.40358 4.41767
64 1UZD CAP 0.008874 0.42241 4.47761
65 4JEJ 1GP 0.007575 0.44145 4.5082
66 3EXS 5RP 0.00008244 0.48816 4.52489
67 1M5W DXP 0.002392 0.43813 4.52675
68 1OX5 1PR 0.0003576 0.50318 4.81928
69 3N9R TD3 0.001824 0.44102 4.81928
70 3C56 PH4 0.004155 0.43708 4.81928
71 5X8G S0N 0.02538 0.4273 4.81928
72 1PS9 FMN 0.01087 0.41964 4.81928
73 1TUF AZ1 0.01463 0.41619 4.81928
74 5C5H 4YB 0.01648 0.41498 4.81928
75 1PS9 FAD 0.03624 0.41323 4.81928
76 5UAO FAD 0.04586 0.4068 4.81928
77 3OVR 5SP 0.0003137 0.49704 4.82456
78 1IR2 CAP 0.0103 0.41915 5
79 2V63 CAP 0.0112 0.41733 5
80 2VDH CAP 0.0119 0.41601 5
81 2V6A CAP 0.01204 0.41402 5
82 2V67 CAP 0.01489 0.41112 5
83 2C6Q NDP 0.0006783 0.50701 5.22088
84 2C6Q IMP 0.0002733 0.5039 5.22088
85 3B0P FMN 0.0001951 0.49593 5.22088
86 1B57 PGH 0.003516 0.42737 5.22088
87 3AXK NDP 0.00958 0.41323 5.42636
88 1WDD CAP 0.01523 0.40893 5.46875
89 1Q6O LG6 0.01469 0.43061 5.55556
90 4Q4K FMN 0.00001611 0.56827 5.62249
91 3KDN CAP 0.0016 0.49094 5.62249
92 4QNW FMN 0.007262 0.42677 5.62249
93 2FJK 13P 0.002357 0.42579 5.62249
94 1F76 FMN 0.01225 0.42158 5.62249
95 2GJN FMN 0.0001198 0.40384 5.62249
96 2Y88 2ER 0.0001072 0.54094 5.7377
97 3OIX FMN 0.001646 0.46267 6.0241
98 1GVE NAP 0.01171 0.43152 6.0241
99 4JB1 NAP 0.02659 0.42543 6.0241
100 4JB1 FAD 0.02745 0.42543 6.0241
101 4BNU 9KQ 0.02195 0.4042 6.0241
102 4NAE 1GP 0.00004151 0.47851 6.22222
103 1OFD FMN 0.001382 0.48261 6.4257
104 2QCD U5P 0.001534 0.45861 6.4257
105 2HSA FMN 0.002821 0.45859 6.4257
106 1OFD AKG 0.003807 0.45708 6.4257
107 4HKP TKW 0.002294 0.45365 6.4257
108 4HKP 16B 0.002279 0.44806 6.4257
109 3MI2 PFU 0.01335 0.4418 6.4257
110 1T3Q FAD 0.01631 0.42819 6.4257
111 1TB3 FMN 0.01491 0.42248 6.4257
112 5U61 7WG 0.02164 0.41962 6.4257
113 4GAA BES 0.01743 0.40044 6.4257
114 1DJN FMN 0.008573 0.42646 6.82731
115 2O4N TPV 0.01221 0.42164 7.07071
116 3S43 478 0.0302 0.40528 7.07071
117 1GY8 NAD 0.0124 0.42788 7.22892
118 2WKV COA 0.0438 0.40125 7.22892
119 1QO8 FAD 0.01862 0.42977 8.03213
120 5TCI MLI 0.001058 0.40906 8.03213
121 2WOE AR6 0.01904 0.40573 8.03213
122 1LQA NDP 0.02994 0.41109 8.43373
123 2F6U CIT 0.00007331 0.4955 8.97436
124 5GJO PLP 0.0005484 0.47149 9.63855
125 1DQX BMP 0.003368 0.44348 9.63855
126 4IGH ORO 0.01501 0.44881 10.0402
127 4IGH 1EA 0.01501 0.44881 10.0402
128 4IGH FMN 0.01501 0.44881 10.0402
129 1N62 FAD 0.02458 0.41963 10.0402
130 4UTU LRY 0.00001622 0.49672 10.4803
131 2DPM SAM 0.0134 0.41505 10.8434
132 5SVV FMN 0.01705 0.40646 10.9489
133 1UJP CIT 0.001473 0.40237 11.0701
134 2VDF OCT 0.006136 0.42389 11.6466
135 1GQ2 NAP 0.03461 0.40096 12.0482
136 4UTW RFW 0.00001495 0.55043 12.6638
137 3HF3 FMN 0.005538 0.43267 13.253
138 2ZRU FMN 0.003567 0.4621 14.4578
139 2WET FAD 0.02702 0.42101 16.8675
140 1RBL CAP 0.01045 0.42051 18.3486
141 1UZH CAP 0.01229 0.4153 19.6721
Pocket No.: 2; Query (leader) PDB : 5EYW; Ligand: PGA; 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: 5eyw.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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