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Receptor
PDB id Resolution Class Description Source Keywords
1RP7 2.09 Å EC: 1.2.4.1 E. COLI PYRUVATE DEHYDROGENASE INHIBITOR COMPLEX ESCHERICHIA COLI, ESCHERICHIA COLI O157:H7 THDP THIAMIN-THIAZOLONE DIPHOSPHATE PYRUVATE DEHYDROGENASE OXIDOREDUCTASE
Ref.: STRUCTURAL DETERMINANTS OF ENZYME BINDING AFFINITY: THE E1 COMPONENT OF PYRUVATE DEHYDROGENASE FROM ESCHERICHIA COLI IN COMPLEX WITH THE INHIBITOR THIAMIN THIAZOLONE DIPHOSPHATE. BIOCHEMISTRY V. 43 2405 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:890;
B:888;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
TZD A:889;
B:887;
Valid;
Valid;
none;
none;
Ki > 0.003 uM
440.306 C12 H18 N4 O8 P2 S Cc1nc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1RP7 2.09 Å EC: 1.2.4.1 E. COLI PYRUVATE DEHYDROGENASE INHIBITOR COMPLEX ESCHERICHIA COLI, ESCHERICHIA COLI O157:H7 THDP THIAMIN-THIAZOLONE DIPHOSPHATE PYRUVATE DEHYDROGENASE OXIDOREDUCTASE
Ref.: STRUCTURAL DETERMINANTS OF ENZYME BINDING AFFINITY: THE E1 COMPONENT OF PYRUVATE DEHYDROGENASE FROM ESCHERICHIA COLI IN COMPLEX WITH THE INHIBITOR THIAMIN THIAZOLONE DIPHOSPHATE. BIOCHEMISTRY V. 43 2405 2004
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3LQ4 Kd = 5.97 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
2 2G25 - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
3 2QTA Kd = 1.75 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
4 2IEA - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
5 1L8A - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
6 1RP7 Ki > 0.003 uM TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
7 2G28 - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
8 3LQ2 Kd = 5.97 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
9 2QTC - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
10 3LPL Kd = 2.39 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3LQ4 Kd = 5.97 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
2 2G25 - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
3 2QTA Kd = 1.75 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
4 2IEA - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
5 1L8A - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
6 1RP7 Ki > 0.003 uM TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
7 2G28 - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
8 3LQ2 Kd = 5.97 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
9 2QTC - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
10 3LPL Kd = 2.39 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3LQ4 Kd = 5.97 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
2 2G25 - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
3 2QTA Kd = 1.75 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
4 2IEA - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
5 1L8A - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
6 1RP7 Ki > 0.003 uM TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
7 2G28 - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
8 3LQ2 Kd = 5.97 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
9 2QTC - TDK C15 H26 N4 O11 P3 S Cc1c(sc([n....
10 3LPL Kd = 2.39 uM TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TZD; Similar ligands found: 30
No: Ligand ECFP6 Tc MDL keys Tc
1 TZD 1 1
2 TDM 0.716049 0.910256
3 TDN 0.690476 0.8875
4 THD 0.682353 0.855422
5 8N9 0.682353 0.855422
6 TD7 0.644444 0.888889
7 8FL 0.638554 0.986667
8 8EL 0.638554 0.910256
9 8EF 0.48913 0.85
10 TPU 0.47191 0.768293
11 TPW 0.466667 0.815789
12 PYI 0.451613 0.782051
13 TPP 0.451613 0.883117
14 THY 0.435644 0.839506
15 R1T 0.43299 0.805195
16 S1T 0.43299 0.805195
17 1TP 0.431373 0.841463
18 G8G 0.430108 0.894737
19 TDW 0.428571 0.860759
20 HTL 0.428571 0.873418
21 1U0 0.42 0.765432
22 8EO 0.416667 0.839506
23 THV 0.415842 0.85
24 MP5 0.413333 0.631579
25 WWF 0.411765 0.829268
26 AUJ 0.411765 0.819277
27 TOG 0.409524 0.841463
28 V4E 0.40404 0.883117
29 TDL 0.403846 0.821429
30 TDK 0.4 0.819277
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1RP7; Ligand: TZD; Similar sites found with APoc: 106
This union binding pocket(no: 1) in the query (biounit: 1rp7.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 5XIO HFG 0.803213
2 3AHC TPP 1.18343
3 1OZH HE3 1.23675
4 2C42 PYR 1.24153
5 2C42 TPP 1.24153
6 1IZC PYR 1.47493
7 4D5G TPP 1.52801
8 4D5G FAD 1.52801
9 3K5I AIR 1.73697
10 2O1S TDP 1.77134
11 4BC5 5FX 1.85874
12 4X1B MLI 1.91458
13 1T9D P22 1.92024
14 5WKC TP9 1.92024
15 1T9D FAD 1.92024
16 1T9D PYD 1.92024
17 1T9D 1MM 1.92024
18 1T9D P25 1.92024
19 5WKC AUJ 1.92024
20 3CXO 3LR 1.92771
21 1GQ2 OXL 1.98198
22 1ZGS XMM 2.01342
23 3EYA TDP 2.36794
24 2YIC TPP 2.53456
25 2IHT TPP 2.6178
26 2IHU TP9 2.6178
27 1UPA TPP 2.6178
28 1H5R G1P 2.73038
29 4WBD CIT 2.77264
30 3B8I OXL 2.78746
31 3IAE D7K 2.80702
32 3WG3 A2G GAL NAG FUC 2.80899
33 2UZ1 TPP 2.84192
34 5B48 TDN 2.95082
35 2C31 TZD 2.99296
36 2C31 ADP 2.99296
37 3CV2 OXL 3.00752
38 2NXW TPP 3.00885
39 2G50 PYR 3.01887
40 3HWW AKG 3.05755
41 4L9Z OXL 3.24484
42 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 3.34728
43 2Z48 A2G 3.47222
44 4IKZ AFS 3.5503
45 1YBH P22 3.55932
46 2J0W ASP 3.56347
47 1U0J ADP 4.11985
48 1FDJ 2FP 4.13223
49 3KFF ZBT 4.32099
50 3KFF XBT 4.32099
51 4RJK TPP 4.37828
52 4RJK TDL 4.37828
53 5NM7 GLY 4.51128
54 5TQZ GLC 4.66667
55 4HZ0 1AV 4.69484
56 6GI2 8SW 4.96454
57 1GXS DKA 5.06329
58 5B47 PYR 5.09554
59 5B47 TPP 5.09554
60 1ZPD DPX 5.10563
61 5KBE IPH 5.24017
62 5AZC PGT 5.33333
63 2CUN 3PG 5.36585
64 2X7J TPP 5.46358
65 4B5W PYR 5.46875
66 1Q19 SSC 5.76541
67 1QS0 TDP 5.91716
68 5AEW BNL 6.10022
69 5B0I BOG 6.12245
70 5A7V MAN 6.18557
71 4D06 NAR 7.42049
72 2GNK ATP 8.03571
73 2VBF TPP 8.07018
74 1QPB TPP 8.17052
75 1QPB PYM 8.17052
76 5MWJ EBU 8.30861
77 5EXE 5SR 8.59873
78 2VK4 TPP 8.70337
79 3AI7 TPP 8.90493
80 4ZOH MCN 9.52381
81 2VHL GLP 9.59596
82 5A9A UTP 9.87654
83 5XU2 TPP 9.89957
84 5XU2 F6R 9.89957
85 5XU2 8EL 9.89957
86 2ZSC BTN 9.92908
87 1C3M MAN MAN 10.2041
88 1TKB N1T 10.472
89 5N53 8NB 11.7949
90 4PYA 2X3 11.8012
91 3CYI ATP 11.8182
92 5FS0 5JC 11.8483
93 1R9J TPP 11.8871
94 4KXV TDP DX5 13.9717
95 2R5N TPP 14.0508
96 2R5N RP5 14.0508
97 2R5N R5P 14.0508
98 1UMD TDP COI 14.5062
99 2NUO BGC 17.2131
100 2NU5 NAG 17.2131
101 2GUD MAN 17.2131
102 2GUC MAN 17.2131
103 1LNX URI 17.284
104 1ITZ TPP 17.7778
105 1OLS TDP 20
106 5ND5 TPP 27.0231
Pocket No.: 2; Query (leader) PDB : 1RP7; Ligand: TZD; Similar sites found with APoc: 31
This union binding pocket(no: 2) in the query (biounit: 1rp7.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 3WIR BGC 0.91623
2 4DDY DN6 2.28137
3 5OC1 ANN 2.30088
4 5WZN A2G 2.5
5 3HQP OXL 2.80561
6 5JVB 2PO 2.85714
7 2X00 GYN 3.52423
8 5U97 PIT 3.80228
9 5LV1 78T 3.92857
10 5ESO ISC 4.00697
11 5ESO TDP 4.00697
12 3JQ8 DX3 4.16667
13 4K6B GLU 4.34783
14 5CPR 539 4.47761
15 1VBO MAN 4.69799
16 1VBO MAN MAN MAN 4.69799
17 6G47 SIA 4.78469
18 2CJ9 SSA 5.17241
19 1U0A BGC BGC BGC BGC 5.60748
20 3X27 TRP 6.26866
21 5A5D 5LC 6.57439
22 2GGX NPJ 7.5
23 1VR0 3SL 8.90688
24 1XQP 8HG 8.98438
25 1KJ1 MAN 9.17431
26 5OFW 9TW 10.3139
27 5VIT MLI 12.1212
28 2GUD BMA 17.2131
29 2HYR BGC GLC 17.2131
30 2HYQ MAN MAN 17.2131
31 4OIT MAN 25.6637
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