Receptor
PDB id Resolution Class Description Source Keywords
1UMD 1.9 Å EC: 1.2.4.4 BRANCHED-CHAIN 2-OXO ACID DEHYDROGENASE (E1) FROM THERMUS THERMOPHILUS HB8 WITH 4-METHYL-2-OXOPENTANOATE AS AN I NTERMEDIATE THERMUS THERMOPHILUS ALPHA(2)BETA(2) TETRAMER STRUCTURAL GENOMICS RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI OXIDOREDUCTASE
Ref.: LIGAND-INDUCED CONFORMATIONAL CHANGES AND A REACTION INTERMEDIATE IN BRANCHED-CHAIN 2-OXO ACID DEHYDROGENASE (E1) FROM THERMUS THERMOPHILUS HB8, AS REVEALED BY X-RAY CRYSTALLOGRAPHY J.MOL.BIOL. V. 337 1011 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:1401;
C:2401;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
TDP COI A:1402;
C:2402;
Valid;
Valid;
none;
none;
submit data
507.421 n/a S1C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1UMD 1.9 Å EC: 1.2.4.4 BRANCHED-CHAIN 2-OXO ACID DEHYDROGENASE (E1) FROM THERMUS THERMOPHILUS HB8 WITH 4-METHYL-2-OXOPENTANOATE AS AN I NTERMEDIATE THERMUS THERMOPHILUS ALPHA(2)BETA(2) TETRAMER STRUCTURAL GENOMICS RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI OXIDOREDUCTASE
Ref.: LIGAND-INDUCED CONFORMATIONAL CHANGES AND A REACTION INTERMEDIATE IN BRANCHED-CHAIN 2-OXO ACID DEHYDROGENASE (E1) FROM THERMUS THERMOPHILUS HB8, AS REVEALED BY X-RAY CRYSTALLOGRAPHY J.MOL.BIOL. V. 337 1011 2004
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1UMD - TDP COI n/a n/a
2 1UMB - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
3 1UMC - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1UMD - TDP COI n/a n/a
2 1UMB - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
3 1UMC - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1UMD - TDP COI n/a n/a
2 1UMB - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
3 1UMC - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TDP COI; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 TDP COI 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1UMD; Ligand: TDP COI; Similar sites found: 49
This union binding pocket(no: 1) in the query (biounit: 1umd.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1YBH P22 0.001586 0.4615 2.17984
2 2C31 ADP 0.001122 0.4652 3.81471
3 2C31 TZD 0.00116 0.4652 3.81471
4 5ESO TDP 0.0005137 0.44944 4.01235
5 5ESO ISC 0.0005137 0.44944 4.01235
6 2ZL4 ALA ALA ALA ALA 0.02196 0.41544 4.08163
7 1YQT ADP 0.01294 0.42721 4.35967
8 3SAO DBH 0.009915 0.43846 4.375
9 3AHC TPP 0.0001634 0.46382 4.62963
10 1ZPD DPX 0.0001828 0.46025 4.62963
11 3AI7 TPP 0.0000004786 0.55705 4.90463
12 2C42 PYR 0.0007445 0.43729 4.90463
13 2C42 TPP 0.0007445 0.43729 4.90463
14 2UZ1 TPP 0.00003257 0.48466 4.93827
15 1QPB PYM 0.0002445 0.45184 4.93827
16 1QPB TPP 0.0002537 0.4512 4.93827
17 3IAE D7K 0.00004082 0.45038 4.93827
18 1OZH HE3 0.0003748 0.47649 5.24691
19 2VK4 TPP 0.0001909 0.45432 5.24691
20 3UDG TMP 0.004728 0.40734 5.31561
21 5B48 TDN 0.001183 0.40487 5.44959
22 2VBF TPP 0.0001322 0.4659 5.8642
23 1ITZ TPP 0.000002933 0.53642 6.53951
24 2R5N TPP 0.000008616 0.46552 7.08447
25 2R5N R5P 0.00001065 0.46233 7.08447
26 2R5N RP5 0.00001061 0.45788 7.08447
27 1T9D P22 0.001352 0.47621 7.23781
28 1T9D PYD 0.007042 0.42503 7.23781
29 3I9U DTU 0.04998 0.40123 8.36502
30 2X7J TPP 0.000152 0.45823 8.71935
31 5EXE 5SR 0.0006164 0.44059 8.9172
32 1VBO MAN MAN MAN 0.03177 0.40232 9.39597
33 1V5F FAD 0.007745 0.42385 9.53679
34 1UPA TPP 0.0002318 0.45099 9.5679
35 2IHT TPP 0.0002512 0.44961 9.5679
36 2IHU TP9 0.0003829 0.40302 9.5679
37 2NXW TPP 0.00006364 0.44011 10.0817
38 4RJK TPP 0.00008496 0.45666 10.3542
39 4RJK TDL 0.0001101 0.44193 10.3542
40 1TKB N1T 0.000009134 0.46138 10.8992
41 3EYA TDP 0.00008458 0.46829 12.2616
42 2Q28 TPP 0.001459 0.41943 12.6543
43 3GNE FLC 0.03638 0.40117 13.4921
44 1RP7 TZD 0.000001687 0.5277 14.5062
45 2YIC TPP 0.0000000002818 0.65886 19.4444
46 5ND5 TPP 0.000002644 0.51787 20.7084
47 1R9J TPP 0.000003816 0.53174 27.248
48 4KXV TDP DX5 0.000151 0.40208 27.7778
49 2O1S TDP 0.00002795 0.52842 29.321
Pocket No.: 2; Query (leader) PDB : 1UMD; Ligand: TDP COI; Similar sites found: 5
This union binding pocket(no: 2) in the query (biounit: 1umd.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3CK8 BCD 0.0206 0.41692 3.08642
2 4XWM CBI 0.01587 0.42266 4.93827
3 1T0S BML 0.0245 0.40712 10.1852
4 4HA6 PXM 0.02021 0.41936 10.8025
5 2FVK DUC 0.03251 0.40625 10.8025
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