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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 P(=O)...
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 with APoc: 91
This union binding pocket(no: 1) in the query (biounit: 1umd.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1U3G ADP 2.1164
2 4WBD CIT 2.16049
3 1YBH P22 2.17984
4 5K8P 6R8 2.77778
5 5Z21 OXM 3.07263
6 3ITJ CIT 3.08642
7 1IZC PYR 3.53982
8 5XU2 TPP 3.54223
9 5XU2 F6R 3.54223
10 5XU2 8EL 3.54223
11 1O5Q PYR 3.60656
12 5A96 GTP 3.61446
13 4CSD MFU 3.67647
14 2C31 TZD 3.81471
15 2C31 ADP 3.81471
16 5ESO ISC 4.01235
17 5ESO TDP 4.01235
18 2ZL4 ALA ALA ALA ALA 4.08163
19 3HWW AKG 4.32099
20 1YQT ADP 4.35967
21 3SAO DBH 4.375
22 3AHC TPP 4.62963
23 1ZPD DPX 4.62963
24 1FAO 4IP 4.7619
25 3AI7 TPP 4.90463
26 2C42 TPP 4.90463
27 2C42 PYR 4.90463
28 3IAE D7K 4.93827
29 2UZ1 TPP 4.93827
30 1QPB TPP 4.93827
31 1QPB PYM 4.93827
32 1OZH HE3 5.24691
33 2VK4 TPP 5.24691
34 3UDG TMP 5.31561
35 5B48 TDN 5.44959
36 4D5G TPP 5.55556
37 4D5G FAD 5.55556
38 2HIM ASN 5.58659
39 2VBF TPP 5.8642
40 5AOV GLV 5.95238
41 5AZC PGT 6
42 6DEN TP9 6.48148
43 6DEN G8A 6.48148
44 6DEN FAD 6.48148
45 1ITZ TPP 6.53951
46 6F7X MFU 6.66667
47 2R5N TPP 7.08447
48 2R5N RP5 7.08447
49 2R5N R5P 7.08447
50 3HQP OXL 7.08447
51 1T9D FAD 7.23781
52 1T9D 1MM 7.23781
53 1T9D P25 7.23781
54 5WKC TP9 7.23781
55 1T9D P22 7.23781
56 5WKC AUJ 7.23781
57 1T9D PYD 7.23781
58 1Q19 SSC 7.62943
59 3I9U DTU 8.36502
60 3L6C MLI 8.55457
61 2X7J TPP 8.71935
62 5EXE 5SR 8.9172
63 1VBO MAN MAN MAN 9.39597
64 1V5F TPP 9.53679
65 1V5F FAD 9.53679
66 2IHU TP9 9.5679
67 1UPA TPP 9.5679
68 2IHT TPP 9.5679
69 2NXW TPP 10.0817
70 4RJK TPP 10.3542
71 4RJK TDL 10.3542
72 2FVK DUC 10.8025
73 5YIZ EF2 10.8108
74 5YJ1 6EL 10.8108
75 5YJ0 EF2 10.8108
76 1TKB N1T 10.8992
77 5NM7 GLY 11.6541
78 3EYA TDP 12.2616
79 4KGD TDP 12.5341
80 4KGD FAD 12.5341
81 5B47 PYR 12.5341
82 5B47 TPP 12.5341
83 2Q28 TPP 12.6543
84 3GNE FLC 13.4921
85 1RP7 TZD 14.5062
86 3FSJ D7K 16.6213
87 2YIC TPP 19.4444
88 5ND5 TPP 20.7084
89 1R9J TPP 27.248
90 4KXV TDP DX5 27.7778
91 2O1S TDP 29.321
Pocket No.: 2; Query (leader) PDB : 1UMD; Ligand: TDP COI; Similar sites found with APoc: 13
This union binding pocket(no: 2) in the query (biounit: 1umd.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 3CK8 BCD 3.08642
2 4RQL SNE 4.01235
3 4XWM CBI 4.93827
4 2PK4 ACA 5
5 2PSJ CEI 5.01567
6 5V7I 8Z1 5.17711
7 6B2W AG2 5.55556
8 4H9T HL4 7.09877
9 3B12 FAH 7.56579
10 1T0S BML 10.1852
11 4HA6 PXM 10.8025
12 4GNC ASO 11.3712
13 5Y02 MXN 22.4299
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