Receptor
PDB id Resolution Class Description Source Keywords
5ND5 1.74 Å EC: 2.2.1.1 CRYSTAL STRUCTURE OF TRANSKETOLASE FROM CHLAMYDOMONAS REINHA COMPLEX WITH TPP AND MG2+ CHLAMYDOMONAS REINHARDTII TRANSFERASE CALVIN-BENSON CYCLE THIAMINE PYROPHOSPHATE MADEPENDENT ACTIVATION
Ref.: STRUCTURAL BASIS FOR THE MAGNESIUM-DEPENDENT ACTIVA TRANSKETOLASE FROM CHLAMYDOMONAS REINHARDTII. BIOCHIM. BIOPHYS. ACTA V.1861 2132 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
TPP B:801;
A:801;
Valid;
Valid;
none;
none;
submit data
425.314 C12 H19 N4 O7 P2 S Cc1c(...
MG A:800;
B:800;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5ND5 1.74 Å EC: 2.2.1.1 CRYSTAL STRUCTURE OF TRANSKETOLASE FROM CHLAMYDOMONAS REINHA COMPLEX WITH TPP AND MG2+ CHLAMYDOMONAS REINHARDTII TRANSFERASE CALVIN-BENSON CYCLE THIAMINE PYROPHOSPHATE MADEPENDENT ACTIVATION
Ref.: STRUCTURAL BASIS FOR THE MAGNESIUM-DEPENDENT ACTIVA TRANSKETOLASE FROM CHLAMYDOMONAS REINHARDTII. BIOCHIM. BIOPHYS. ACTA V.1861 2132 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 5ND5 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5ND5 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 1ITZ - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1R9J - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 1NGS - E4P C4 H9 O7 P C([C@H]([C....
3 1TKB Ki = 0.8 uM N1T C13 H19 N3 O7 P2 S Cc1ccc(c(n....
4 1TRK - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
5 1GPU - THD C14 H22 N4 O9 P2 S Cc1ncc(c(n....
6 5HYV - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
7 5I5E - 5SP C5 H11 O8 P C([C@H]([C....
8 5I51 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
9 5HJE - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
10 5ND5 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
11 1ITZ - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
12 1QGD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
13 2R5N Kd = 700 uM R5P C5 H11 O8 P C(C(C(C(C=....
14 2R8O - T5X C17 H30 N4 O15 P3 S Cc1c(sc([n....
15 2R8P - T6F C18 H32 N4 O16 P3 S Cc1c(sc([n....
16 5HHT - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TPP; Similar ligands found: 41
No: Ligand ECFP6 Tc MDL keys Tc
1 TPP 1 1
2 V4E 0.891892 1
3 TDP 0.84 0.985714
4 TPS 0.816901 0.957143
5 TMV 0.769231 0.958333
6 2TP 0.725 0.932432
7 VNP 0.721519 0.958904
8 VIB 0.621622 0.75
9 PYI 0.581395 0.887324
10 TDW 0.566667 0.972222
11 HTL 0.566667 0.958904
12 N1T 0.556818 0.985714
13 FTP 0.551724 0.835616
14 THV 0.548387 0.958904
15 TPW 0.546512 0.9
16 WWF 0.542553 0.933333
17 TD6 0.540816 0.921053
18 THY 0.536842 0.945946
19 TOG 0.536082 0.921053
20 TDL 0.53125 0.897436
21 THW 0.530612 0.958904
22 TD9 0.53 0.921053
23 TD8 0.53 0.921053
24 TDK 0.525773 0.921053
25 D7K 0.490566 0.909091
26 S1T 0.489362 0.887324
27 R1T 0.489362 0.887324
28 TPU 0.483146 0.842105
29 5SR 0.479167 0.945205
30 T5X 0.476636 0.897436
31 T6F 0.476636 0.897436
32 1U0 0.474227 0.84
33 8PA 0.459459 0.945946
34 TZD 0.451613 0.883117
35 O2T 0.45098 0.909091
36 TDM 0.443299 0.894737
37 TDN 0.415842 0.871795
38 THD 0.411765 0.839506
39 MP5 0.407895 0.676056
40 TD7 0.40566 0.85
41 DPX 0.4 0.734177
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5ND5; Ligand: TPP; Similar sites found: 37
This union binding pocket(no: 1) in the query (biounit: 5nd5.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3AI7 TPP 0.00000000005291 0.69512 1.15607
2 2YIC TPP 0.00003405 0.46398 1.44509
3 2VK4 TPP 0.0001967 0.44593 1.59858
4 2IHT TPP 0.0006608 0.43998 2.6178
5 2IHU TP9 0.003141 0.42432 2.6178
6 1UPA TPP 0.001305 0.41644 2.6178
7 1ZPD DPX 0.0003888 0.45441 2.64085
8 2UZ1 TPP 0.00006555 0.4647 3.01954
9 2VBF TPP 0.0001148 0.47644 3.03468
10 4LOC OXM 0.01181 0.4167 3.16456
11 1TZJ A3B 0.03041 0.40297 3.5503
12 4RJK TPP 0.0004465 0.42456 3.67776
13 1T9D PYD 0.002504 0.44355 3.84047
14 1YQT ADP 0.03458 0.40107 3.90335
15 3LA3 2FT 0.02467 0.40777 5.34979
16 2VFK AMP 0.01236 0.42501 5.85366
17 2VZZ SCA 0.006149 0.40448 6.42202
18 2OZL TPP 0.0000002484 0.56156 6.57534
19 2X7J TPP 0.0006012 0.42787 6.62252
20 3EXH TPP 0.0000003319 0.58308 6.68693
21 1W2D ADP 0.01679 0.40757 6.79245
22 3AHC TPP 0.01475 0.41635 7.65896
23 5B48 TDN 0.000798 0.40572 7.86885
24 1JI0 ATP 0.02996 0.40284 7.91667
25 3ZCB ATP 0.0148 0.40271 8.06452
26 1QPB PYM 0.0001613 0.46689 8.17052
27 1QPB TPP 0.0001613 0.46689 8.17052
28 3P7G MAN 0.01898 0.42003 8.21918
29 3EYA TDP 0.0004842 0.44552 8.56102
30 4Y8D 49J 0.03273 0.40082 9.28571
31 2XKO AKG 0.01893 0.41393 11.236
32 2O1S TDP 0.000001402 0.50288 13.3655
33 3DVA TPW 0.0000002086 0.55968 20
34 1W85 TDP 0.000000291 0.56003 20.0617
35 1UMD TDP COI 0.000002644 0.51787 20.7084
36 1RP7 TZD 0.0000000102 0.599 27.0231
37 4MA6 28E 0.01794 0.41451 35.0318
Pocket No.: 2; Query (leader) PDB : 5ND5; Ligand: TPP; 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: 5nd5.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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