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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 (33)
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 5XSA - 8EL C12 H20 N4 O7 P2 S Cc1ncc(c(n....
8 5I5E - 5SP C5 H11 O8 P C([C@H]([C....
9 5XU9 - 8N9 C14 H22 N4 O9 P2 S Cc1ncc(c(n....
10 5XRV - F6R C6 H13 O9 P C([C@H]([C....
11 5XS6 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
12 5XSB - 8EL C12 H20 N4 O7 P2 S Cc1ncc(c(n....
13 5XSM - 8EO C12 H21 N4 O7 P2 S Cc1ncc(c(n....
14 5XUF - 8FL C12 H20 N4 O8 P2 S Cc1ncc(c(n....
15 5XVT - 8FL C12 H20 N4 O8 P2 S Cc1ncc(c(n....
16 5XTV - 8EF C12 H20 N4 O7 P2 S Cc1ncc(c(n....
17 5XQK - T5X C17 H30 N4 O15 P3 S Cc1c(sc([n....
18 5XPS - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
19 5I51 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
20 5XU2 - F6R C6 H13 O9 P C([C@H]([C....
21 5XT4 - T6F C18 H32 N4 O16 P3 S Cc1c(sc([n....
22 5XTX - 8ML C18 H33 N4 O16 P3 S Cc1ncc(c(n....
23 5XT0 - T6F C18 H32 N4 O16 P3 S Cc1c(sc([n....
24 5XQA - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
25 5XTL - 8GF C5 H7 N3 Cc1nccc(n1....
26 5HJE - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
27 5ND5 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
28 1ITZ - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
29 1QGD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
30 2R5N Kd = 700 uM R5P C5 H11 O8 P C(C(C(C(C=....
31 2R8O - T5X C17 H30 N4 O15 P3 S Cc1c(sc([n....
32 2R8P - T6F C18 H32 N4 O16 P3 S Cc1c(sc([n....
33 5HHT - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TPP; Similar ligands found: 47
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 AUJ 0.55914 0.921053
13 N1T 0.556818 0.985714
14 FTP 0.551724 0.835616
15 THV 0.548387 0.958904
16 TPW 0.546512 0.9
17 WWF 0.542553 0.933333
18 TD6 0.540816 0.921053
19 THY 0.536842 0.945946
20 TOG 0.536082 0.921053
21 TDL 0.53125 0.897436
22 THW 0.530612 0.958904
23 TD8 0.53 0.921053
24 TD9 0.53 0.921053
25 TDK 0.525773 0.921053
26 D7K 0.490566 0.909091
27 S1T 0.489362 0.887324
28 R1T 0.489362 0.887324
29 TPU 0.483146 0.842105
30 5SR 0.479167 0.945205
31 T6F 0.476636 0.897436
32 T5X 0.476636 0.897436
33 1U0 0.474227 0.84
34 8PA 0.459459 0.945946
35 8FL 0.457447 0.894737
36 8EO 0.457447 0.92
37 TZD 0.451613 0.883117
38 O2T 0.45098 0.909091
39 TDM 0.443299 0.894737
40 8EL 0.442105 0.894737
41 G8G 0.44086 0.805195
42 TDN 0.415842 0.871795
43 THD 0.411765 0.839506
44 8N9 0.411765 0.839506
45 MP5 0.407895 0.676056
46 TD7 0.40566 0.85
47 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 with APoc: 101
This union binding pocket(no: 1) in the query (biounit: 5nd5.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 3AI7 TPP 1.15607
3 2YIC TPP 1.44509
4 3SZB I1E 1.5896
5 2VK4 TPP 1.59858
6 4WBD CIT 1.66359
7 3ITJ CIT 1.77515
8 2NUN ADP 1.85759
9 6FYQ PLP 1.8595
10 3ZX4 2M8 1.9305
11 2NXW TPP 1.9469
12 5E70 RCD 1.96078
13 3MD0 GDP 1.97183
14 4D5G FAD 2.03735
15 4D5G TPP 2.03735
16 3NOJ PYR 2.10084
17 5AJU RP5 2.18978
18 4I90 CHT 2.31023
19 5H06 MAL 2.34375
20 6A46 DCM 2.34375
21 1UPA TPP 2.6178
22 2IHT TPP 2.6178
23 2IHU TP9 2.6178
24 1ZPD DPX 2.64085
25 1OZH HE3 2.65018
26 1B7A OPE 2.68817
27 5ESO ISC 2.78746
28 5ESO TDP 2.78746
29 5A96 GTP 2.81124
30 4G86 BNT 2.8169
31 3IAE D7K 2.98246
32 2UZ1 TPP 3.01954
33 2VBF TPP 3.03468
34 4LOC OXM 3.16456
35 4LCQ URQ 3.26923
36 2IYA UDP 3.30189
37 1QS0 TDP 3.5503
38 1TZJ A3B 3.5503
39 3B6R CRN 3.67454
40 4RJK TPP 3.67776
41 4RJK TDL 3.67776
42 5EXE 5SR 3.82166
43 1T9D P25 3.84047
44 1T9D 1MM 3.84047
45 1T9D FAD 3.84047
46 5WKC TP9 3.84047
47 5WKC AUJ 3.84047
48 1T9D PYD 3.84047
49 5ZI9 FLC 3.84615
50 1YQT ADP 3.90335
51 2C31 TZD 4.0493
52 2C31 ADP 4.0493
53 4JJF N2I 4.06977
54 5XPI 8C3 4.4586
55 3AB4 THR 4.49438
56 4B5W PYR 4.6875
57 3LA3 2FT 5.34979
58 5W6Y TRP 5.37975
59 6CI9 F3V 5.40541
60 2WPB ZZI 5.59211
61 2VWT PYR 5.61798
62 2GCG DGY 5.75758
63 1ONI BEZ 5.7971
64 2VFK AMP 5.85366
65 2WW4 ADP 6.00707
66 2VZZ SCA 6.42202
67 2OZL TPP 6.57534
68 2X7J TPP 6.62252
69 3EXH TPP 6.68693
70 2IYF UDP 6.74699
71 1W2D ADP 6.79245
72 5URY PAM 6.84932
73 1U6R IOM 7.36842
74 3AHC TPP 7.65896
75 5B48 TDN 7.86885
76 1JI0 ATP 7.91667
77 3ZCB ATP 8.06452
78 4C01 QY9 8.15603
79 1QPB TPP 8.17052
80 1QPB PYM 8.17052
81 3P7G MAN 8.21918
82 3EYA TDP 8.56102
83 4NTO 1PW 8.69565
84 4Y8D 49J 9.28571
85 1VRP IOM 9.44882
86 5B47 TPP 10.1974
87 5B47 PYR 10.1974
88 3GUZ PAF 10.2273
89 1CFV E3G 10.9244
90 2XKO AKG 11.236
91 3B8I OXL 11.4983
92 1C3X 8IG 12.406
93 2O1S TDP 13.3655
94 4M1U A2G MBG 14.2857
95 3I6B KDO 15.5556
96 1OLS TDP 16.5
97 3DVA TPW 20
98 1W85 TDP 20.0617
99 1UMD TDP COI 20.7084
100 1RP7 TZD 27.0231
101 4MA6 28E 35.0318
Pocket No.: 2; Query (leader) PDB : 5ND5; Ligand: TPP; Similar sites found with APoc: 16
This union binding pocket(no: 2) in the query (biounit: 5nd5.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 2FVK DUC 1.43113
2 1T3D CYS 2.07612
3 2Q8M AMP 2.40964
4 3QDK QDK 2.62238
5 4K6B GLU 3.10559
6 5ZBL AMP 3.44828
7 4FBL SPD 4.27046
8 5G6U YJM 4.5977
9 1Q8P MAN MMA 4.7619
10 2BMB PMM 4.77064
11 4OWK NGA 5.7971
12 4K7O EKZ 7.14286
13 2J0B UDP 8.57143
14 2PZE ATP 10.4803
15 5MLJ 9ST 16.9643
16 5FQ0 FLC 18.4211
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