Receptor
PDB id Resolution Class Description Source Keywords
5I5E 1.62 Å EC: 2.2.1.1 CRYSTAL STRUCTURE OF TRANSKETOLASE MUTANTS-H66/261C COMPLEX XYLULOSE-5-PHOAPHATE FROM PICHIA STIPITIS SCHEFFERSOMYCES STIPITIS CBS 6054 TRANSKETOLASE XYLULOSE-5-PHOSPHATE TRANSFERASE
Ref.: STRUCTURAL AND BIOCHEMICAL INTERROGATION ON TRANSKE FROM PICHIA STIPITIS FOR NEW FUNCTIONALITY PROTEIN ENG. DES. SEL. 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
TPP A:701;
 Valid;
 none;
 submit data
425.314 C12 H19 N4 O7 P2 S Cc1c(...
CA A:703;
 Part of Protein;
 none;
 submit data
40.078 Ca [Ca+2...
5SP A:702;
 Valid;
 none;
 submit data
230.11 C5 H11 O8 P C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5XU2 0.97 Å EC: 2.2.1.1 CRYSTAL STRUCTURE OF TRANSKETOLASE IN COMPLEX WITH TPP_III A FRUCTOSE-6-PHOSPHATE FROM PICHIA STIPITIS SCHEFFERSOMYCES STIPITIS CBS 6054 TRANSKETOLASE TRANSFERASE
Ref.: EVIDENCE OF DIRADICALS INVOLVED IN THE YEAST TRANSK CATALYZED KETO-TRANSFERRING REACTIONS. CHEMBIOCHEM V. 19 2395 2018
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 5HYV - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 5XSA - 8EL C12 H20 N4 O7 P2 S Cc1ncc(c(n....
3 5I5E - 5SP C5 H11 O8 P C([C@H]([C....
4 5XU9 - 8N9 C14 H22 N4 O9 P2 S Cc1ncc(c(n....
5 5XRV - F6R C6 H13 O9 P C([C@H]([C....
6 5XS6 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
7 5XSB - 8EL C12 H20 N4 O7 P2 S Cc1ncc(c(n....
8 5XSM - 8EO C12 H21 N4 O7 P2 S Cc1ncc(c(n....
9 5XUF - 8FL C12 H20 N4 O8 P2 S Cc1ncc(c(n....
10 5XVT - 8FL C12 H20 N4 O8 P2 S Cc1ncc(c(n....
11 5XTV - 8EF C12 H20 N4 O7 P2 S Cc1ncc(c(n....
12 5XQK - T5X C17 H30 N4 O15 P3 S Cc1c(sc([n....
13 5XPS - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
14 5I51 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
15 5XU2 - F6R C6 H13 O9 P C([C@H]([C....
16 5XT4 - T6F C18 H32 N4 O16 P3 S Cc1c(sc([n....
17 5XTX - 8ML C18 H33 N4 O16 P3 S Cc1ncc(c(n....
18 5XT0 - T6F C18 H32 N4 O16 P3 S Cc1c(sc([n....
19 5XQA - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
20 5XTL - 8GF C5 H7 N3 Cc1nccc(n1....
21 5HJE - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
70% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1NGS - E4P C4 H9 O7 P C([C@H]([C....
2 1TKB Kd = 0.000000064 M N1T C13 H19 N3 O7 P2 S Cc1ccc(c(n....
3 1TRK - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
4 1GPU - THD C14 H22 N4 O9 P2 S Cc1ncc(c(n....
5 5HYV - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
6 5XSA - 8EL C12 H20 N4 O7 P2 S Cc1ncc(c(n....
7 5I5E - 5SP C5 H11 O8 P C([C@H]([C....
8 5XU9 - 8N9 C14 H22 N4 O9 P2 S Cc1ncc(c(n....
9 5XRV - F6R C6 H13 O9 P C([C@H]([C....
10 5XS6 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
11 5XSB - 8EL C12 H20 N4 O7 P2 S Cc1ncc(c(n....
12 5XSM - 8EO C12 H21 N4 O7 P2 S Cc1ncc(c(n....
13 5XUF - 8FL C12 H20 N4 O8 P2 S Cc1ncc(c(n....
14 5XVT - 8FL C12 H20 N4 O8 P2 S Cc1ncc(c(n....
15 5XTV - 8EF C12 H20 N4 O7 P2 S Cc1ncc(c(n....
16 5XQK - T5X C17 H30 N4 O15 P3 S Cc1c(sc([n....
17 5XPS - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
18 5I51 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
19 5XU2 - F6R C6 H13 O9 P C([C@H]([C....
20 5XT4 - T6F C18 H32 N4 O16 P3 S Cc1c(sc([n....
21 5XTX - 8ML C18 H33 N4 O16 P3 S Cc1ncc(c(n....
22 5XT0 - T6F C18 H32 N4 O16 P3 S Cc1c(sc([n....
23 5XQA - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
24 5XTL - 8GF C5 H7 N3 Cc1nccc(n1....
25 5HJE - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
50% Homology Family (35)
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 Kd = 0.000000064 M 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 6TJ8 - NDQ C12 H19 N4 O8 P2 S Cc1c(sc[n+....
29 6TJ9 - 5SP C5 H11 O8 P C([C@H]([C....
30 1QGD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
31 2R5N Kd = 700 uM R5P C5 H11 O8 P C(C(C(C(C=....
32 2R8O - T5X C17 H30 N4 O15 P3 S Cc1c(sc([n....
33 2R8P - T6F C18 H32 N4 O16 P3 S Cc1c(sc([n....
34 5HHT - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
35 1ITZ - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: TPP; Similar ligands found: 48
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 NDQ 0.769231 0.909091
6 TMV 0.769231 0.958333
7 2TP 0.725 0.932432
8 VNP 0.721519 0.958904
9 VIB 0.621622 0.75
10 PYI 0.581395 0.887324
11 HTL 0.566667 0.958904
12 TDW 0.566667 0.972222
13 AUJ 0.55914 0.921053
14 N1T 0.556818 0.985714
15 FTP 0.551724 0.835616
16 THV 0.548387 0.958904
17 TPW 0.546512 0.9
18 WWF 0.542553 0.933333
19 TD6 0.540816 0.921053
20 THY 0.536842 0.945946
21 TOG 0.536082 0.921053
22 TDL 0.53125 0.897436
23 THW 0.530612 0.958904
24 TD9 0.53 0.921053
25 TD8 0.53 0.921053
26 TDK 0.525773 0.921053
27 D7K 0.490566 0.909091
28 R1T 0.489362 0.887324
29 S1T 0.489362 0.887324
30 TPU 0.483146 0.842105
31 5SR 0.479167 0.945205
32 T6F 0.476636 0.897436
33 T5X 0.476636 0.897436
34 1U0 0.474227 0.84
35 8PA 0.459459 0.945946
36 8EO 0.457447 0.92
37 8FL 0.457447 0.894737
38 TZD 0.451613 0.883117
39 O2T 0.45098 0.909091
40 TDM 0.443299 0.894737
41 8EL 0.442105 0.894737
42 G8G 0.44086 0.805195
43 TDN 0.415842 0.871795
44 THD 0.411765 0.839506
45 8N9 0.411765 0.839506
46 MP5 0.407895 0.676056
47 TD7 0.40566 0.85
48 DPX 0.4 0.734177
Ligand no: 2; Ligand: 5SP; Similar ligands found: 48
No: Ligand ECFP6 Tc MDL keys Tc
1 5SP 1 1
2 HMS 1 1
3 5RP 1 1
4 RUB 0.657895 0.944444
5 XBP 0.657895 0.944444
6 TG6 0.641026 0.972222
7 F6R 0.641026 0.972222
8 I22 0.609756 0.972222
9 DER 0.594595 0.891892
10 DEZ 0.594595 0.891892
11 DXP 0.578947 0.815789
12 RES 0.536585 0.673469
13 R10 0.512195 0.891892
14 PA5 0.512195 0.891892
15 P6F 0.5 0.944444
16 GOS 0.5 0.916667
17 P6T 0.5 0.944444
18 M2P 0.5 0.916667
19 2FP 0.5 0.944444
20 LG6 0.488372 0.891892
21 6PG 0.488372 0.891892
22 HG3 0.485714 0.783784
23 PAN 0.466667 0.673469
24 9C2 0.456522 0.66
25 4TP 0.452381 0.75
26 A5P 0.45 0.944444
27 LX1 0.45 0.815789
28 DX5 0.45 0.944444
29 LXP 0.45 0.944444
30 RBL 0.444444 0.638889
31 QDK 0.444444 0.638889
32 XUL 0.444444 0.638889
33 S6P 0.439024 0.916667
34 KD0 0.425532 0.891892
35 E4P 0.425 0.861111
36 5FX 0.421053 0.605263
37 DG6 0.418605 0.918919
38 R52 0.418605 0.916667
39 TX4 0.418605 0.632653
40 R5P 0.418605 0.916667
41 3PG 0.410256 0.837838
42 H4P 0.408163 0.772727
43 52L 0.408163 0.723404
44 DG2 0.404762 0.810811
45 O1B 0.403846 0.686275
46 G6Q 0.4 0.916667
47 M6R 0.4 0.75
48 AGP 0.4 0.75
Similar Ligands (3D)
Ligand no: 1; Ligand: TPP; Similar ligands found: 4
No: Ligand Similarity coefficient
1 8EF 0.9955
2 TP9 0.9752
3 HTD 0.9623
4 HE3 0.9027
Ligand no: 2; Ligand: 5SP; Similar ligands found: 308
No: Ligand Similarity coefficient
1 1AE 0.9433
2 HSA 0.9126
3 EUH 0.9113
4 MF3 0.9103
5 5OY 0.9085
6 5WN 0.9069
7 6C5 0.9066
8 HC4 0.9065
9 EUE 0.9043
10 MRU 0.9033
11 PMV 0.9025
12 P9E 0.9020
13 AZM 0.9018
14 5TO 0.9011
15 RP3 0.9009
16 CUW 0.9009
17 E8U 0.9005
18 M28 0.9003
19 ZEC 0.8998
20 STX 0.8994
21 SG3 0.8994
22 S0W 0.8985
23 GGG 0.8985
24 F98 0.8979
25 1PS 0.8974
26 JFM 0.8969
27 PNP 0.8953
28 GLY GLY GLY 0.8945
29 3W6 0.8944
30 3W3 0.8944
31 4NP 0.8942
32 S0E 0.8941
33 Y3L 0.8935
34 657 0.8933
35 DAH 0.8930
36 AES 0.8924
37 P81 0.8921
38 3W8 0.8920
39 C82 0.8919
40 6C9 0.8915
41 HPP 0.8911
42 PLP 0.8903
43 TYR 0.8902
44 OOG 0.8901
45 MP5 0.8900
46 6FR 0.8896
47 ATX 0.8891
48 BGT 0.8886
49 LSQ 0.8883
50 TZP 0.8883
51 IPE 0.8881
52 IYR 0.8879
53 IPR 0.8875
54 F6P 0.8874
55 4JE 0.8873
56 P80 0.8869
57 TRP 0.8869
58 9VQ 0.8867
59 AHL 0.8867
60 4CF 0.8865
61 CIR 0.8865
62 9GB 0.8863
63 2FM 0.8862
64 33S 0.8860
65 RDV 0.8859
66 LGT 0.8859
67 ENW 0.8856
68 DHC 0.8854
69 N4E 0.8853
70 SYE 0.8853
71 ENO 0.8851
72 FER 0.8850
73 R1P 0.8849
74 7MW 0.8849
75 5OO 0.8847
76 GAE 0.8846
77 8NB 0.8846
78 4BL 0.8842
79 MZM 0.8840
80 P93 0.8838
81 88L 0.8837
82 9YT 0.8837
83 5DL 0.8836
84 IJ6 0.8835
85 PRO GLY 0.8829
86 8SZ 0.8829
87 4NS 0.8829
88 D5X 0.8828
89 B41 0.8826
90 ARG 0.8826
91 RYV 0.8824
92 RP5 0.8822
93 VFG 0.8821
94 DED 0.8820
95 6C8 0.8820
96 HSX 0.8820
97 PLR 0.8816
98 LUQ 0.8815
99 6C4 0.8814
100 HXY 0.8813
101 2OR 0.8812
102 1X4 0.8810
103 2JJ 0.8809
104 6KT 0.8808
105 TA6 0.8807
106 14W 0.8803
107 KPC 0.8800
108 4MB 0.8800
109 E79 0.8798
110 1FD 0.8797
111 BL0 0.8795
112 G6P 0.8795
113 GRQ 0.8794
114 PFF 0.8793
115 QIV 0.8793
116 HPO 0.8789
117 3ZB 0.8789
118 GNW 0.8788
119 5PV 0.8787
120 AJG 0.8784
121 5LA 0.8784
122 XI7 0.8782
123 VM1 0.8779
124 RCV 0.8777
125 FOM 0.8776
126 UN1 0.8773
127 VD9 0.8773
128 M3L 0.8772
129 HCA 0.8770
130 GGB 0.8769
131 4BY 0.8766
132 GJK 0.8765
133 EZL 0.8765
134 D9Z 0.8764
135 DZA 0.8764
136 NAG 0.8762
137 UA5 0.8762
138 XRX 0.8761
139 9NB 0.8756
140 4BF 0.8755
141 UNJ 0.8753
142 ZYX 0.8753
143 YI6 0.8753
144 EQW 0.8747
145 CS2 0.8746
146 DTY 0.8745
147 NFZ 0.8744
148 2O8 0.8744
149 BHU 0.8744
150 64Z 0.8742
151 HJ7 0.8741
152 BGP 0.8740
153 6ZX 0.8740
154 PAU 0.8739
155 SKF 0.8738
156 4AF 0.8737
157 CFA 0.8734
158 IOP 0.8733
159 428 0.8727
160 YIE 0.8723
161 PUE 0.8719
162 DA3 0.8719
163 O45 0.8718
164 PTB 0.8718
165 JBZ 0.8716
166 PPT 0.8716
167 EVF 0.8715
168 F90 0.8713
169 AHC 0.8711
170 IS2 0.8711
171 5O6 0.8710
172 36M 0.8708
173 KYN 0.8707
174 VFM 0.8707
175 TU0 0.8706
176 6FG 0.8705
177 DHM 0.8701
178 LEL 0.8701
179 MLY 0.8700
180 MAJ 0.8699
181 TBJ 0.8698
182 BSA 0.8693
183 DLT 0.8693
184 0A9 0.8692
185 F4K 0.8692
186 RGP 0.8691
187 4I8 0.8690
188 3VW 0.8689
189 Z13 0.8689
190 3EB 0.8687
191 I2E 0.8687
192 A7N 0.8687
193 F1P 0.8686
194 STT 0.8683
195 GP1 0.8681
196 X1R 0.8677
197 M1T 0.8677
198 ZZU 0.8675
199 0F3 0.8674
200 BG6 0.8673
201 GCO 0.8673
202 ABF 0.8672
203 JF5 0.8671
204 6HO 0.8669
205 DMA 0.8669
206 H35 0.8666
207 EGV 0.8665
208 7QD 0.8663
209 HLP 0.8663
210 G14 0.8663
211 C26 0.8663
212 TEG 0.8662
213 DI6 0.8662
214 LO1 0.8662
215 DJN 0.8660
216 EYV 0.8660
217 58X 0.8659
218 DVQ 0.8659
219 S8P 0.8659
220 NNH 0.8658
221 GZ2 0.8657
222 1HS 0.8657
223 AJ1 0.8656
224 KPA 0.8656
225 YPN 0.8655
226 0NX 0.8652
227 DI9 0.8651
228 NPI 0.8651
229 TB8 0.8651
230 80G 0.8650
231 KDG 0.8648
232 TZM 0.8648
233 4BX 0.8646
234 7FU 0.8643
235 ISC 0.8643
236 D8X 0.8639
237 EPE 0.8636
238 A98 0.8635
239 NF3 0.8635
240 MSL 0.8633
241 TYC 0.8633
242 K3D 0.8633
243 9BF 0.8632
244 4R1 0.8631
245 GO2 0.8630
246 PHI 0.8629
247 6HN 0.8628
248 YIP 0.8626
249 5LD 0.8623
250 5GT 0.8622
251 7O4 0.8622
252 MD6 0.8620
253 TYL 0.8620
254 363 0.8617
255 SOJ 0.8612
256 GHQ 0.8609
257 SWX 0.8609
258 NOK 0.8609
259 J1K 0.8608
260 RA7 0.8607
261 2J3 0.8606
262 Q06 0.8605
263 2NP 0.8604
264 P7Y 0.8604
265 SOR 0.8599
266 LYS 0.8598
267 2QC 0.8597
268 IOS 0.8597
269 PPN 0.8596
270 J6W 0.8593
271 S62 0.8589
272 0UL 0.8585
273 9W5 0.8584
274 JAH 0.8584
275 FIX 0.8582
276 K4V 0.8580
277 8V8 0.8580
278 ENV 0.8579
279 FUD 0.8578
280 4Z9 0.8574
281 API 0.8573
282 PBA 0.8572
283 GVA 0.8571
284 MMS 0.8568
285 GWM 0.8565
286 F1X 0.8564
287 NY4 0.8563
288 LRW 0.8562
289 3VR 0.8558
290 EXY 0.8557
291 ALE 0.8555
292 VGS 0.8551
293 MN9 0.8548
294 CXH 0.8546
295 HDL 0.8545
296 SZ7 0.8540
297 OQC 0.8536
298 6FB 0.8536
299 GLP 0.8534
300 HAR 0.8533
301 5DS 0.8532
302 GVY 0.8529
303 ZZA 0.8527
304 D6P 0.8525
305 KLE 0.8525
306 1N5 0.8524
307 K82 0.8521
308 5F5 0.8513
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5XU2; Ligand: 8EL; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5xu2.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5XU2; Ligand: 8EL; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5xu2.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5XU2; Ligand: TPP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5xu2.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5XU2; Ligand: TPP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5xu2.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5XU2; Ligand: F6R; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5xu2.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5XU2; Ligand: F6R; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5xu2.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
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