Receptor
PDB id Resolution Class Description Source Keywords
1HO4 2.3 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE IN COM PYRIDOXINE 5'-PHOSPHATE AND INORGANIC PHOSPHATE ESCHERICHIA COLI TIM BARREL OPEN-CLOSED TRANSITION ENZYME-PRODUCT COMPLEX CHANNEL BIOSYNTHETIC PROTEIN
Ref.: STRUCTURAL BASIS FOR THE FUNCTION OF PYRIDOXINE 5'-SYNTHASE. STRUCTURE V. 9 245 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:901;
B:903;
C:902;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
94.971 O4 P [O-]P...
PXP A:802;
B:804;
C:803;
D:801;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
249.158 C8 H12 N O6 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1M5W 1.96 Å NON-ENZYME: OTHER 1.96 A CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE COMPLEX WITH 1-DEOXY-D-XYLULOSE PHOSPHATE ESCHERICHIA COLI TIM BARREL PROTEIN-SUBSTRATE COMPLEX MULTI-BINDING STATESBIOSYNTHETIC PROTEIN
Ref.: MULTISTATE BINDING IN PYRIDOXINE 5'-PHOSPHATE SYNTH A CRYSTAL STRUCTURE IN COMPLEX WITH 1-DEOXY-D-XYLUL PHOSPHATE BIOCHEMISTRY V. 41 11649 2002
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 1M5W Kd = 54 uM DXP C5 H11 O7 P CC(=O)[C@H....
2 1HO4 - PXP C8 H12 N O6 P Cc1c(c(c(c....
3 1IXO - G3P C3 H9 O6 P C([C@H](CO....
4 1IXN - G3P C3 H9 O6 P C([C@H](CO....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 1M5W Kd = 54 uM DXP C5 H11 O7 P CC(=O)[C@H....
2 1HO4 - PXP C8 H12 N O6 P Cc1c(c(c(c....
3 1IXO - G3P C3 H9 O6 P C([C@H](CO....
4 1IXN - G3P C3 H9 O6 P C([C@H](CO....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 1M5W Kd = 54 uM DXP C5 H11 O7 P CC(=O)[C@H....
2 1HO4 - PXP C8 H12 N O6 P Cc1c(c(c(c....
3 1IXO - G3P C3 H9 O6 P C([C@H](CO....
4 1IXN - G3P C3 H9 O6 P C([C@H](CO....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PXP; Similar ligands found: 87
No: Ligand ECFP6 Tc MDL keys Tc
1 PXP 1 1
2 PMP 0.7 0.888889
3 GT1 0.686275 0.886792
4 PLG 0.583333 0.8
5 IN5 0.583333 0.842105
6 PLR 0.568627 0.843137
7 PLS 0.5625 0.830508
8 PP3 0.555556 0.813559
9 PDA 0.555556 0.813559
10 PDD 0.555556 0.813559
11 P1T 0.555556 0.761905
12 CKT 0.546875 0.813559
13 33P 0.546875 0.827586
14 IK2 0.546875 0.761905
15 PMG 0.544118 0.727273
16 2BO 0.538462 0.844828
17 TLP 0.538462 0.844828
18 2BK 0.538462 0.844828
19 PMH 0.538462 0.710145
20 5PA 0.538462 0.761905
21 PLP 0.537037 0.862745
22 UEG 0.531915 0.734694
23 PPD 0.530303 0.8
24 C6P 0.530303 0.8
25 PDG 0.529412 0.774194
26 PGU 0.529412 0.774194
27 PZP 0.527273 0.830189
28 PLA 0.522388 0.75
29 OJQ 0.522388 0.690141
30 PY5 0.522388 0.75
31 QLP 0.521739 0.727273
32 P0P 0.517857 0.9
33 76U 0.514286 0.761905
34 PLP PMP 0.508772 0.836364
35 CBA 0.507246 0.803279
36 7TS 0.507246 0.671233
37 7XF 0.507246 0.774194
38 ILP 0.507246 0.786885
39 N5F 0.507042 0.761905
40 EA5 0.507042 0.738462
41 LCS 0.5 0.643836
42 DCS 0.5 0.680556
43 LPI 0.5 0.716418
44 PL2 0.5 0.75
45 PY6 0.492958 0.727273
46 HEY 0.492958 0.75
47 0PR 0.486486 0.786885
48 3LM 0.486111 0.727273
49 ORX 0.486111 0.761905
50 PSZ 0.486111 0.738462
51 PL8 0.48 0.676056
52 9YM 0.479452 0.803279
53 PE1 0.479452 0.761905
54 KAM 0.473684 0.761905
55 AN7 0.46875 0.796296
56 7B9 0.467532 0.705882
57 RW2 0.466667 0.738462
58 PL4 0.466667 0.761905
59 PXG 0.466667 0.8
60 FOO 0.461538 0.741379
61 PPG 0.460526 0.734375
62 RMT 0.454545 0.730159
63 AQ3 0.45 0.75
64 1D0 0.45 0.738462
65 EVM 0.449275 0.810345
66 2B1 0.448718 0.657143
67 DN9 0.448718 0.710145
68 EPC 0.446154 0.781818
69 GT0 0.444444 0.679245
70 MPM 0.441176 0.741379
71 EXT 0.439394 0.758621
72 KOU 0.434783 0.824561
73 FEV 0.434783 0.704918
74 2B6 0.432099 0.630137
75 0JO 0.426471 0.704918
76 4LM 0.426471 0.716667
77 PLP CYS 0.422535 0.741935
78 PLP SER 0.42029 0.766667
79 F0G 0.42029 0.754386
80 PXM 0.415094 0.62963
81 PL6 0.410959 0.716667
82 6DF 0.410959 0.767857
83 HCP 0.408451 0.733333
84 P3D 0.408451 0.754098
85 PFM 0.405405 0.704918
86 PLP 2KZ 0.402778 0.766667
87 5B6 0.402299 0.779661
Similar Ligands (3D)
Ligand no: 1; Ligand: PXP; Similar ligands found: 413
No: Ligand Similarity coefficient
1 NPL 0.9683
2 G6P 0.9644
3 BG6 0.9594
4 X04 0.9548
5 4R1 0.9529
6 GLP 0.9505
7 1QV 0.9474
8 MP5 0.9430
9 L21 0.9346
10 3LJ 0.9343
11 M6D 0.9335
12 M6P 0.9329
13 QMS 0.9315
14 N2M 0.9292
15 A6P 0.9284
16 6HP 0.9264
17 STT 0.9252
18 5WN 0.9222
19 M3Q 0.9204
20 D6G 0.9202
21 FER 0.9197
22 F5C 0.9196
23 IOS 0.9194
24 QIF 0.9193
25 SG2 0.9177
26 2GQ 0.9147
27 GI3 0.9142
28 F1X 0.9141
29 EUE 0.9136
30 BGP 0.9121
31 F1P 0.9118
32 790 0.9113
33 5OO 0.9113
34 ZIP 0.9110
35 V1T 0.9102
36 YF3 0.9101
37 F6P 0.9099
38 9F8 0.9099
39 CFA 0.9089
40 NAG 0.9086
41 GI1 0.9084
42 GJK 0.9084
43 IOP 0.9069
44 P9T 0.9055
45 TU0 0.9047
46 O2Y 0.9043
47 A5P 0.9038
48 H35 0.9026
49 S0E 0.9024
50 57O 0.9019
51 CMU 0.9017
52 P2L 0.9011
53 F40 0.9008
54 TNX 0.9002
55 BY5 0.9000
56 5WM 0.8999
57 KLV 0.8993
58 G1P 0.8992
59 IPD 0.8992
60 F52 0.8988
61 SYE 0.8983
62 ENG 0.8979
63 9BF 0.8976
64 NBV 0.8976
65 NPA 0.8972
66 8MP 0.8970
67 IAC 0.8967
68 P7Y 0.8965
69 3JM 0.8962
70 GB4 0.8961
71 3Y7 0.8959
72 GZV 0.8958
73 SBK 0.8958
74 ZON 0.8957
75 1VQ 0.8955
76 TOM 0.8954
77 CPW 0.8953
78 HA6 0.8952
79 LIP 0.8952
80 F06 0.8949
81 3D8 0.8948
82 5V7 0.8947
83 AKD 0.8943
84 4KR 0.8940
85 NQH 0.8940
86 ZEA 0.8939
87 ABF 0.8938
88 TB8 0.8935
89 3VX 0.8933
90 HPT 0.8933
91 657 0.8931
92 505 0.8930
93 AJD 0.8927
94 HSX 0.8926
95 TRP 0.8925
96 2VQ 0.8924
97 NFK 0.8923
98 SXX 0.8923
99 GXG 0.8919
100 ARP 0.8919
101 54X 0.8918
102 MD6 0.8918
103 SG6 0.8918
104 6J5 0.8917
105 IL5 0.8917
106 2HC 0.8915
107 X1P 0.8915
108 68A 0.8913
109 GDL 0.8909
110 22L 0.8907
111 AMR 0.8906
112 MBP 0.8902
113 XYP XIF 0.8902
114 XIF XYP 0.8901
115 ONZ 0.8900
116 H4B 0.8899
117 HWD 0.8899
118 HBI 0.8898
119 CTE 0.8894
120 XFE 0.8893
121 FWD 0.8891
122 KYN 0.8890
123 NTF 0.8889
124 QUB 0.8888
125 YKG 0.8886
126 E9S 0.8885
127 UQ1 0.8882
128 I4D 0.8881
129 1BW 0.8881
130 FTV 0.8878
131 PTS 0.8876
132 3IL 0.8875
133 CLU 0.8874
134 N7I 0.8873
135 NLA 0.8872
136 DTR 0.8872
137 T6Z 0.8868
138 KF5 0.8867
139 H2B 0.8866
140 EXD 0.8865
141 12R 0.8865
142 CHQ 0.8865
143 DHC 0.8860
144 FUZ 0.8859
145 6Q3 0.8858
146 NFM 0.8857
147 CX4 0.8857
148 RVE 0.8856
149 9E3 0.8856
150 AC2 0.8853
151 S3C 0.8852
152 3RI 0.8852
153 4AB 0.8850
154 327 0.8847
155 67Y 0.8847
156 GA2 0.8847
157 ZEC 0.8846
158 A4V 0.8840
159 EYV 0.8839
160 GO8 0.8838
161 RGG 0.8838
162 OSB 0.8836
163 YO5 0.8836
164 5WU 0.8836
165 6DP 0.8834
166 S0G 0.8827
167 EXL 0.8827
168 SIZ 0.8827
169 89J 0.8826
170 ZEZ 0.8823
171 NBG 0.8822
172 MPP 0.8820
173 BEU 0.8819
174 DTE 0.8819
175 YX1 0.8813
176 STZ 0.8813
177 NHT 0.8813
178 8NX 0.8812
179 CWD 0.8811
180 CR1 0.8810
181 GI4 0.8810
182 61M 0.8810
183 D1Y 0.8809
184 5OF 0.8808
185 4Z9 0.8807
186 N91 0.8806
187 8U3 0.8804
188 LTN 0.8804
189 B41 0.8804
190 96Z 0.8803
191 ALN 0.8803
192 MUR 0.8802
193 XYP XYP 0.8799
194 MTS 0.8798
195 2KU 0.8797
196 3N1 0.8793
197 3B4 0.8791
198 2K8 0.8791
199 I2E 0.8791
200 ALX 0.8790
201 2LT 0.8790
202 4WF 0.8790
203 55D 0.8786
204 JF2 0.8785
205 CH8 0.8784
206 S7G 0.8784
207 EUH 0.8784
208 BWD 0.8782
209 BIO 0.8781
210 535 0.8780
211 BNX 0.8780
212 I59 0.8779
213 B5A 0.8779
214 NGA 0.8778
215 KED 0.8777
216 PYU 0.8777
217 0FR 0.8776
218 ZYV 0.8776
219 IBM 0.8775
220 TZP 0.8774
221 5WS 0.8774
222 M5H 0.8774
223 SKF 0.8773
224 RP5 0.8772
225 7ZL 0.8770
226 EVF 0.8766
227 PVQ 0.8763
228 KG1 0.8762
229 DAH 0.8761
230 IBC 0.8761
231 BM3 0.8760
232 3SU 0.8760
233 Q5M 0.8759
234 FPL 0.8759
235 PE2 0.8759
236 3M8 0.8759
237 4GP 0.8759
238 TSR 0.8758
239 X0T 0.8757
240 FNA 0.8757
241 K82 0.8757
242 MUX 0.8756
243 B61 0.8754
244 GPM 0.8749
245 4OG 0.8749
246 4Z1 0.8748
247 IWD 0.8747
248 ZIQ 0.8747
249 PW1 0.8746
250 GFP 0.8743
251 MQG 0.8742
252 GXD 0.8741
253 TA6 0.8739
254 JXK 0.8739
255 NEO 0.8738
256 AVO 0.8738
257 5E4 0.8738
258 ALE 0.8737
259 AX3 0.8736
260 B21 0.8733
261 MUK 0.8733
262 TXW 0.8732
263 ITW 0.8731
264 TMG 0.8730
265 ZSP 0.8729
266 SLY 0.8729
267 EXG 0.8728
268 TLG 0.8726
269 S8A 0.8726
270 WV7 0.8725
271 W8G 0.8723
272 GC2 0.8722
273 SJK 0.8716
274 EXR 0.8716
275 B23 0.8715
276 D9Z 0.8715
277 6DQ 0.8714
278 9GP 0.8713
279 TLM 0.8711
280 ZYQ 0.8710
281 HQ6 0.8709
282 C9E 0.8708
283 M9N 0.8707
284 TOH 0.8706
285 MXD 0.8705
286 MFZ 0.8705
287 DBS 0.8704
288 7AP 0.8704
289 DDU 0.8703
290 2FX 0.8703
291 GC3 0.8701
292 BQ2 0.8700
293 GRF 0.8700
294 GRX 0.8699
295 MW5 0.8699
296 B4O 0.8699
297 878 0.8697
298 C4E 0.8697
299 CC5 0.8697
300 Z25 0.8697
301 FT6 0.8697
302 CG8 0.8695
303 ENO 0.8694
304 EYY 0.8692
305 MJ5 0.8691
306 7MX 0.8690
307 DY5 0.8689
308 3L1 0.8689
309 A1Y 0.8688
310 PBG 0.8688
311 CGW 0.8686
312 7PJ 0.8685
313 92O 0.8685
314 EYJ 0.8685
315 CL9 0.8684
316 PVK 0.8684
317 ZHA 0.8683
318 52F 0.8682
319 5RP 0.8682
320 M02 0.8680
321 JYT 0.8678
322 APS 0.8677
323 1A7 0.8675
324 P80 0.8675
325 4FE 0.8673
326 OQC 0.8671
327 3IB 0.8670
328 CP7 0.8670
329 78U 0.8670
330 NCV 0.8668
331 Q9P 0.8668
332 MFR 0.8667
333 3GC 0.8666
334 AWE 0.8666
335 EQA 0.8665
336 56N 0.8662
337 0J5 0.8661
338 EYM 0.8660
339 BHS 0.8660
340 HC4 0.8658
341 MPU 0.8655
342 CKU 0.8655
343 8Y7 0.8654
344 HHV 0.8654
345 NOK 0.8651
346 BGN 0.8650
347 3D1 0.8650
348 K3Q 0.8650
349 54E 0.8649
350 EVO 0.8647
351 R5P 0.8646
352 6J9 0.8644
353 3AK 0.8643
354 BIE 0.8640
355 NIY 0.8640
356 1Q4 0.8640
357 CKI 0.8635
358 MMS 0.8635
359 78P 0.8634
360 GL6 0.8633
361 OUB 0.8633
362 5JT 0.8630
363 AUY 0.8627
364 S0W 0.8627
365 DBQ 0.8627
366 L07 0.8627
367 YOF 0.8626
368 CCV 0.8625
369 LOG 0.8624
370 AHC 0.8624
371 BB4 0.8623
372 MIG 0.8622
373 GNR 0.8620
374 BPY 0.8620
375 C0W 0.8617
376 UN4 0.8617
377 TZM 0.8615
378 RNK 0.8615
379 IYR 0.8615
380 NIP 0.8614
381 TL6 0.8614
382 NAL 0.8610
383 4NP 0.8606
384 4MB 0.8605
385 HPP 0.8605
386 2LX 0.8599
387 5TY 0.8594
388 LJ4 0.8591
389 LSQ 0.8588
390 P81 0.8588
391 4NS 0.8587
392 JVA 0.8583
393 0J4 0.8579
394 OX2 0.8575
395 6HO 0.8574
396 2UD 0.8573
397 AAN 0.8569
398 D87 0.8568
399 DI6 0.8567
400 848 0.8564
401 092 0.8563
402 CP6 0.8562
403 JY2 0.8559
404 B2Y 0.8557
405 22T 0.8552
406 THM 0.8551
407 3IP 0.8550
408 UAY 0.8547
409 VUP 0.8545
410 4BX 0.8544
411 Z21 0.8541
412 5O6 0.8538
413 C82 0.8524
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1M5W; Ligand: DXP; 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: 1m5w.bio4) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1M5W; Ligand: DXP; 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: 1m5w.bio4) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1M5W; Ligand: DXP; 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: 1m5w.bio2) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1M5W; Ligand: DXP; 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: 1m5w.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1M5W; Ligand: DXP; 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: 1m5w.bio3) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1M5W; Ligand: DXP; 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: 1m5w.bio3) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 1m5w.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 1m5w.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 1m5w.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 1m5w.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 1m5w.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 1m5w.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
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