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 1256 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 1068 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 922 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
Ligand no: 1; Ligand: PXP; Similar ligands found: 84
No: Ligand ECFP6 Tc MDL keys Tc
1 PXP 1 1
2 PMP 0.7 0.888889
3 GT1 0.686275 0.886792
4 IN5 0.583333 0.842105
5 PLG 0.583333 0.8
6 PLR 0.568627 0.843137
7 PLS 0.5625 0.830508
8 P1T 0.555556 0.761905
9 PP3 0.555556 0.813559
10 PDD 0.555556 0.813559
11 PDA 0.555556 0.813559
12 IK2 0.546875 0.761905
13 33P 0.546875 0.827586
14 PMG 0.544118 0.727273
15 2BK 0.538462 0.844828
16 TLP 0.538462 0.844828
17 5PA 0.538462 0.761905
18 2BO 0.538462 0.844828
19 PMH 0.538462 0.710145
20 PLP 0.537037 0.862745
21 UEG 0.531915 0.734694
22 C6P 0.530303 0.8
23 PPD 0.530303 0.8
24 PDG 0.529412 0.774194
25 PGU 0.529412 0.774194
26 PZP 0.527273 0.830189
27 PLA 0.522388 0.75
28 PY5 0.522388 0.75
29 QLP 0.521739 0.727273
30 P0P 0.517857 0.9
31 76U 0.514286 0.761905
32 7TS 0.507246 0.671233
33 CBA 0.507246 0.803279
34 ILP 0.507246 0.786885
35 7XF 0.507246 0.774194
36 N5F 0.507042 0.761905
37 EA5 0.507042 0.738462
38 LCS 0.5 0.643836
39 PL2 0.5 0.75
40 DCS 0.5 0.680556
41 PY6 0.492958 0.727273
42 HEY 0.492958 0.75
43 PSZ 0.486111 0.738462
44 ORX 0.486111 0.761905
45 3LM 0.486111 0.727273
46 PL8 0.48 0.676056
47 PE1 0.479452 0.761905
48 9YM 0.479452 0.803279
49 KAM 0.473684 0.761905
50 AN7 0.46875 0.796296
51 7B9 0.467532 0.705882
52 RW2 0.466667 0.738462
53 PXG 0.466667 0.8
54 PL4 0.466667 0.761905
55 GLY PLP 0.461538 0.741379
56 FOO 0.461538 0.741379
57 PPG 0.460526 0.734375
58 1D0 0.45 0.738462
59 AQ3 0.45 0.75
60 2B1 0.448718 0.657143
61 EPC 0.446154 0.781818
62 GT0 0.444444 0.679245
63 MPM 0.441176 0.741379
64 PLP PMP 0.439394 0.733333
65 EXT 0.439394 0.758621
66 KOU 0.434783 0.824561
67 2B6 0.432099 0.630137
68 SER PLP 0.428571 0.807018
69 PLP SER 0.426471 0.741379
70 4LM 0.426471 0.716667
71 0JO 0.426471 0.704918
72 PXM 0.415094 0.62963
73 6DF 0.410959 0.767857
74 PL6 0.410959 0.716667
75 P3D 0.408451 0.754098
76 PLP ALO 0.408451 0.79661
77 PLP 2TL 0.408451 0.789474
78 HCP 0.408451 0.733333
79 PFM 0.405405 0.704918
80 GLU PLP 0.405405 0.716667
81 PLP CYS 0.402778 0.775862
82 PLP 2KZ 0.402778 0.766667
83 PLP BH2 0.402778 0.789474
84 5B6 0.402299 0.779661
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found: 45
This union binding pocket(no: 1) in the query (biounit: 1m5w.bio4) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1LBT T80 0.01908 0.4083 None
2 3MJY FMN 0.02568 0.41658 2.46914
3 3MJY IJZ 0.02568 0.41658 2.46914
4 4WZH FMN 0.02178 0.41298 2.46914
5 4LUT DCS 0.02193 0.40164 2.46914
6 3GD9 GLC BGC BGC BGC 0.01532 0.40339 3.29218
7 4JIQ FMN 0.03327 0.40323 3.29218
8 2C91 NAP 0.04404 0.40595 3.5503
9 1QXW M1C 0.01242 0.4161 3.7037
10 2B4G FMN 0.0378 0.40159 3.7037
11 4UTW RFW 0.0009004 0.46955 3.93013
12 5A5W GUO 0.008782 0.44925 3.95257
13 4QYS PLP SEP 0.02254 0.41079 4.11523
14 3A5Z KAA 0.03031 0.40538 4.18848
15 5CSS G3P 0.009055 0.40983 4.42478
16 4NAE 1GP 0.009569 0.41159 4.44444
17 5KY3 GFB 0.03222 0.40118 4.52675
18 2Q8Z NUP 0.005353 0.44184 4.93827
19 4ZOW CLM 0.02145 0.40568 4.93827
20 1WDD CAP 0.0235 0.40364 4.93827
21 4HKP TKW 0.009692 0.42684 5.34979
22 2QCD U5P 0.01049 0.42166 5.34979
23 4HKP 16B 0.01347 0.4143 5.34979
24 3CTL S6P 0.007001 0.43066 5.62771
25 2VDH CAP 0.008648 0.42772 5.76132
26 1UZH CAP 0.01411 0.41675 5.76132
27 1UZD CAP 0.02865 0.40082 5.76132
28 3OVR 5SP 0.0004906 0.49371 6.14035
29 5FBF DCM 0.02266 0.40611 6.17284
30 2FFC U5P 0.009565 0.42189 6.58436
31 1PI5 SM2 0.03781 0.41938 6.99588
32 1N62 MCN 0.02027 0.42641 7.22892
33 1Q6O LG6 0.01494 0.40818 7.40741
34 4J56 FAD 0.04657 0.41349 8.23045
35 3U2U UDP 0.04762 0.40201 8.23045
36 1DQX BMP 0.006728 0.43333 9.0535
37 1RBL CAP 0.02146 0.40892 9.17431
38 3C56 PH4 0.02313 0.404 9.46502
39 3KDN CAP 0.0345 0.42239 9.87654
40 1MJH ATP 0.02838 0.40103 12.3457
41 3EXS 5RP 0.003735 0.4089 13.5747
42 1OVD FMN 0.02988 0.41719 16.4609
43 1JCM 137 0.001744 0.45737 18.5185
44 2Y88 2ER 0.04142 0.40841 20.9877
45 2FLI DX5 0.0002213 0.50945 23.6364
Pocket No.: 2; Query (leader) PDB : 1M5W; Ligand: DXP; 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: 1m5w.bio4) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found: 71
This union binding pocket(no: 3) in the query (biounit: 1m5w.bio2) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1U0A BGC BGC BGC BGC 0.008482 0.42058 1.86916
2 2OO0 PLP 0.01118 0.41454 2.05761
3 4BI7 PGA 0.001779 0.44441 2.46914
4 1QDS PGA 0.002467 0.44023 2.46914
5 4V15 PLP 0.00339 0.43597 2.46914
6 5GJO PLP 0.007876 0.42005 2.46914
7 2BP1 NDP 0.02976 0.41526 2.46914
8 2F6U CIT 0.01103 0.40294 2.5641
9 1LYX PGA 0.002365 0.44617 2.88066
10 4YMZ 13P 0.002384 0.4382 2.88066
11 1PZ1 NAP 0.01266 0.42677 2.88066
12 2J3M PRI 0.01163 0.42432 2.88066
13 2Z6J FMN 0.02295 0.41568 2.88066
14 2J3M ATP 0.02014 0.41035 2.88066
15 1X54 4AD 0.02374 0.4096 2.88066
16 2Z6C FMN 0.02328 0.40213 3.10078
17 2BTM PGA 0.001635 0.4462 3.29218
18 3ATY FMN 0.02309 0.41023 3.29218
19 4O12 2QG 0.0435 0.44454 3.39321
20 5IXJ THR 0.01395 0.42846 3.7037
21 2YPI PGA 0.001337 0.42732 3.7037
22 2NVA PL2 0.01204 0.42652 3.7037
23 1W8S FBP 0.01599 0.40463 3.7037
24 3KRU FMN 0.04916 0.40125 3.7037
25 3B0P FMN 0.001808 0.40003 3.7037
26 4Q4K FMN 0.01003 0.43069 3.92157
27 4UTU LRY 0.0007063 0.42109 3.93013
28 3REU ATP 0.01004 0.41891 4.11523
29 3PC3 P1T 0.01755 0.41186 4.11523
30 3TAO PGH 0.002146 0.4432 4.11985
31 5L9G MO0 0.003233 0.44587 4.52675
32 5EYW PGA 0.002392 0.43813 4.52675
33 1TRD PGH 0.007418 0.41907 4.52675
34 2RJH DCS 0.01176 0.41133 4.52675
35 1SW0 PGA 0.003575 0.43482 4.93827
36 4ZLU 4PW 0.04673 0.40453 4.93827
37 4ZLU ADP 0.04673 0.40453 4.93827
38 4A3U FMN 0.02885 0.40066 4.93827
39 3MI2 PFU 0.01262 0.44767 5.34979
40 2IRY DGT 0.01129 0.41632 5.34979
41 3IES M24 0.04804 0.40387 5.34979
42 4WUJ FMN 0.02387 0.40157 5.44218
43 2V63 CAP 0.004849 0.44065 5.76132
44 2V6A CAP 0.004607 0.43996 5.76132
45 1EIX BMQ 0.002343 0.45088 6.12245
46 3TTC ADP 0.02671 0.40546 6.39269
47 2PLK P3D 0.005091 0.43956 6.58436
48 1KBJ FMN 0.03503 0.40204 6.58436
49 1KBI PYR 0.04009 0.40023 6.58436
50 1TUF AZ1 0.00558 0.44249 6.99588
51 4IGH 1EA 0.03843 0.42966 7.40741
52 4IGH FMN 0.03843 0.42966 7.40741
53 4IGH ORO 0.03843 0.42966 7.40741
54 3W9Z FMN 0.00599 0.43224 7.81893
55 1NJJ ORX 0.01564 0.41445 7.81893
56 1WLE SRP 0.02225 0.40314 7.81893
57 1TB3 FMN 0.04544 0.40091 7.81893
58 1YIQ PQQ 0.02901 0.40053 7.81893
59 1V7C HEY 0.02176 0.41565 8.23045
60 5FLJ QUE 0.02493 0.40395 8.60215
61 1BWV CAP 0.007181 0.42823 9.46502
62 3N9R TD3 0.0161 0.40001 9.46502
63 3OIX FMN 0.0219 0.40998 9.87654
64 1UWK NAD 0.04076 0.41754 11.1111
65 1UWK URO 0.04076 0.41754 11.1111
66 2W90 6PG 0.02162 0.41173 11.5226
67 4JEJ 1GP 0.001806 0.44952 12.3457
68 4R38 RBF 0.005214 0.43721 14.2857
69 4J75 TYM 0.04136 0.40075 14.4033
70 2OEM 1AE 0.007872 0.41779 22.6337
71 1X1Z BMP 0.007528 0.46019 27.1605
Pocket No.: 4; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found: 37
This union binding pocket(no: 6) in the query (biounit: 1m5w.bio3) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4I9A NCN 0.006305 0.42621 1.23457
2 4AIA ADK 0.02498 0.40129 2.12766
3 2Z6I FMN 0.004063 0.42145 2.46914
4 4I3G BGC 0.04105 0.40378 2.46914
5 1ONX ASP 0.04892 0.40344 2.46914
6 3ZGJ RMN 0.02783 0.41685 2.88066
7 3C8F MT2 0.001083 0.48713 3.29218
8 1EYE PMM 0.003667 0.44962 3.29218
9 3GLC R5P 0.002736 0.45598 4.11523
10 3WQD PLP 999 0.002778 0.44291 4.11523
11 2C6Q IMP 0.009127 0.40072 4.11523
12 3A6T 8OG 0.01432 0.41277 4.65116
13 4RW3 IPD 0.003714 0.45885 4.93827
14 1Z44 FMN 0.009284 0.42551 4.93827
15 1Z42 FMN 0.02515 0.40762 4.93827
16 4EWN 0VR 0.006477 0.42932 5.13834
17 5OCS FMN 0.01589 0.40422 5.34979
18 3DGB MUC 0.03215 0.40222 5.34979
19 2V68 CAP 0.007324 0.41646 5.76132
20 2V67 CAP 0.008315 0.4109 5.76132
21 1IR2 CAP 0.008465 0.41055 5.76132
22 1DBT U5P 0.0003613 0.47973 6.69456
23 5TVM PUT 0.03244 0.41549 6.99588
24 5TH5 MET 0.03715 0.40944 7.81893
25 2BO9 VAL 0.03432 0.41188 8.64198
26 1GXU 2HP 0.03696 0.41269 8.79121
27 4IXH IMP 0.002663 0.42619 9.0535
28 1L5Y BEF 0.008394 0.43618 9.67742
29 4KBA 1QM 0.04139 0.4036 10.2881
30 2Y69 CHD 0.03028 0.40992 11.8421
31 1O68 KIV 0.01133 0.43801 11.9342
32 2VD9 IN5 0.01967 0.40613 13.1687
33 1UJP CIT 0.001147 0.4609 14.3911
34 1LBF 137 0.000332 0.45371 16.4609
35 2G50 PYR 0.04171 0.40973 17.6955
36 1AJ0 PH2 0.003748 0.4407 18.107
37 1AJ0 SAN 0.004599 0.42557 18.107
Pocket No.: 7; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 1M5W; Ligand: DXP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
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