Receptor
PDB id Resolution Class Description Source Keywords
1G79 2 Å EC: 1.4.3.5 X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE COMPLEXED WITH PYRIDOXAL 5'-PHOSPHATE AT 2.0 A RESOLUTION ESCHERICHIA COLI PLP COMPLEX FMN COMPLEX PYRIDOXINE 5-prime -PHOSPHATE OXIDOREDU
Ref.: X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-P OXIDASE COMPLEXED WITH PYRIDOXAL 5'-PHOSPHATE AT 2. RESOLUTION. J.MOL.BIOL. V. 310 817 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BME A:300;
Invalid;
none;
submit data
78.133 C2 H6 O S C(CS)...
FMN A:250;
Valid;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
PLP A:260;
A:270;
Valid;
Valid;
none;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
PO4 A:280;
A:290;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1G79 2 Å EC: 1.4.3.5 X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE COMPLEXED WITH PYRIDOXAL 5'-PHOSPHATE AT 2.0 A RESOLUTION ESCHERICHIA COLI PLP COMPLEX FMN COMPLEX PYRIDOXINE 5-prime -PHOSPHATE OXIDOREDU
Ref.: X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-P OXIDASE COMPLEXED WITH PYRIDOXAL 5'-PHOSPHATE AT 2. RESOLUTION. J.MOL.BIOL. V. 310 817 2001
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1G76 - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 1G79 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 1G78 - PLP C8 H10 N O6 P Cc1c(c(c(c....
4 1G77 - PLP C8 H10 N O6 P Cc1c(c(c(c....
5 1JNW - PLP C8 H10 N O6 P Cc1c(c(c(c....
6 1DNL - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1G76 - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 1G79 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 1G78 - PLP C8 H10 N O6 P Cc1c(c(c(c....
4 1G77 - PLP C8 H10 N O6 P Cc1c(c(c(c....
5 1JNW - PLP C8 H10 N O6 P Cc1c(c(c(c....
6 1DNL - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1G76 - PLP C8 H10 N O6 P Cc1c(c(c(c....
2 1G79 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 1G78 - PLP C8 H10 N O6 P Cc1c(c(c(c....
4 1G77 - PLP C8 H10 N O6 P Cc1c(c(c(c....
5 1JNW - PLP C8 H10 N O6 P Cc1c(c(c(c....
6 1DNL - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FMN; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 RS3 0.571429 0.831169
4 FAS 0.543307 0.876543
5 FAD 0.543307 0.876543
6 FAE 0.539062 0.865854
7 DAL FAD PER 0.5 0.833333
8 LFN 0.475 0.643836
9 C3F 0.473684 0.74359
10 CF4 0.463918 0.734177
11 FAY 0.446043 0.864198
12 FNR 0.444444 0.909091
13 RFL 0.442857 0.845238
14 4LS 0.411215 0.875
15 1VY 0.406593 0.769231
16 DLZ 0.404494 0.782051
Ligand no: 2; Ligand: PLP; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP 1 1
2 PZP 0.729167 0.843137
3 EXT 0.62069 0.8
4 AN7 0.603448 0.918367
5 EPC 0.603448 0.862745
6 FOO 0.59322 0.849057
7 PLR 0.58 0.895833
8 4LM 0.57377 0.818182
9 0JO 0.57377 0.803571
10 P3D 0.571429 0.704918
11 MPM 0.564516 0.814815
12 KOU 0.555556 0.836364
13 HCP 0.546875 0.77193
14 6DF 0.545455 0.811321
15 PXL 0.541667 0.659574
16 Z98 0.537313 0.75
17 PXP 0.537037 0.862745
18 PMP 0.527273 0.767857
19 P0P 0.527273 0.916667
20 PL6 0.522388 0.818182
21 GT1 0.517857 0.830189
22 PFM 0.514706 0.803571
23 LLP 0.5 0.737705
24 PL5 0.479452 0.775862
25 PUS 0.479452 0.707692
26 MPL 0.473684 0.836364
27 PLG 0.46875 0.75
28 IN5 0.46875 0.758621
29 P89 0.466667 0.714286
30 PLP PUT 0.463768 0.684211
31 5DK 0.460526 0.725806
32 O1G 0.454545 0.75
33 PLP ABU 0.450704 0.706897
34 PLT 0.439024 0.762712
35 X04 0.431034 0.851852
36 PP3 0.426471 0.762712
37 P1T 0.426471 0.714286
38 PDD 0.426471 0.762712
39 PDA 0.426471 0.762712
40 IK2 0.42029 0.714286
41 33P 0.42029 0.745763
42 2BO 0.414286 0.793103
43 PLS 0.414286 0.779661
44 PMH 0.414286 0.619718
45 5PA 0.414286 0.714286
46 TLP 0.414286 0.793103
47 2BK 0.414286 0.793103
48 C6P 0.408451 0.75
49 PPD 0.408451 0.75
50 QLP 0.405405 0.681818
51 MP5 0.403509 0.666667
52 PY5 0.402778 0.703125
53 PLA 0.402778 0.703125
54 HEY 0.4 0.703125
55 PLP PHE 0.4 0.732143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1G79; Ligand: PLP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1g79.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1G79; Ligand: PLP; Similar sites found: 74
This union binding pocket(no: 2) in the query (biounit: 1g79.bio1) has 40 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3F81 STT 0.001391 0.4989 None
2 1TUV VK3 0.01658 0.44154 None
3 2E1A MSE 0.006405 0.42713 None
4 4F4S EFO 0.01412 0.41667 None
5 3UEC ALA ARG TPO LYS 0.01706 0.43325 1.36986
6 2NCD ADP 0.007816 0.43335 1.83486
7 4PTZ FMN 0.009528 0.40006 2.09424
8 3SHR CMP 0.01283 0.40978 2.29358
9 2Y7P SAL 0.001512 0.46006 2.75229
10 2ZO9 MLI 0.00428 0.4276 2.75229
11 1SQ5 PAU 0.009388 0.42462 2.75229
12 1WDA BAG 0.007643 0.4238 2.75229
13 3MAG 3MA 0.04929 0.42236 2.75229
14 1SQ5 ADP 0.005851 0.4198 2.75229
15 4F8L GAL 0.04337 0.43289 2.75862
16 2ASF CIT 0.0000001383 0.54647 2.91971
17 4K30 NLG 0.007517 0.42894 3.125
18 3A3B FMN 0.01161 0.43501 3.15789
19 3A3B RBF 0.01836 0.42444 3.15789
20 1RZM E4P 0.009281 0.44131 3.21101
21 4COQ SAN 0.02176 0.41763 3.21101
22 1Y42 TYR 0.02276 0.40734 3.21101
23 1UF5 CDT 0.01669 0.40495 3.21101
24 1SS4 GSH 0.002202 0.50856 3.26797
25 1SS4 CIT 0.04045 0.43811 3.26797
26 1ULE GLA GAL NAG 0.007586 0.45231 3.33333
27 4E28 9MZ 0.03359 0.40853 3.66972
28 1YOA FMN 0.009594 0.47133 3.77358
29 1YOA FAD 0.01193 0.40329 3.77358
30 2Q37 3AL 0.03435 0.40349 3.8674
31 1D8C GLV 0.03841 0.42752 4.12844
32 2BES RES 0.007466 0.41547 4.12844
33 1FW1 GSH 0.002889 0.42788 4.16667
34 4LHM AZZ 0.002504 0.45617 4.58716
35 2Z9V PXM 0.007488 0.42902 4.58716
36 1EJE FMN 0.007245 0.42217 4.6875
37 3CF6 SP1 0.0114 0.40053 4.79042
38 3LTW HLZ 0.00189 0.46833 5.04587
39 4DYO SD4 0.01072 0.41741 5.04587
40 2RC5 FAD 0.01036 0.41183 5.04587
41 3S9K CIT 0.001447 0.53884 5.08475
42 2QCX PF1 0.001176 0.47128 5.50459
43 2Q8H TF4 0.0247 0.43223 5.50459
44 4B4D FAD 0.01294 0.40453 5.50459
45 3ZPG 5GP 0.002227 0.48803 5.9633
46 1Z44 FMN 0.0005979 0.45509 5.9633
47 3QDT A2G GAL 0.0007873 0.50267 6.29371
48 3BY8 MLT 0.009767 0.44021 6.33803
49 1G8S MET 0.001572 0.47214 6.42202
50 1I0Z OXM 0.02328 0.43362 6.42202
51 4KOA NDP 0.002026 0.42547 6.42202
52 2V5E SCR 0.002424 0.49544 6.5
53 2BH9 NAP 0.006616 0.40971 6.88073
54 1PEA ACM 0.01867 0.43219 7.79817
55 4IXW IXW 0.009826 0.41906 7.79817
56 3NFZ 3NF 0.00868 0.41278 8.25688
57 1G7C 5GP 0.03179 0.40799 8.51064
58 4RJK PYR 0.002023 0.48171 8.7156
59 1C1L GAL BGC 0.007927 0.4447 9.48905
60 3A1I UNU 0.002012 0.4437 9.63303
61 3P3N AKG 0.008855 0.43634 9.63303
62 3GCM 5GP 0.01814 0.46078 9.7561
63 2XDQ MGX 0.007141 0.46108 10.0917
64 3QV9 QV7 0.00288 0.45336 10.0917
65 4CCO OGA 0.01425 0.41649 10.5505
66 1O9U ADZ 0.01573 0.44276 14.6789
67 2QLX RM4 0.02184 0.42286 15.7407
68 1QO0 BMD 0.01066 0.43249 20.4082
69 1T0S BML 0.001251 0.4924 22.093
70 3R5W F42 0.001827 0.44985 22.3214
71 1UO5 PIH 0.01457 0.46074 26.4706
72 1T9M FMN 0.0000005158 0.6211 46.729
73 4HMT NNV 0.0000004322 0.48552 47.7064
74 4HMT FMN 0.0000005331 0.47628 47.7064
Pocket No.: 3; Query (leader) PDB : 1G79; Ligand: FMN; Similar sites found: 73
This union binding pocket(no: 3) in the query (biounit: 1g79.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3F81 STT 0.001182 0.4989 None
2 1TUV VK3 0.01442 0.44154 None
3 2E1A MSE 0.007332 0.4212 None
4 4F4S EFO 0.02051 0.40621 None
5 3UEC ALA ARG TPO LYS 0.01504 0.43325 1.36986
6 1MZV AMP 0.005614 0.4215 1.37615
7 2NCD ADP 0.006299 0.43427 1.83486
8 3SHR CMP 0.01072 0.40978 2.29358
9 2Y7P SAL 0.001361 0.45837 2.75229
10 2ZO9 MLI 0.006887 0.41562 2.75229
11 1SQ5 ADP 0.009305 0.40821 2.75229
12 1WDA BAG 0.01569 0.40699 2.75229
13 4F8L GAL 0.03856 0.43289 2.75862
14 2ASF CIT 0.00000009296 0.54647 2.91971
15 3A2Y TS5 0.003971 0.41093 3.04569
16 4K30 NLG 0.00888 0.42236 3.125
17 3A3B FMN 0.01007 0.43497 3.15789
18 3A3B RBF 0.01607 0.4243 3.15789
19 1RZM E4P 0.007936 0.44131 3.21101
20 4COQ SAN 0.01933 0.41693 3.21101
21 1SS4 GSH 0.001918 0.50856 3.26797
22 1SS4 CIT 0.01743 0.47392 3.26797
23 1ULE GLA GAL NAG 0.006511 0.45231 3.33333
24 1Y9Q MED 0.02627 0.41058 3.64583
25 4E28 9MZ 0.029 0.40853 3.66972
26 1YOA FMN 0.006131 0.47923 3.77358
27 1YOA FAD 0.01002 0.40329 3.77358
28 4IF4 BEF 0.02575 0.41542 3.84615
29 2Q37 3AL 0.02951 0.40349 3.8674
30 2BES RES 0.007629 0.41171 4.12844
31 1FW1 GSH 0.003129 0.42295 4.16667
32 3RF4 FUN 0.02771 0.40038 4.31034
33 4LHM AZZ 0.002087 0.45617 4.58716
34 2Z9V PXM 0.006547 0.42823 4.58716
35 1V6A TRE 0.02137 0.40995 4.58716
36 1EJE FMN 0.006113 0.42217 4.6875
37 3LTW HLZ 0.00158 0.46833 5.04587
38 4DYO SD4 0.009417 0.41653 5.04587
39 2RC5 FAD 0.008961 0.41136 5.04587
40 3S9K CIT 0.001266 0.53884 5.08475
41 2QCX PF1 0.001595 0.46149 5.50459
42 2Q8H TF4 0.02941 0.42507 5.50459
43 4B4D FAD 0.01099 0.4044 5.50459
44 3ZPG 5GP 0.004842 0.46661 5.9633
45 1Z44 FMN 0.0004754 0.45509 5.9633
46 3QDT A2G GAL 0.01052 0.44172 6.29371
47 3BY8 MLT 0.01582 0.42661 6.33803
48 1G8S MET 0.004948 0.44495 6.42202
49 1I0Z OXM 0.02135 0.43249 6.42202
50 4KOA NDP 0.001626 0.42538 6.42202
51 3PLN U5P 0.01882 0.40788 6.42202
52 2V5E SCR 0.008688 0.4613 6.5
53 1YRX FMN 0.006375 0.40692 6.61157
54 2BH9 NAP 0.006071 0.40773 6.88073
55 1PEA ACM 0.01507 0.43376 7.79817
56 3NFZ 3NF 0.007178 0.41278 8.25688
57 4RJK PYR 0.007844 0.47306 8.7156
58 1C1L GAL BGC 0.02835 0.41412 9.48905
59 3P3N AKG 0.03831 0.40274 9.63303
60 3A1I UNU 0.01634 0.40214 9.63303
61 3GCM 5GP 0.01627 0.46078 9.7561
62 2XDQ MGX 0.01627 0.43876 10.0917
63 3QV9 QV7 0.00949 0.42613 10.0917
64 1O9U ADZ 0.02293 0.43083 14.6789
65 4OYA 1VE 0.006633 0.40405 14.6789
66 2QLX RM4 0.04835 0.40259 15.7407
67 1QO0 BMD 0.01278 0.42545 20.4082
68 1T0S BML 0.008083 0.44754 22.093
69 3R5W F42 0.001519 0.44985 22.3214
70 1UO5 PIH 0.01473 0.45724 26.4706
71 1T9M FMN 0.000000395 0.6211 46.729
72 4HMT NNV 0.0000005399 0.50191 47.7064
73 4HMT FMN 0.0000003932 0.50011 47.7064
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