Receptor
PDB id Resolution Class Description Source Keywords
1DFO 2.4 Å EC: 2.1.2.1 CRYSTAL STRUCTURE AT 2.4 ANGSTROM RESOLUTION OF E. COLI SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH GLYCINE A ND 5-FORMYL TETRAHYDROFOLATE ESCHERICHIA COLI ALPHA PLP ASPARTATE AMINO TRANSFERASE (AAT)-LIKE FOLD
Ref.: CRYSTAL STRUCTURE AT 2.4 A RESOLUTION OF E. COLI SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH GLYCINE SUBSTRATE AND 5-FORMYL TETRAHYDROFOLATE. J.MOL.BIOL. V. 296 155 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FFO A:1002;
B:2002;
C:3002;
D:4002;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
473.439 C20 H23 N7 O7 c1cc(...
PLG A:1001;
B:2001;
C:3001;
D:4001;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
306.209 C10 H15 N2 O7 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1DFO 2.4 Å EC: 2.1.2.1 CRYSTAL STRUCTURE AT 2.4 ANGSTROM RESOLUTION OF E. COLI SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH GLYCINE A ND 5-FORMYL TETRAHYDROFOLATE ESCHERICHIA COLI ALPHA PLP ASPARTATE AMINO TRANSFERASE (AAT)-LIKE FOLD
Ref.: CRYSTAL STRUCTURE AT 2.4 A RESOLUTION OF E. COLI SERINE HYDROXYMETHYLTRANSFERASE IN COMPLEX WITH GLYCINE SUBSTRATE AND 5-FORMYL TETRAHYDROFOLATE. J.MOL.BIOL. V. 296 155 2000
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1DFO - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2VMO - GLY PLP n/a n/a
2 2VMQ - GLY PLP n/a n/a
3 2W7F - SER PLP n/a n/a
4 2W7L - PLP ALO n/a n/a
5 1KKP - PLP SER n/a n/a
6 2VMP - SER PLP n/a n/a
7 1YJY - PLP SER n/a n/a
8 2VMW - SER PLP n/a n/a
9 2W7K - SER PLP n/a n/a
10 1KL1 - PLP GLY n/a n/a
11 2W7J - GLY PLP n/a n/a
12 2W7M - GLY PLP n/a n/a
13 2VMX - PLP ALO n/a n/a
14 1YJZ - PLP C8 H10 N O6 P Cc1c(c(c(c....
15 2VMT - SER PLP n/a n/a
16 2W7G - PLP ALO n/a n/a
17 1YJS - PLP GLY n/a n/a
18 4WXG - 2BO C12 H19 N2 O8 P Cc1c(c(c(c....
19 4WXB - CIT C6 H8 O7 C(C(=O)O)C....
20 4WXF - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
21 1DFO - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2VMO - GLY PLP n/a n/a
2 2VMQ - GLY PLP n/a n/a
3 2W7F - SER PLP n/a n/a
4 2W7L - PLP ALO n/a n/a
5 1KKP - PLP SER n/a n/a
6 2VMP - SER PLP n/a n/a
7 1YJY - PLP SER n/a n/a
8 2VMW - SER PLP n/a n/a
9 2W7K - SER PLP n/a n/a
10 1KL1 - PLP GLY n/a n/a
11 2W7J - GLY PLP n/a n/a
12 2W7M - GLY PLP n/a n/a
13 2VMX - PLP ALO n/a n/a
14 1YJZ - PLP C8 H10 N O6 P Cc1c(c(c(c....
15 2VMT - SER PLP n/a n/a
16 2W7G - PLP ALO n/a n/a
17 1YJS - PLP GLY n/a n/a
18 4WXG - 2BO C12 H19 N2 O8 P Cc1c(c(c(c....
19 4WXB - CIT C6 H8 O7 C(C(=O)O)C....
20 4WXF - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
21 5GVN ic50 = 90 nM G6F C26 H25 F N4 O3 Cc1c2c(n[n....
22 4TN4 - 33G C25 H20 F N5 O Cc1c2c(n[n....
23 5GVL ic50 = 42 nM GI8 C24 H23 N5 O2 S Cc1c2c(n[n....
24 5GVM ic50 = 186 nM G57 C26 H23 F3 N4 O3 Cc1c2c(n[n....
25 5GVK Kd = 99 nM G45 C24 H24 N6 O3 S2 Cc1c2c(n[n....
26 5GVP ic50 = 165 nM GCF C27 H25 F3 N4 O3 Cc1c2c(n[n....
27 1DFO - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FFO; Similar ligands found: 25
No: Ligand ECFP6 Tc MDL keys Tc
1 FFO 1 1
2 C2F 0.739583 0.957747
3 FON 0.683168 1
4 THG 0.617647 0.926471
5 1YJ 0.617647 0.926471
6 MEF 0.550459 0.881579
7 TLL 0.530435 0.931507
8 1YA 0.508929 0.970588
9 THF 0.504505 0.943662
10 THH 0.495495 0.8
11 9L9 0.456311 0.855072
12 DHF 0.45045 0.926471
13 3TZ 0.440678 0.723684
14 83A 0.438596 0.77027
15 DZF 0.429825 0.788732
16 FOL 0.429825 0.802817
17 GHC 0.429825 0.6625
18 28Z 0.428571 0.780822
19 29D 0.428571 0.780822
20 29C 0.428571 0.780822
21 MHF 0.416667 0.881579
22 GHW 0.412281 0.670886
23 21V 0.401709 0.847222
24 DDF 0.401709 0.847222
25 TMF 0.4 0.866667
Ligand no: 2; Ligand: PLG; Similar ligands found: 70
No: Ligand ECFP6 Tc MDL keys Tc
1 PLG 1 1
2 IK2 0.666667 0.890625
3 EA5 0.661972 0.921875
4 PDD 0.651515 0.918033
5 PP3 0.651515 0.918033
6 P1T 0.651515 0.890625
7 PDA 0.651515 0.918033
8 PPD 0.647059 0.966667
9 33P 0.641791 0.901639
10 PLA 0.637681 0.90625
11 5PA 0.632353 0.890625
12 2BK 0.632353 0.918033
13 PLS 0.632353 0.934426
14 TLP 0.632353 0.918033
15 2BO 0.632353 0.918033
16 IN5 0.630769 0.885246
17 C6P 0.623188 0.934426
18 PDG 0.619718 0.935484
19 PGU 0.619718 0.935484
20 PY5 0.614286 0.876923
21 PMG 0.611111 0.878788
22 PL2 0.611111 0.794118
23 76U 0.60274 0.890625
24 KAM 0.597403 0.890625
25 ILP 0.597222 0.888889
26 7XF 0.597222 0.904762
27 CBA 0.597222 0.875
28 PSZ 0.594595 0.808824
29 N5F 0.594595 0.920635
30 QLP 0.589041 0.878788
31 PXP 0.583333 0.8
32 HEY 0.581081 0.90625
33 PY6 0.581081 0.850746
34 PMP 0.57377 0.866667
35 ORX 0.573333 0.890625
36 3LM 0.573333 0.850746
37 PE1 0.565789 0.890625
38 GT1 0.564516 0.746032
39 PMH 0.56338 0.706667
40 PXG 0.551282 0.873016
41 PL4 0.551282 0.890625
42 RW2 0.551282 0.835821
43 7TS 0.533333 0.714286
44 AQ3 0.53012 0.876923
45 DCS 0.526316 0.746667
46 9YM 0.506329 0.818182
47 PL8 0.487805 0.791667
48 PLP ALO 0.48 0.870968
49 1D0 0.476744 0.835821
50 7B9 0.47619 0.826087
51 PLP 2KZ 0.473684 0.84127
52 PLP 0.46875 0.75
53 PLR 0.467742 0.704918
54 P0P 0.454545 0.75
55 PPG 0.452381 0.861538
56 PZP 0.439394 0.754098
57 AN7 0.438356 0.754098
58 CAN PLP 0.433735 0.848485
59 GLY PLP 0.432432 0.85
60 FOO 0.432432 0.790323
61 LCS 0.432099 0.688312
62 2B6 0.426966 0.653846
63 PL6 0.425 0.793651
64 4LM 0.421053 0.738462
65 0JO 0.421053 0.727273
66 GBC PLP 0.418605 0.828125
67 GAB PLP 0.418605 0.828125
68 0LD 0.412371 0.627907
69 KOU 0.410256 0.809524
70 PLP SER 0.402597 0.790323
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1DFO; Ligand: FFO; Similar sites found: 5
This union binding pocket(no: 1) in the query (biounit: 1dfo.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2D24 XYS XYS 0.0227 0.41059 2.63789
2 2TOH HBI 0.02153 0.40109 2.91545
3 4WOH 4NP 0.02112 0.40479 3.61446
4 1H6H PIB 0.02071 0.40852 4.1958
5 4REI 3MV 0.01854 0.40498 5.29801
Pocket No.: 2; Query (leader) PDB : 1DFO; Ligand: PLG; Similar sites found: 105
This union binding pocket(no: 2) in the query (biounit: 1dfo.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4E1O PLP PVH 0.0005101 0.43575 1.19904
2 5G09 6DF 0.002356 0.41877 1.19904
3 1D3V ABH 0.009661 0.40642 1.54799
4 5W71 PLP 0.0001472 0.47954 1.67866
5 1JS3 PLP 142 0.0002472 0.46478 1.67866
6 2WK9 PLG 0.000005018 0.45377 1.79949
7 2WK9 PLP 0.00004589 0.43337 1.79949
8 4R5Z PMP 0.001608 0.41505 1.90736
9 4I06 X8A 0.009966 0.40214 1.96078
10 2HW1 FRU 0.01189 0.42066 2.01342
11 3FQ8 PMP 0.0003123 0.46202 2.15827
12 2HHP FLC 0.01842 0.45712 2.15827
13 5G4J EXT 0.0007535 0.44388 2.15827
14 4ZSY RW2 0.0005675 0.4382 2.15827
15 1CZA G6P 0.01422 0.40625 2.15827
16 1AJS PLA 0.0005106 0.42943 2.18447
17 4AZJ SEP PLP 0.0002445 0.45358 2.22222
18 5K8B PDG 0.00009287 0.46257 2.23325
19 2VAR KDG 0.0109 0.40781 2.23642
20 2VAR KDF 0.01531 0.4008 2.23642
21 4ZM4 PLP 0.0001972 0.48453 2.39808
22 4ZM4 P3B 0.001076 0.43318 2.39808
23 3PD6 PMP 0.0001617 0.50058 2.49377
24 3PDB PMP 0.0001968 0.49034 2.49377
25 2X5F PLP 0.003886 0.43364 2.63789
26 3E2Y PMP 0.000988 0.4572 2.68293
27 4M2K PLP 0.0008848 0.47049 2.70936
28 3ZRR PXG 0.000002354 0.54565 2.86458
29 1WB4 SXX 0.0007561 0.48396 2.8777
30 1VJO PLP 0.0001067 0.49112 3.05344
31 3A8U PLP 0.002853 0.45423 3.35731
32 2OGA PGU 0.002651 0.41055 3.50877
33 1S20 TLA 0.01694 0.40664 3.52941
34 1WYV PLP AOA 0.00007732 0.49188 3.83693
35 5WYF ILP 0.0002801 0.4579 4.07674
36 2R5C C6P 0.001859 0.42313 4.07674
37 2R5E QLP 0.001993 0.42184 4.07674
38 1MLY ACZ PLP 0.005707 0.40586 4.1958
39 4UOX PLP 0.001256 0.45227 4.55635
40 4UOX PUT 0.003042 0.42546 4.55635
41 4UOX PLP PUT 0.006408 0.40716 4.55635
42 3B1E P1T 0.004627 0.42123 4.59184
43 1M32 PLP 0.0008179 0.48022 4.64481
44 1LC8 33P 0.001348 0.40077 4.67033
45 1GCK ASP PLP 0.004287 0.40776 4.67532
46 1UU1 PMP HSA 0.001289 0.42425 4.79616
47 2ZC0 PMP 0.001329 0.43736 4.914
48 5LUB 3Y7 0.01716 0.41071 4.96183
49 5I8T LAC 0.008159 0.42726 5.02793
50 4BA5 PXG 0.0002265 0.47638 5.03597
51 4JE5 PLP 0.008395 0.41739 5.03597
52 5IWQ PLP 0.007702 0.41498 5.03597
53 4JE5 PMP 0.01029 0.41309 5.03597
54 5JP0 BGC 0.02685 0.40065 5.03597
55 3BS8 PMP 0.003725 0.42993 5.27578
56 1ELU PDA 0.0002582 0.46397 5.38462
57 1ELU CSS 0.001472 0.42229 5.38462
58 2JG1 TA6 0.006572 0.42256 5.45455
59 4K2M O1G 0.0007072 0.4282 5.51559
60 1ZC9 PMP 0.002078 0.42484 5.51559
61 4ADC PLP 0.002022 0.40351 5.7554
62 2UZH IPE 0.006291 0.43606 6.06061
63 3CQ5 PMP 0.0005987 0.48522 6.23306
64 2OAT PFM 0.002737 0.4235 6.23501
65 4UHO PLP 0.008344 0.42676 6.71463
66 2TPL HPP 0.0009456 0.40851 6.71463
67 5DDW 5B6 0.0008015 0.4315 6.95444
68 5DJ3 5DK 0.001577 0.43001 7.18085
69 4B98 PXG 0.001296 0.43784 7.19424
70 4HVK PMP 0.00002694 0.54585 7.32984
71 1PMO PLR 0.0002211 0.48794 7.43405
72 4FL0 PLP 0.006291 0.41914 7.43405
73 4IY7 KOU 0.0007795 0.4391 7.80856
74 4IY7 0JO 0.0007945 0.43874 7.80856
75 4IYO 0JO 0.0008762 0.43695 7.80856
76 5VYQ TYD 0.01609 0.41319 7.84314
77 2Z9V PXM 0.0006459 0.48354 7.90816
78 2R2N PMP 0.004495 0.42606 7.91367
79 1LW4 TLP 0.0001014 0.47119 8.06916
80 1LW4 PLP 0.00005626 0.4703 8.06916
81 2FYF PLP 0.00006098 0.52822 8.29146
82 4E3Q PMP 0.00003859 0.53071 8.39329
83 2HOX P1T 0.003328 0.416 8.39329
84 1E5F PLP 0.0001926 0.47955 8.66337
85 1GZ4 FUM 0.02665 0.40453 9.11271
86 4RKC PMP 0.001652 0.44192 9.29648
87 3VP6 HLD 0.000004688 0.50023 9.59233
88 1U08 PLP 0.0004561 0.47875 10.3627
89 5W70 9YM 0.0000868 0.47941 10.5516
90 1DJ9 KAM 0.000008405 0.54093 10.6771
91 1V1A KDG 0.004894 0.43354 10.6796
92 5X30 7XF 0.0002256 0.4665 11.3065
93 5X30 4LM 0.0003036 0.46566 11.3065
94 5X2Z 3LM 0.0006283 0.41352 11.3065
95 4LNL PLG 0.00003765 0.51774 11.4114
96 4LNL 2BO 0.00003971 0.5105 11.4114
97 3BWN PMP 0.001027 0.4564 11.7647
98 3BWN PMP PHE 0.003818 0.40462 11.7647
99 1SFF IK2 0.0006831 0.44152 12.2302
100 1B9I PXG 0.0008481 0.41932 13.1443
101 4AOA IK2 0.0003412 0.46835 13.1894
102 3WGC PLG 0.00002695 0.51809 15.8358
103 1FC4 AKB PLP 0.0000137 0.51904 17.9856
104 1GEX PLP HSA 0.001556 0.40088 21.3429
105 2XBN PMP 0.0005368 0.45547 32.8537
Pocket No.: 3; Query (leader) PDB : 1DFO; Ligand: PLG; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1dfo.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1DFO; Ligand: FFO; 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: 1dfo.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1DFO; Ligand: FFO; Similar sites found: 2
This union binding pocket(no: 5) in the query (biounit: 1dfo.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3BRN SRO 0.02248 0.40068 4.4586
2 3W6G FLC 0.02097 0.40072 7.87037
Pocket No.: 6; Query (leader) PDB : 1DFO; Ligand: PLG; Similar sites found: 5
This union binding pocket(no: 6) in the query (biounit: 1dfo.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4UP4 NDG 0.02007 0.40849 3.74065
2 4OSP 2V4 0.02391 0.40325 4.56274
3 1XI9 PLP 0.01938 0.40368 7.88177
4 1CL2 PPG 0.003577 0.41109 8.35443
5 2ZL4 ALA ALA ALA ALA 0.02724 0.40193 8.63309
Pocket No.: 7; Query (leader) PDB : 1DFO; Ligand: FFO; 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: 1dfo.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 1DFO; Ligand: PLG; 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: 1dfo.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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