Receptor
PDB id Resolution Class Description Source Keywords
4WXG 2 Å EC: 2.1.2.1 CRYSTAL STRUCTURE OF L-SERINE HYDROXYMETHYLTRANSFERASE IN CO A MIXTURE OF L-ALLO-THREONINE AND GLYCINE STREPTOCOCCUS THERMOPHILUS ALDOLASE TRANSFERASE ALDEHYDES CATALYSIS CATALYTIC DOMAIDIMERIZATION GLYCINE HYDROXYMETHYLTRANSFERASE L-ALLO-THREPROTEIN BINDING THREONINE ALDOLASE
Ref.: ENGINEERED L-SERINE HYDROXYMETHYLTRANSFERASE FROM STREPTOCOCCUS THERMOPHILUS FOR THE SYNTHESIS OF ALP ALPHA-DIALKYL-ALPHA-AMINO ACIDS. ANGEW.CHEM.INT.ED.ENGL. V. 54 3013 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2BO A:501;
C:501;
Valid;
Valid;
Atoms found MORE than expected: % Diff = 1.174;
Atoms found MORE than expected: % Diff = 1.174;
submit data
350.262 C12 H19 N2 O8 P Cc1c(...
GOL A:503;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NA C:502;
A:502;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4WXG 2 Å EC: 2.1.2.1 CRYSTAL STRUCTURE OF L-SERINE HYDROXYMETHYLTRANSFERASE IN CO A MIXTURE OF L-ALLO-THREONINE AND GLYCINE STREPTOCOCCUS THERMOPHILUS ALDOLASE TRANSFERASE ALDEHYDES CATALYSIS CATALYTIC DOMAIDIMERIZATION GLYCINE HYDROXYMETHYLTRANSFERASE L-ALLO-THREPROTEIN BINDING THREONINE ALDOLASE
Ref.: ENGINEERED L-SERINE HYDROXYMETHYLTRANSFERASE FROM STREPTOCOCCUS THERMOPHILUS FOR THE SYNTHESIS OF ALP ALPHA-DIALKYL-ALPHA-AMINO ACIDS. ANGEW.CHEM.INT.ED.ENGL. V. 54 3013 2015
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4WXG - 2BO C12 H19 N2 O8 P Cc1c(c(c(c....
2 4WXB - CIT C6 H8 O7 C(C(=O)O)C....
3 4WXF - 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: 2BO; Similar ligands found: 70
No: Ligand ECFP6 Tc MDL keys Tc
1 2BO 1 1
2 2BK 1 1
3 TLP 1 1
4 ILP 0.791045 0.934426
5 PP3 0.753846 0.966102
6 PDA 0.753846 0.966102
7 PDD 0.753846 0.966102
8 PLS 0.705882 0.95
9 C6P 0.695652 0.918033
10 PPD 0.695652 0.918033
11 PY5 0.685714 0.890625
12 IN5 0.681818 0.932203
13 7XF 0.666667 0.888889
14 PDG 0.666667 0.888889
15 PGU 0.666667 0.888889
16 N5F 0.662162 0.875
17 ORX 0.662162 0.875
18 QLP 0.657534 0.835821
19 PLP ALO 0.657143 0.949153
20 PE1 0.653333 0.875
21 PY6 0.648649 0.863636
22 PLG 0.632353 0.918033
23 76U 0.626667 0.846154
24 CBA 0.621622 0.919355
25 33P 0.619718 0.885246
26 PL4 0.615385 0.875
27 P1T 0.605634 0.875
28 KAM 0.6 0.875
29 IK2 0.597222 0.846154
30 5PA 0.589041 0.875
31 EA5 0.576923 0.848485
32 PLA 0.573333 0.890625
33 AQ3 0.571429 0.861538
34 HEY 0.564103 0.861538
35 3LM 0.556962 0.863636
36 PMP 0.553846 0.881356
37 PMG 0.551282 0.863636
38 GT1 0.545455 0.786885
39 PXP 0.538462 0.844828
40 PSZ 0.5375 0.820895
41 PMH 0.526316 0.739726
42 PXG 0.518072 0.887097
43 RW2 0.518072 0.820895
44 PL2 0.5125 0.753623
45 DCS 0.5125 0.756757
46 7TS 0.5 0.746667
47 9YM 0.47619 0.830769
48 PLP 2KZ 0.4625 0.854839
49 PL8 0.45977 0.753425
50 PLR 0.454545 0.745763
51 7B9 0.449438 0.785714
52 PPG 0.443182 0.818182
53 P0P 0.442857 0.793103
54 KOU 0.4375 0.852459
55 PLP 2TL 0.432099 0.881356
56 0JO 0.43038 0.738462
57 CAN PLP 0.425287 0.80597
58 PUS 0.420455 0.708333
59 1D0 0.419355 0.848485
60 PL6 0.416667 0.75
61 PLP 0.414286 0.793103
62 4LM 0.4125 0.777778
63 PLP SER 0.4125 0.833333
64 Z98 0.411765 0.8
65 EPC 0.410256 0.783333
66 AN7 0.410256 0.766667
67 PZP 0.408451 0.766667
68 LCS 0.406977 0.697368
69 FOO 0.405063 0.803279
70 GLY PLP 0.405063 0.803279
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4WXG; Ligand: 2BO; Similar sites found: 75
This union binding pocket(no: 1) in the query (biounit: 4wxg.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ZC0 PMP 0.001706 0.40114 1.7199
2 5WYF ILP 0.00046 0.4289 1.86916
3 1JS3 PLP 142 0.0002712 0.46921 2.1028
4 3CQ5 PMP 0.001391 0.47217 2.16802
5 3PD6 PMP 0.0001665 0.50628 2.24439
6 3PDB PMP 0.0002388 0.41674 2.24439
7 4E1O PLP PVH 0.000778 0.42988 2.33645
8 3FQ8 PMP 0.001177 0.42627 2.34192
9 1SFF IK2 0.001033 0.43966 2.34742
10 4ZSY RW2 0.001627 0.42748 2.57009
11 1OXO IK2 0.003159 0.43266 2.74314
12 5U23 TQP 0.00212 0.42654 2.87958
13 5K8B PDG 0.0001969 0.45301 2.97767
14 1DJ9 KAM 0.00001018 0.47159 3.03738
15 5IWQ PLP 0.01046 0.41365 3.03738
16 2B6N ALA PRO THR 0.03338 0.40212 3.23741
17 5DDW 5B6 0.001395 0.4303 3.27103
18 1M32 PLP 0.0005262 0.4959 3.27869
19 1PMO PLR 0.0002029 0.42178 3.50467
20 4IYO 0JO 0.001041 0.43952 3.52645
21 4IY7 KOU 0.001067 0.41802 3.52645
22 4IY7 0JO 0.001192 0.41631 3.52645
23 1F6D UDP 0.01038 0.4179 3.7234
24 4ZM4 PLP 0.0003718 0.47789 3.73832
25 5W71 9YM 0.0009797 0.45177 3.73832
26 5W71 PLP 0.0001892 0.43195 3.73832
27 4ZM4 P3B 0.002145 0.426 3.73832
28 2FYF PLP 0.00005556 0.42623 3.76884
29 4UHO PLP 0.01278 0.42219 4.20561
30 4ZAH T5K 0.0008303 0.41191 4.29293
31 5G09 6DF 0.002168 0.40398 4.34783
32 2R2N PMP 0.00594 0.42551 4.47059
33 2OAT PFM 0.003713 0.42297 4.6729
34 1ELU PDA 0.0005255 0.42718 4.87179
35 1ELU CSS 0.002226 0.40824 4.87179
36 4AOA IK2 0.0006197 0.41034 4.90654
37 5X30 7XF 0.00017 0.44105 5.02513
38 5X2Z 3LM 0.0008827 0.43483 5.02513
39 5X30 4LM 0.0002916 0.42749 5.02513
40 5DJ3 5DK 0.00009172 0.44976 5.05319
41 3B1E P1T 0.008972 0.41296 5.10204
42 4YDD MGD 0.03447 0.40313 5.14019
43 4YDD MD1 0.03447 0.40313 5.14019
44 2OGA PGU 0.002189 0.40749 5.26316
45 4R5Z PMP 0.003791 0.40875 5.44959
46 2R5E QLP 0.002719 0.42156 5.59441
47 2R5C C6P 0.002782 0.4009 5.59441
48 4E3Q PMP 0.00007472 0.41956 5.60748
49 1WYV PLP AOA 0.0001471 0.44001 5.84112
50 5G4J EXT 0.001018 0.44397 6.30841
51 2C1P FNZ 0.0194 0.40445 6.45161
52 4AZJ SEP PLP 0.0001995 0.44764 6.94444
53 4OSP 2V4 0.01927 0.41289 7.22433
54 1LW4 TLP 0.0001584 0.44225 8.93372
55 1LW4 PLP 0.00007938 0.44117 8.93372
56 3VWX GSH 0.0314 0.40177 9.00901
57 1O8B ABF 0.01015 0.42274 9.13242
58 3VP6 HLD 0.000003211 0.53257 9.57944
59 1AJS PLA 0.0005981 0.4382 9.95146
60 1WB4 SXX 0.001698 0.4694 10.4377
61 4K2M O1G 0.001216 0.42918 10.7477
62 3WGC PLG 0.00005656 0.45068 11.4369
63 1FC4 AKB PLP 0.00001667 0.52241 11.6822
64 5KGS 6SR 0.00487 0.42441 11.9159
65 4BA5 PXG 0.0002791 0.42078 12.4183
66 1MDZ DCS 0.004649 0.4147 13.7405
67 1MDZ PLP 0.004348 0.4147 13.7405
68 3DR4 G4M 0.003465 0.42585 13.8107
69 2WK9 PLG 0.00001461 0.51899 14.2523
70 2WK9 PLP 0.00007057 0.48693 14.2523
71 2Y91 98J 0.01757 0.41114 16.2264
72 5W70 9YM 0.000128 0.44935 17.0561
73 2PO3 T4K 0.008627 0.40445 18.3962
74 3NUB UD0 0.001378 0.43439 20.6128
75 4BXF AKG 0.02677 0.40782 47.3684
Pocket No.: 2; Query (leader) PDB : 4WXG; Ligand: 2BO; 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: 4wxg.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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