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-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-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 10 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 (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 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 6YMF - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
22 1DFO - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
50% Homology Family (45)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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 6UXI - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
19 6UXL - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
20 6UXJ Kd = 17 uM FFO C20 H23 N7 O7 c1cc(ccc1C....
21 4WXG - 2BO C12 H19 N2 O8 P Cc1c(c(c(c....
22 4WXB - CIT C6 H8 O7 C(C(=O)O)C....
23 4WXF - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
24 6SMW Ki = 119.4 uM LYA C20 H21 N5 O6 c1cc(ccc1C....
25 6SMR Ki = 179.3 uM MTX C20 H22 N8 O5 CN(Cc1cnc2....
26 6YMF - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
27 6QVL - 4DW C20 H19 N5 O6 c1cc(ccc1C....
28 6QVG - GLY C2 H5 N O2 C(C(=O)O)N
29 5V7I - GLY C2 H5 N O2 C(C(=O)O)N
30 5GVN ic50 = 90 nM G6F C26 H25 F N4 O3 Cc1c2c(n[n....
31 5XMV - 8AU C24 H20 Cl F3 N4 O Cc1c2c(n[n....
32 5YFZ - 8UO C24 H28 F N5 O3 Cc1c2c(n[n....
33 5XMQ - 8A6 C32 H30 F3 N5 O3 S Cc1c2c(n[n....
34 4TN4 - 33G C25 H20 F N5 O Cc1c2c(n[n....
35 5GVL ic50 = 42 nM GI8 C24 H23 N5 O2 S Cc1c2c(n[n....
36 5XMP - 8A3 C27 H25 F6 N5 O3 S Cc1c2c(n[n....
37 5GVM ic50 = 186 nM G57 C26 H23 F3 N4 O3 Cc1c2c(n[n....
38 5XMS - 8B3 C24 H20 F4 N4 O Cc1c2c(n[n....
39 5YG4 - 8UF C25 H28 F N5 O3 Cc1c2c(n[n....
40 5XMU - 8A0 C25 H23 F3 N4 O Cc1ccccc1c....
41 5YG3 - 8UC C23 H20 F N5 O Cc1c2c(n[n....
42 5GVK ic50 = 99 nM G45 C24 H24 N6 O3 S2 Cc1c2c(n[n....
43 5YG2 - N05 C25 H30 F N5 O3 Cc1c2c(n[n....
44 5GVP ic50 = 165 nM GCF C27 H25 F3 N4 O3 Cc1c2c(n[n....
45 1DFO - PLG C10 H15 N2 O7 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 2BO; Similar ligands found: 79
No: Ligand ECFP6 Tc MDL keys Tc
1 TLP 1 1
2 2BO 1 1
3 2BK 1 1
4 ILP 0.791045 0.934426
5 PDD 0.753846 0.966102
6 PP3 0.753846 0.966102
7 PDA 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 PGU 0.666667 0.888889
14 PDG 0.666667 0.888889
15 7XF 0.666667 0.888889
16 ORX 0.662162 0.875
17 N5F 0.662162 0.875
18 LPI 0.657534 0.850746
19 QLP 0.657534 0.835821
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 0PR 0.615385 0.903226
27 PL4 0.615385 0.875
28 P1T 0.605634 0.875
29 KAM 0.6 0.875
30 IK2 0.597222 0.846154
31 5PA 0.589041 0.875
32 EA5 0.576923 0.848485
33 PLA 0.573333 0.890625
34 AQ3 0.571429 0.861538
35 HEY 0.564103 0.861538
36 3LM 0.556962 0.863636
37 PMP 0.553846 0.881356
38 PMG 0.551282 0.863636
39 GT1 0.545455 0.786885
40 PXP 0.538462 0.844828
41 PSZ 0.5375 0.820895
42 PMH 0.526316 0.739726
43 RW2 0.518072 0.820895
44 PXG 0.518072 0.887097
45 PL2 0.5125 0.753623
46 DCS 0.5125 0.756757
47 7TS 0.5 0.746667
48 DN9 0.5 0.814286
49 CKT 0.493506 0.870968
50 9YM 0.47619 0.830769
51 PLP 2KZ 0.4625 0.854839
52 F0G 0.461538 0.816667
53 PL8 0.45977 0.753425
54 PLR 0.454545 0.745763
55 7B9 0.449438 0.785714
56 FEJ 0.445783 0.836066
57 PPG 0.443182 0.818182
58 P0P 0.442857 0.793103
59 OJQ 0.439024 0.72
60 KOU 0.4375 0.852459
61 PLP PMP 0.43662 0.833333
62 0JO 0.43038 0.738462
63 RMT 0.422222 0.787879
64 PLP 2TL 0.421687 0.933333
65 CAN PLP 0.420455 0.794118
66 PUS 0.420455 0.708333
67 1D0 0.419355 0.848485
68 PL6 0.416667 0.75
69 EVM 0.414634 0.83871
70 PLP 0.414286 0.793103
71 4LM 0.4125 0.777778
72 Z98 0.411765 0.8
73 AN7 0.410256 0.766667
74 EPC 0.410256 0.783333
75 PZP 0.408451 0.766667
76 PLP SER 0.407407 0.885246
77 LCS 0.406977 0.697368
78 FOO 0.405063 0.803279
79 FEV 0.402439 0.765625
Similar Ligands (3D)
Ligand no: 1; Ligand: 2BO; Similar ligands found: 16
No: Ligand Similarity coefficient
1 SER PLP 0.9592
2 PLP ALO 0.9391
3 PM9 0.9127
4 MET PLP 0.9100
5 PLP MET 0.9081
6 PLP 2ML 0.9013
7 MPM 0.8958
8 L7N 0.8932
9 PLP CYS 0.8918
10 HCP 0.8914
11 KET 0.8900
12 PLI 0.8890
13 ASP PLP 0.8867
14 PLP GLY 0.8785
15 GLY PLP 0.8781
16 PLP 0A0 0.8648
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4WXG; Ligand: 2BO; 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: 4wxg.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4WXG; Ligand: 2BO; 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: 4wxg.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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