Receptor
PDB id Resolution Class Description Source Keywords
1KKP 1.93 Å EC: 2.1.2.1 CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE COMPLEX SERINE GEOBACILLUS STEAROTHERMOPHILUS SHMT PLP TETRAHYDROFOLATE TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF BINARY AND TERNARY COMPLEXES O HYDROXYMETHYLTRANSFERASE FROM BACILLUS STEAROTHERMO INSIGHTS INTO THE CATALYTIC MECHANISM. J.BIOL.CHEM. V. 277 17161 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PLP SER A:501;
Valid;
none;
submit data
318.222 n/a P(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VMQ 1.67 Å EC: 2.1.2.1 STRUCTURE OF N341ABSSHMT CRYSTALLIZED IN THE PRESENCE OF L- ALLO-THR BACILLUS STEAROTHERMOPHILUS PLP-DEPENDENT ENZYMES SERINE HYDROXYMETHYLTRANSFERASE SHMT N341A TRANSFERASE FOLATE BINDING PYRIDOXAL PHOSPHATE ONE-CARBON METABOLISM
Ref.: STRUCTURAL AND FUNCTIONAL STUDIES OF BACILLUS STEAROTHERMOPHILUS SERINE HYDROXYMETHYLTRANSFERASE: THE ROLE OF ASN(341), TYR(60) AND PHE(351) IN TETRAHYDROFOLATE BINDING. BIOCHEM.J. V. 418 635 2009
Members (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 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
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: PLP SER; Similar ligands found: 34
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP SER 1 1
2 PLP 2TL 0.757576 0.949153
3 PLP CYS 0.742424 0.901639
4 LEU PLP 0.735294 0.918033
5 PLP BH2 0.720588 0.916667
6 SEP PLP 0.720588 0.916667
7 GLU PLP 0.690141 0.887097
8 TYR PLP 0.644737 0.901639
9 PLP 2ML 0.621622 0.919355
10 PLP 0A0 0.60274 0.919355
11 PLP PMP 0.5625 0.912281
12 ASP PLP 0.56 0.847458
13 PLP HSA 0.555556 0.80303
14 PLP 2KZ 0.533333 0.9
15 CAN PLP 0.518519 0.833333
16 ACZ PLP 0.455556 0.859375
17 GAB PLP 0.453488 0.885246
18 PLP ALO 0.444444 0.8
19 PMP 0.434783 0.864407
20 SER PLP 0.432099 0.786885
21 PLP 999 0.421687 0.770492
22 PXP 0.42029 0.766667
23 PPD 0.419753 0.84127
24 GLY PLP 0.417722 0.783333
25 PDA 0.417722 0.916667
26 PP3 0.417722 0.916667
27 PDD 0.417722 0.916667
28 IN5 0.415584 0.883333
29 OJQ 0.414634 0.684211
30 PMP HSA 0.411111 0.746269
31 GT1 0.408451 0.714286
32 2BO 0.407407 0.885246
33 2BK 0.407407 0.885246
34 TLP 0.407407 0.885246
Similar Ligands (3D)
Ligand no: 1; Ligand: PLP SER; Similar ligands found: 43
No: Ligand Similarity coefficient
1 PLS 0.9903
2 0JO 0.9777
3 P1T 0.9742
4 PLG 0.9624
5 FOO 0.9602
6 C6P 0.9579
7 EVM 0.9563
8 KOU 0.9541
9 L7N 0.9509
10 DCS 0.9465
11 CKT 0.9392
12 PLI 0.9382
13 F0G 0.9353
14 PMH 0.9353
15 PLP GLY 0.9340
16 5PA 0.9330
17 7TS 0.9324
18 MET PLP 0.9201
19 EPC 0.9161
20 MPM 0.9156
21 LCS 0.9132
22 IK2 0.9129
23 PLP AOA 0.9129
24 PLP MET 0.9110
25 4LM 0.9087
26 PM9 0.9071
27 AN7 0.9069
28 FEV 0.9030
29 7XF 0.8983
30 PLA 0.8945
31 HCP 0.8906
32 KET 0.8896
33 PY5 0.8848
34 3QP 0.8768
35 ILP 0.8721
36 PGU 0.8719
37 8JF 0.8695
38 PPE 0.8693
39 07U 0.8667
40 FEJ 0.8605
41 3LM 0.8595
42 PY6 0.8546
43 855 0.8539
Similar Binding Sites (Proteins are less than 50% similar to leader) APoc FAQ
Feedback