Receptor
PDB id Resolution Class Description Source Keywords
5XMS 2.45 Å EC: 2.-.-.- PLASMODIUM VIVAX SHMT BOUND WITH PLP-GLYCINE AND GS498 PLASMODIUM VIVAX ALPHA AND BETA PROTEIN METHYLTRANSFERASE ACTIVITY TRANSFERTRANSFERASE INHIBITOR COMPLEX
Ref.: CONFORMATIONAL ASPECTS IN THE DESIGN OF INHIBITORS SERINE HYDROXYMETHYLTRANSFERASE (SHMT): BIPHENYL, A SULFONAMIDE, AND ARYL SULFONE MOTIFS CHEMISTRY V. 23 14345 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PLG C:501;
A:501;
B:501;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
306.209 C10 H15 N2 O7 P Cc1c(...
CL A:503;
C:503;
 Invalid;
Invalid;
 none;
none;
 submit data
35.453 Cl [Cl-]
8B3 B:502;
A:502;
C:502;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
456.435 C24 H20 F4 N4 O Cc1c2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5GVL 2.5 Å EC: 2.-.-.- PLASMODIUM VIVAX SHMT BOUND WITH PLP-GLYCINE AND GS182 PLASMODIUM VIVAX (STRAIN SALVADOR I) ALPHA AND BETA PROTEIN METHYLTRANSFERASE ACTIVITY TRANSFERTRANSFERASE INHIBITOR COMPLEX
Ref.: ANTIMALARIAL INHIBITORS TARGETING SERINE HYDROXYMETHYLTRANSFERASE (SHMT) WITH IN VIVO EFFICA ANALYSIS OF THEIR BINDING MODE BASED ON X-RAY COCRY STRUCTURES J. MED. CHEM. V. 60 4840 2017
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 313 families.
1 5GVN ic50 = 90 nM G6F C26 H25 F N4 O3 Cc1c2c(n[n....
2 5XMV - 8AU C24 H20 Cl F3 N4 O Cc1c2c(n[n....
3 5YFZ - 8UO C24 H28 F N5 O3 Cc1c2c(n[n....
4 5XMQ - 8A6 C32 H30 F3 N5 O3 S Cc1c2c(n[n....
5 4TN4 - 33G C25 H20 F N5 O Cc1c2c(n[n....
6 5GVL ic50 = 42 nM GI8 C24 H23 N5 O2 S Cc1c2c(n[n....
7 5XMP - 8A3 C27 H25 F6 N5 O3 S Cc1c2c(n[n....
8 5GVM ic50 = 186 nM G57 C26 H23 F3 N4 O3 Cc1c2c(n[n....
9 5XMS - 8B3 C24 H20 F4 N4 O Cc1c2c(n[n....
10 5YG4 - 8UF C25 H28 F N5 O3 Cc1c2c(n[n....
11 5XMU - 8A0 C25 H23 F3 N4 O Cc1ccccc1c....
12 5YG3 - 8UC C23 H20 F N5 O Cc1c2c(n[n....
13 5GVK ic50 = 99 nM G45 C24 H24 N6 O3 S2 Cc1c2c(n[n....
14 5YG2 - N05 C25 H30 F N5 O3 Cc1c2c(n[n....
15 5GVP ic50 = 165 nM GCF C27 H25 F3 N4 O3 Cc1c2c(n[n....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 277 families.
1 5GVN ic50 = 90 nM G6F C26 H25 F N4 O3 Cc1c2c(n[n....
2 5XMV - 8AU C24 H20 Cl F3 N4 O Cc1c2c(n[n....
3 5YFZ - 8UO C24 H28 F N5 O3 Cc1c2c(n[n....
4 5XMQ - 8A6 C32 H30 F3 N5 O3 S Cc1c2c(n[n....
5 4TN4 - 33G C25 H20 F N5 O Cc1c2c(n[n....
6 5GVL ic50 = 42 nM GI8 C24 H23 N5 O2 S Cc1c2c(n[n....
7 5XMP - 8A3 C27 H25 F6 N5 O3 S Cc1c2c(n[n....
8 5GVM ic50 = 186 nM G57 C26 H23 F3 N4 O3 Cc1c2c(n[n....
9 5XMS - 8B3 C24 H20 F4 N4 O Cc1c2c(n[n....
10 5YG4 - 8UF C25 H28 F N5 O3 Cc1c2c(n[n....
11 5XMU - 8A0 C25 H23 F3 N4 O Cc1ccccc1c....
12 5YG3 - 8UC C23 H20 F N5 O Cc1c2c(n[n....
13 5GVK ic50 = 99 nM G45 C24 H24 N6 O3 S2 Cc1c2c(n[n....
14 5YG2 - N05 C25 H30 F N5 O3 Cc1c2c(n[n....
15 5GVP ic50 = 165 nM GCF C27 H25 F3 N4 O3 Cc1c2c(n[n....
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: PLG; Similar ligands found: 78
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 P1T 0.651515 0.890625
6 PDA 0.651515 0.918033
7 PP3 0.651515 0.918033
8 PPD 0.647059 0.966667
9 33P 0.641791 0.901639
10 PLA 0.637681 0.90625
11 TLP 0.632353 0.918033
12 PLS 0.632353 0.934426
13 2BO 0.632353 0.918033
14 5PA 0.632353 0.890625
15 2BK 0.632353 0.918033
16 IN5 0.630769 0.885246
17 C6P 0.623188 0.934426
18 PGU 0.619718 0.935484
19 PDG 0.619718 0.935484
20 PY5 0.614286 0.876923
21 PL2 0.611111 0.794118
22 PMG 0.611111 0.878788
23 DN9 0.61039 0.855072
24 76U 0.60274 0.890625
25 KAM 0.597403 0.890625
26 CBA 0.597222 0.875
27 7XF 0.597222 0.904762
28 ILP 0.597222 0.888889
29 PSZ 0.594595 0.808824
30 N5F 0.594595 0.920635
31 LPI 0.589041 0.865672
32 QLP 0.589041 0.878788
33 PXP 0.583333 0.8
34 HEY 0.581081 0.90625
35 PY6 0.581081 0.850746
36 PMP 0.57377 0.866667
37 ORX 0.573333 0.890625
38 3LM 0.573333 0.850746
39 PE1 0.565789 0.890625
40 GT1 0.564516 0.746032
41 PMH 0.56338 0.706667
42 PXG 0.551282 0.873016
43 PL4 0.551282 0.890625
44 0PR 0.551282 0.919355
45 RW2 0.551282 0.835821
46 7TS 0.533333 0.714286
47 AQ3 0.53012 0.876923
48 CKT 0.527778 0.857143
49 DCS 0.526316 0.746667
50 9YM 0.506329 0.818182
51 PL8 0.487805 0.791667
52 1D0 0.476744 0.835821
53 7B9 0.47619 0.826087
54 PLP 2KZ 0.473684 0.84127
55 PLP 0.46875 0.75
56 PLR 0.467742 0.704918
57 P0P 0.454545 0.75
58 PPG 0.452381 0.861538
59 OJQ 0.448718 0.688312
60 RMT 0.447059 0.776119
61 EVM 0.441558 0.796875
62 PZP 0.439394 0.754098
63 AN7 0.438356 0.754098
64 DOW 0.434343 0.838235
65 FOO 0.432432 0.790323
66 LCS 0.432099 0.688312
67 CAN PLP 0.428571 0.835821
68 FEV 0.428571 0.727273
69 2B6 0.426966 0.653846
70 PLP PMP 0.426471 0.819672
71 PL6 0.425 0.793651
72 0JO 0.421053 0.727273
73 4LM 0.421053 0.738462
74 GAB PLP 0.418605 0.828125
75 F0G 0.415584 0.774194
76 0LD 0.412371 0.627907
77 KOU 0.410256 0.809524
78 PLP CYS 0.4 0.873016
Ligand no: 2; Ligand: 8B3; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 8B3 1 1
2 8A0 0.795455 0.983333
3 8AU 0.769231 0.983607
4 G57 0.598131 0.867647
5 8A6 0.580357 0.686047
6 8A3 0.579439 0.694118
7 GCF 0.567568 0.842857
8 GI8 0.463636 0.774648
9 G6F 0.452991 0.842857
10 G45 0.447368 0.682927
11 8UO 0.431034 0.719512
12 N05 0.420168 0.719512
Similar Ligands (3D)
Ligand no: 1; Ligand: PLG; Similar ligands found: 41
No: Ligand Similarity coefficient
1 GLY PLP 0.9979
2 PLP GLY 0.9962
3 PLI 0.9743
4 PLP SER 0.9624
5 SER PLP 0.9582
6 PLP AOA 0.9423
7 EPC 0.9406
8 PLP ALO 0.9237
9 L7N 0.9094
10 MPM 0.9069
11 PLP 2TL 0.9003
12 HM5 0.8984
13 07U 0.8909
14 96X 0.8897
15 695 0.8812
16 PLP PUT 0.8809
17 LF5 0.8802
18 AKB PLP 0.8793
19 PM9 0.8776
20 9KQ 0.8755
21 MZC 0.8747
22 7CU 0.8742
23 2T4 0.8732
24 36I 0.8727
25 KB8 0.8717
26 EXT 0.8717
27 PLP MET 0.8712
28 MET PLP 0.8712
29 LJW 0.8659
30 6SC 0.8655
31 74U 0.8653
32 66P 0.8653
33 8HH 0.8647
34 HM4 0.8634
35 ROL 0.8617
36 C9Q 0.8612
37 K6B 0.8586
38 K6N 0.8565
39 6DF 0.8550
40 52X 0.8528
41 IRG 0.8525
Ligand no: 2; Ligand: 8B3; Similar ligands found: 3
No: Ligand Similarity coefficient
1 8Z1 0.9481
2 33G 0.9195
3 8UC 0.8622
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5GVL; Ligand: PLG; 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: 5gvl.bio2) has 40 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5GVL; Ligand: PLG; 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: 5gvl.bio2) has 40 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5GVL; Ligand: GI8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5gvl.bio2) has 40 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5GVL; Ligand: GI8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5gvl.bio2) has 40 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5GVL; Ligand: GI8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5gvl.bio1) has 40 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5GVL; Ligand: PLG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5gvl.bio1) has 39 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5GVL; Ligand: GI8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5gvl.bio1) has 39 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5GVL; Ligand: PLG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5gvl.bio1) has 40 residues
No: Leader PDB Ligand Sequence Similarity
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