Receptor
PDB id Resolution Class Description Source Keywords
4BMK 1.62 Å EC: 2.3.1.50 SERINE PALMITOYLTRANSFERASE K265A FROM S. PAUCIMOBILIS WITH BOUND PLP-MYRIOCIN ALDIMINE SPHINGOMONAS PAUCIMOBILIS TRANSFERASE-ANTIBIOTIC COMPLEX TRANSFERASE EXTERNAL ALDIMIINHIBITOR SPHINGOLIPIDS NATURAL PRODUCT ANTIBIOTIC ISP-1
Ref.: THE CHEMICAL BASIS OF SERINE PALMITOYLTRANSFERASE INHIBITION BY MYRIOCIN. J.AM.CHEM.SOC. V. 135 14276 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PLP MYB A:1421;
B:1421;
 Valid;
Valid;
 none;
none;
 submit data
418.383 n/a P(=O)...
GOL A:1423;
A:1424;
 Invalid;
Invalid;
 none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2XBN 1.4 Å EC: 2.3.1.50 INHIBITION OF THE PLP-DEPENDENT ENZYME SERINE PALMITOYLTRANSFERASE BY CYCLOSERINE: EVIDENCE FOR A NOVEL D ECARBOXYLATIVE MECHANISM OF INACTIVATION SPHINGOMONAS PAUCIMOBILIS TRANSFERASE PYRIDOXAL PHOSPHATE
Ref.: INHIBITION OF THE PLP-DEPENDENT ENZYME SERINE PALMITOYLTRANSFERASE BY CYCLOSERINE: EVIDENCE FOR A NOVEL DECARBOXYLATIVE MECHANISM OF INACTIVATION. MOL.BIOSYSTEMS V. 6 1682 2010
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4BMK - PLP MYB n/a n/a
2 2XBN - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
3 2W8W - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
4 2W8J - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4BMK - PLP MYB n/a n/a
2 2XBN - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
3 2W8W - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
4 2W8J - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4BMK - PLP MYB n/a n/a
2 2XBN - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
3 2W8W - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
4 2W8J - PLS C11 H17 N2 O8 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PLP MYB; Similar ligands found: 24
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP MYB 1 1
2 SER PLP 0.564706 0.731343
3 PLP ALO 0.54023 0.716418
4 PLP 999 0.534091 0.716418
5 GLY PLP 0.5 0.676471
6 PLP PUT 0.494382 0.791045
7 PLP ABU 0.483516 0.720588
8 PLP PHE 0.469388 0.666667
9 KOU 0.460674 0.724638
10 EPC 0.453488 0.686567
11 PLP PVH 0.45098 0.657895
12 6DF 0.44086 0.676471
13 FEJ 0.43617 0.685714
14 F0G 0.433333 0.666667
15 PL5 0.428571 0.704225
16 PL6 0.425532 0.710145
17 5DK 0.415842 0.689189
18 EQJ 0.415842 0.689189
19 EVM 0.408602 0.73913
20 PLP 142 0.407407 0.702703
21 4LM 0.406593 0.638889
22 P89 0.405941 0.8
23 MPM 0.402174 0.731343
24 EXT 0.4 0.720588
Similar Ligands (3D)
Ligand no: 1; Ligand: PLP MYB; Similar ligands found: 1
No: Ligand Similarity coefficient
1 KAM 0.8742
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2XBN; Ligand: PMP; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 2xbn.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
1 5TXR PLP 42.1546
2 1DJ9 KAM 46.3542
Pocket No.: 2; Query (leader) PDB : 2XBN; Ligand: PMP; 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: 2xbn.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
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