Receptor
PDB id Resolution Class Description Source Keywords
6KNK 2.3 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF SBNH IN COMPLEX WITH CITRYL-DIAMINOETHA STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MUORGANISM_TAXID: 158878 PLP-DEPENDENT DECARBOXYLASE STAPHYLOFERRIN B BIOSYNTHETIC
Ref.: STRUCTURAL INSIGHTS INTO SUBSTRATE RECOGNITION AND REGULATION OF THE KEY DECARBOXYLASE SBNH IN STAPHYL BIOSYNTHESIS. J.MOL.BIOL. V. 431 4868 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DN9 A:501;
 Valid;
 none;
 submit data
465.349 C16 H24 N3 O11 P Cc1c(...
PO4 C:501;
B:501;
 Invalid;
Invalid;
 none;
none;
 submit data
94.971 O4 P [O-]P...
X3J B:502;
 Valid;
 none;
 submit data
234.207 C8 H14 N2 O6 C(CNC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6KNH 1.76 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF SBNH IN COMPLEX WITH CITRATE, A PLP-DEP DECARBOXYLASE IN STAPHYLOFERRIN B BIOTHESYNTHESIS STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MUORGANISM_TAXID: 158878 PLP-DEPENDENT DECARBOXYLASE STAPHYLOFERRIN B BIOSYNTHETIC
Ref.: STRUCTURAL INSIGHTS INTO SUBSTRATE RECOGNITION AND REGULATION OF THE KEY DECARBOXYLASE SBNH IN STAPHYL BIOSYNTHESIS. J.MOL.BIOL. V. 431 4868 2019
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 62 families.
1 6KNH ic50 = 280 uM CIT C6 H8 O7 C(C(=O)O)C....
2 6KNK - X3J C8 H14 N2 O6 C(CNC(=O)C....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 59 families.
1 6KNH ic50 = 280 uM CIT C6 H8 O7 C(C(=O)O)C....
2 6KNK - X3J C8 H14 N2 O6 C(CNC(=O)C....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 47 families.
1 6KNH ic50 = 280 uM CIT C6 H8 O7 C(C(=O)O)C....
2 6KNK - X3J C8 H14 N2 O6 C(CNC(=O)C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DN9; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 DN9 1 1
2 PLG 0.61039 0.855072
3 PLA 0.559524 0.833333
4 PL2 0.55814 0.76
5 P1T 0.53012 0.794521
6 CBA 0.528736 0.884058
7 EA5 0.52809 0.9
8 IK2 0.52381 0.819444
9 33P 0.52381 0.774648
10 PDD 0.511905 0.788732
11 PP3 0.511905 0.788732
12 PDA 0.511905 0.788732
13 PPD 0.511628 0.855072
14 PMG 0.505618 0.861111
15 2BK 0.5 0.814286
16 HEY 0.5 0.833333
17 2BO 0.5 0.814286
18 TLP 0.5 0.814286
19 76U 0.5 0.84507
20 5PA 0.5 0.84507
21 PLS 0.5 0.855072
22 N5F 0.494505 0.871429
23 PSZ 0.494505 0.705128
24 PDG 0.494382 0.884058
25 PGU 0.494382 0.884058
26 C6P 0.494253 0.828571
27 QLP 0.488889 0.914286
28 LPI 0.488889 0.824324
29 PY5 0.488636 0.833333
30 3LM 0.478261 0.763158
31 ORX 0.478261 0.84507
32 ILP 0.477778 0.791667
33 7XF 0.477778 0.857143
34 IN5 0.47619 0.760563
35 PY6 0.467391 0.810811
36 PXG 0.463158 0.753425
37 PE1 0.457447 0.84507
38 KAM 0.453608 0.819444
39 PMH 0.449438 0.746835
40 PXP 0.448718 0.710145
41 0PR 0.447917 0.816901
42 PL4 0.447917 0.84507
43 RW2 0.447917 0.773333
44 7TS 0.445652 0.753086
45 PMP 0.443038 0.742857
46 9YM 0.442105 0.780822
47 DCS 0.44086 0.807692
48 CKT 0.438202 0.763889
49 GT1 0.4375 0.666667
50 AQ3 0.435644 0.808219
51 PL8 0.428571 0.828947
52 7B9 0.42 0.789474
53 PPG 0.4 0.794521
Ligand no: 2; Ligand: X3J; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 X3J 1 1
2 SF8 0.471698 0.911111
Similar Ligands (3D)
Ligand no: 1; Ligand: DN9; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: X3J; Similar ligands found: 2
No: Ligand Similarity coefficient
1 55D 0.8880
2 ALA LYS 0.8593
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6KNH; Ligand: CIT; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 6knh.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 5GJO PLP 39.0863
2 5GJO PLP 39.0863
Pocket No.: 2; Query (leader) PDB : 6KNH; Ligand: CIT; 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: 6knh.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6KNH; Ligand: CIT; 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: 6knh.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6KNH; Ligand: CIT; 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: 6knh.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
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