Receptor
PDB id Resolution Class Description Source Keywords
5DJ3 2.23 Å EC: 3.-.-.- STRUCTURE OF THE PLP-DEPENDENT L-ARGININE HYDROXYLASE MPPP W ARGININE BOUND STREPTOMYCES WADAYAMENSIS AMINOTRANSFERASE HYDROXYLASE ENDURACIDIDINE PYRIDOXAL 5-prime -PHOSPHATE TRANSFERASE
Ref.: STREPTOMYCES WADAYAMENSIS MPPP IS A PYRIDOXAL 5'-PHOSPHATE-DEPENDENT L-ARGININE ALPHA-DEAMINASE, GAMMA-HYDROXYLASE IN THE ENDURACIDIDINE BIOSYNTHETI PATHWAY. BIOCHEMISTRY V. 54 7029 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5DK B:401;
C:500;
A:500;
D:500;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
403.328 C14 H22 N5 O7 P [H]/N...
MG B:402;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6C9B 1.69 Å EC: 3.-.-.- THE STRUCTURE OF MPPP SOAKED WITH THE PRODUCTS 4HKA AND 2KA STREPTOMYCES WADAYAMENSIS DIMER PRODUCT 4HKA BINDING COMPLEX OXIDASE PLP ANTIBIOTIOXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX
Ref.: STREPTOMYCES WADAYAMENSIS MPPP IS A PLP-DEPENDENT O NOT AN OXYGENASE. BIOCHEMISTRY V. 57 3252 2018
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 312 families.
1 5BK7 - EQJ C14 H22 N5 O7 P [H]/N=C(/N....
2 6C9B - EGV C6 H11 N3 O4 [H]/N=C(/N....
3 5DJ3 - 5DK C14 H22 N5 O7 P [H]/N=C(N)....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 261 families.
1 5BK7 - EQJ C14 H22 N5 O7 P [H]/N=C(/N....
2 6C9B - EGV C6 H11 N3 O4 [H]/N=C(/N....
3 5DJ3 - 5DK C14 H22 N5 O7 P [H]/N=C(N)....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 families.
1 5BK7 - EQJ C14 H22 N5 O7 P [H]/N=C(/N....
2 6C9B - EGV C6 H11 N3 O4 [H]/N=C(/N....
3 5DJ3 - 5DK C14 H22 N5 O7 P [H]/N=C(N)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 5DK; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 EQJ 1 1
2 5DK 1 1
3 PL5 0.7125 0.903226
4 PL6 0.679487 0.854839
5 KOU 0.671053 0.84127
6 PUS 0.630952 0.8
7 F0G 0.615385 0.806452
8 P70 0.593023 0.809524
9 EPC 0.584416 0.774194
10 FEJ 0.571429 0.769231
11 0JO 0.5625 0.784615
12 Q0P 0.55914 0.80303
13 Z98 0.552941 0.904762
14 PLT 0.53125 0.776119
15 SER PLP 0.529412 0.793651
16 4LM 0.52439 0.769231
17 6DF 0.523256 0.734375
18 FEV 0.511905 0.757576
19 EVM 0.505882 0.828125
20 P3D 0.488372 0.888889
21 PLP PHE 0.484211 0.75
22 PFM 0.483146 0.8125
23 MPM 0.482353 0.765625
24 EXT 0.481928 0.83871
25 FOO 0.481928 0.793651
26 PLP ALO 0.47191 0.75
27 AN7 0.46988 0.730159
28 PLP 999 0.466667 0.75
29 PLP PVH 0.464646 0.732394
30 P89 0.463158 0.757143
31 PLP 0.460526 0.725806
32 LUK 0.458333 0.72973
33 LUH 0.458333 0.72973
34 HCP 0.454545 0.784615
35 PZP 0.454545 0.758065
36 PL2 0.445652 0.878788
37 PLP ABU 0.434783 0.809524
38 GLY PLP 0.431818 0.761905
39 3QP 0.426966 0.758065
40 O1G 0.424242 0.714286
41 KET 0.423913 0.828125
42 PLP MYB 0.415842 0.689189
43 PLP PUT 0.413043 0.857143
44 PLS 0.406593 0.818182
45 ORX 0.40625 0.863636
46 C6P 0.402174 0.818182
47 PE1 0.402062 0.863636
48 LPI 0.4 0.763889
49 PP3 0.4 0.776119
50 PDA 0.4 0.776119
51 PDD 0.4 0.776119
52 QLP 0.4 0.8
Similar Ligands (3D)
Ligand no: 1; Ligand: 5DK; Similar ligands found: 1
No: Ligand Similarity coefficient
1 LJS 0.8596
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6C9B; Ligand: EGV; 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: 6c9b.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback