Receptor
PDB id Resolution Class Description Source Keywords
4POW 1.55 Å NON-ENZYME: BINDING STRUCTURE OF THE PBP NOCT IN COMPLEX WITH PYRONOPALINE AGROBACTERIUM TUMEFACIENS PBP CLASS F TRANSPORT PROTEIN
Ref.: AGROBACTERIUM USES A UNIQUE LIGAND-BINDING MODE FOR OPINES AND ACQUIRING A COMPETITIVE ADVANTAGE IN THE CONSTRUCTION ON PLANT HOST. PLOS PATHOG. V. 10 04444 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:306;
A:301;
B:302;
A:304;
A:302;
A:305;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
OP1 A:303;
B:301;
Valid;
Valid;
none;
none;
Kd = 0.57 uM
286.284 C11 H18 N4 O5 [H]/N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4POW 1.55 Å NON-ENZYME: BINDING STRUCTURE OF THE PBP NOCT IN COMPLEX WITH PYRONOPALINE AGROBACTERIUM TUMEFACIENS PBP CLASS F TRANSPORT PROTEIN
Ref.: AGROBACTERIUM USES A UNIQUE LIGAND-BINDING MODE FOR OPINES AND ACQUIRING A COMPETITIVE ADVANTAGE IN THE CONSTRUCTION ON PLANT HOST. PLOS PATHOG. V. 10 04444 2014
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 510 families.
1 5OT8 Kd = 52 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
2 5OT9 Kd = 84.4 uM AOZ C9 H13 N3 O4 CC(C(=O)O)....
3 5OTC Kd = 23 uM AQK C7 H14 N2 O4 C(C[C@@H](....
4 4POW Kd = 0.57 uM OP1 C11 H18 N4 O5 [H]/N=C(N)....
5 5ITO Kd = 68.9 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
6 5ITP Kd = 6.1 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
7 4POX Kd = 3.7 uM 2W2 C11 H20 N4 O6 [H]/N=C(/N....
8 5OTA Kd = 4.4 uM AQQ C8 H16 N2 O4 C[C@H](C(=....
9 4PP0 - OP1 C11 H18 N4 O5 [H]/N=C(N)....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 391 families.
1 5OT8 Kd = 52 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
2 5OT9 Kd = 84.4 uM AOZ C9 H13 N3 O4 CC(C(=O)O)....
3 5OTC Kd = 23 uM AQK C7 H14 N2 O4 C(C[C@@H](....
4 4POW Kd = 0.57 uM OP1 C11 H18 N4 O5 [H]/N=C(N)....
5 5ITO Kd = 68.9 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
6 5ITP Kd = 6.1 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
7 4POX Kd = 3.7 uM 2W2 C11 H20 N4 O6 [H]/N=C(/N....
8 5OTA Kd = 4.4 uM AQQ C8 H16 N2 O4 C[C@H](C(=....
9 4PP0 - OP1 C11 H18 N4 O5 [H]/N=C(N)....
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 149 families.
1 1WDN Kd = 0.5 uM GLN C5 H10 N2 O3 C(CC(=O)N)....
2 4POW Kd = 0.57 uM OP1 C11 H18 N4 O5 [H]/N=C(N)....
3 5ITO Kd = 68.9 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
4 5ITP Kd = 6.1 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
5 4POX Kd = 3.7 uM 2W2 C11 H20 N4 O6 [H]/N=C(/N....
6 5OTA Kd = 4.4 uM AQQ C8 H16 N2 O4 C[C@H](C(=....
7 4PP0 - OP1 C11 H18 N4 O5 [H]/N=C(N)....
8 2Y7I - ARG C6 H15 N4 O2 C(C[C@@H](....
9 4G4P Kd = 0.13 uM GLN C5 H10 N2 O3 C(CC(=O)N)....
10 2PVU Kd = 0.49 uM LYS C6 H15 N2 O2 C(CC[NH3+]....
11 2Q2C Kd = 0.42 uM HIS C6 H10 N3 O2 c1c([nH+]c....
12 4YMX Kd = 79 nM ARG C6 H15 N4 O2 C(C[C@@H](....
13 1LST - LYS C6 H15 N2 O2 C(CC[NH3+]....
14 1LAF Kd = 14 nM ARG C6 H15 N4 O2 C(C[C@@H](....
15 5OWF Kd = 1.59 uM GLN C5 H10 N2 O3 C(CC(=O)N)....
16 1LAH Kd = 30 nM ORN C5 H12 N2 O2 C(C[C@@H](....
17 2PYY Kd = 0.2 uM GLU C5 H9 N O4 C(CC(=O)O)....
18 1HSL Kd = 0.064 uM HIS C6 H10 N3 O2 c1c([nH+]c....
19 1HPB Kd = 0.03 uM HIS C6 H10 N3 O2 c1c([nH+]c....
20 3VV5 - SLZ C5 H12 N2 O2 S C(CSC[C@@H....
21 3VVE - LYS C6 H15 N2 O2 C(CC[NH3+]....
22 3VVF - ARG C6 H15 N4 O2 C(C[C@@H](....
23 3VVD - ORN C5 H12 N2 O2 C(C[C@@H](....
24 5L9O Kd = 4 uM GOP C11 H22 N2 O8 C(CC(=O)N)....
25 4ZV1 Kd = 5.7 uM ARG C6 H15 N4 O2 C(C[C@@H](....
26 4ZV2 Kd = 1.2 mM GLN C5 H10 N2 O3 C(CC(=O)N)....
27 5ORG Kd = 9 nM 6DB C9 H18 N4 O4 [H]/N=C(/N....
28 4KQP Kd = 1.49 uM GLN C5 H10 N2 O3 C(CC(=O)N)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: OP1; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 OP1 1 1
2 PCX 0.532258 0.875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4POW; Ligand: OP1; 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: 4pow.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4POW; Ligand: OP1; 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: 4pow.bio2) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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