Receptor
PDB id Resolution Class Description Source Keywords
5L9O 1.84 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTURE OF AGROBACTERIUM TUMEFACIENS C58 STRAIN PB COMPLEX WITH GLUCOPINE AGROBACTERIUM FABRUM (STRAIN C58 / ATCORGANISM_TAXID: 176299 PERIPLASMIC BINDING PROTEIN ABC TRANSPORTER SYNTHETIC OPINTRANSPORT PROTEIN
Ref.: STRUCTURAL BASIS FOR HIGH SPECIFICITY OF AMADORI CO AND MANNOPINE OPINE BINDING IN BACTERIAL PATHOGENS. J.BIOL.CHEM. V. 291 22638 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOP B:301;
A:301;
 Valid;
Valid;
 none;
none;
 Kd = 4 uM
310.301 C11 H22 N2 O8 C(CC(...
EDO A:304;
B:302;
B:305;
A:303;
A:307;
A:302;
A:305;
B:303;
A:306;
B:304;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
CA B:306;
A:308;
 Invalid;
Invalid;
 none;
none;
 submit data
40.078 Ca [Ca+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5L9O 1.84 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTURE OF AGROBACTERIUM TUMEFACIENS C58 STRAIN PB COMPLEX WITH GLUCOPINE AGROBACTERIUM FABRUM (STRAIN C58 / ATCORGANISM_TAXID: 176299 PERIPLASMIC BINDING PROTEIN ABC TRANSPORTER SYNTHETIC OPINTRANSPORT PROTEIN
Ref.: STRUCTURAL BASIS FOR HIGH SPECIFICITY OF AMADORI CO AND MANNOPINE OPINE BINDING IN BACTERIAL PATHOGENS. J.BIOL.CHEM. V. 291 22638 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 232 families.
1 5LOM - SNW C11 H20 N2 O8 C1[C@H]([C....
2 5L9O Kd = 4 uM GOP C11 H22 N2 O8 C(CC(=O)N)....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 197 families.
1 5LOM - SNW C11 H20 N2 O8 C1[C@H]([C....
2 5L9O Kd = 4 uM GOP C11 H22 N2 O8 C(CC(=O)N)....
50% Homology Family (46)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 165 families.
1 1WDN Kd = 0.5 uM GLN C5 H10 N2 O3 C(CC(=O)N)....
2 6MLA Kd = 42 uM ARG C6 H15 N4 O2 C(C[C@@H](....
3 1LAG Kd = 500 nM HIS C6 H10 N3 O2 c1c([nH+]c....
4 6MLI Kd = 3700 uM HIS C6 H10 N3 O2 c1c([nH+]c....
5 6MLO Kd = 0.8 uM ARG C6 H15 N4 O2 C(C[C@@H](....
6 6MLN Kd = 29 nM ARG C6 H15 N4 O2 C(C[C@@H](....
7 6ML9 Kd = 5 uM ARG C6 H15 N4 O2 C(C[C@@H](....
8 6MKW Kd = 17 uM HIS C6 H10 N3 O2 c1c([nH+]c....
9 6MLG Kd = 9 uM ARG C6 H15 N4 O2 C(C[C@@H](....
10 6MLP Kd = 200 uM HIS C6 H10 N3 O2 c1c([nH+]c....
11 1LST - LYS C6 H15 N2 O2 C(CC[NH3+]....
12 1LAF Kd = 14 nM ARG C6 H15 N4 O2 C(C[C@@H](....
13 5OWF Kd = 1.59 uM GLN C5 H10 N2 O3 C(CC(=O)N)....
14 6MKU Kd = 70 nM ARG C6 H15 N4 O2 C(C[C@@H](....
15 6MLJ Kd = 55 nM ARG C6 H15 N4 O2 C(C[C@@H](....
16 6MLE Kd = 1 nM ARG C6 H15 N4 O2 C(C[C@@H](....
17 1LAH Kd = 30 nM ORN C5 H12 N2 O2 C(C[C@@H](....
18 6A8S Kd = 0.000000064 M CYS C3 H7 N O2 S C([C@@H](C....
19 6A80 Kd = 0.000000064 M CYS C3 H7 N O2 S C([C@@H](C....
20 6AA1 - CIT C6 H8 O7 C(C(=O)O)C....
21 5OT8 Kd = 52 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
22 5OT9 Kd = 84.4 uM AOZ C9 H13 N3 O4 CC(C(=O)O)....
23 5OTC Kd = 23 uM AQK C7 H14 N2 O4 C(C[C@@H](....
24 4POW Kd = 0.58 uM OP1 C11 H18 N4 O5 [H]/N=C(N)....
25 5ITO Kd = 68.9 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
26 5ITP Kd = 9.9 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
27 4POX Kd = 3.7 uM 2W2 C11 H20 N4 O6 [H]/N=C(/N....
28 5OTA Kd = 4.4 uM AQQ C8 H16 N2 O4 C[C@H](C(=....
29 4PP0 - OP1 C11 H18 N4 O5 [H]/N=C(N)....
30 6SVF - ARG C6 H15 N4 O2 C(C[C@@H](....
31 6Q3U - ARG C6 H15 N4 O2 C(C[C@@H](....
32 2Y7I - ARG C6 H15 N4 O2 C(C[C@@H](....
33 4G4P Kd = 0.13 uM GLN C5 H10 N2 O3 C(CC(=O)N)....
34 2PVU Kd = 0.49 uM LYS C6 H15 N2 O2 C(CC[NH3+]....
35 2Q2C Kd = 0.42 uM HIS C6 H10 N3 O2 c1c([nH+]c....
36 4YMX Kd = 79 nM ARG C6 H15 N4 O2 C(C[C@@H](....
37 2PYY Kd = 0.000023 M GLU C5 H9 N O4 C(CC(=O)O)....
38 1HSL Kd = 0.064 uM HIS C6 H10 N3 O2 c1c([nH+]c....
39 1HPB Kd = 0.03 uM HIS C6 H10 N3 O2 c1c([nH+]c....
40 3VVF - ARG C6 H15 N4 O2 C(C[C@@H](....
41 3VVD - ORN C5 H12 N2 O2 C(C[C@@H](....
42 5L9O Kd = 4 uM GOP C11 H22 N2 O8 C(CC(=O)N)....
43 4ZV1 Kd = 5.73 uM ARG C6 H15 N4 O2 C(C[C@@H](....
44 4ZV2 Kd = 1170 uM GLN C5 H10 N2 O3 C(CC(=O)N)....
45 5ORG Kd = 0.009 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
46 4KQP Kd = 0.9 uM GLN C5 H10 N2 O3 C(CC(=O)N)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GOP; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 GOP 1 1
2 MO0 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: GOP; Similar ligands found: 3
No: Ligand Similarity coefficient
1 N7T 0.9927
2 SNW 0.9217
3 N72 0.9170
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5L9O; Ligand: GOP; 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: 5l9o.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5L9O; Ligand: GOP; 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: 5l9o.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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