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 209 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 175 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 (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: GOP; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 MO0 1 1
2 GOP 1 1
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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