Receptor
PDB id Resolution Class Description Source Keywords
5itp 1.85 Å NON-ENZYME: BINDING STRUCTURE OF THE PERIPLASMIC BINDING PROTEIN NOCT FROM A.TUM IN COMPLEX WITH OCTOPINE AGROBACTERIUM FABRUM PERIPLASMIC BINDING PROTEIN OPINE MEMBRANE PROTEIN
Ref.: FITNESS COSTS RESTRICT NICHE EXPANSION BY GENERALIS NICHE-CONSTRUCTING PATHOGENS. ISME J V. 11 374 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:304;
A:303;
A:307;
A:308;
A:302;
A:305;
A:306;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
6DB B:301;
A:301;
Valid;
Valid;
none;
none;
Kd = 9.9 uM
246.264 C9 H18 N4 O4 [H]/N...
PEG A:309;
Invalid;
none;
submit data
106.12 C4 H10 O3 C(COC...
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 552 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 = 0.58 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 = 9.9 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 426 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 = 0.58 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 = 9.9 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 (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: 6DB; Similar ligands found: 10
No: Ligand ECFP6 Tc MDL keys Tc
1 6DB 1 1
2 2W2 0.6 0.897436
3 AAG 0.583333 0.9
4 AQQ 0.577778 0.810811
5 M3R 0.54902 0.770833
6 CMA 0.519231 0.833333
7 SUG 0.490909 0.833333
8 L06 0.489796 0.731707
9 G3M 0.45098 0.804878
10 HRG 0.411765 0.842105
Similar Ligands (3D)
Ligand no: 1; Ligand: 6DB; Similar ligands found: 2
No: Ligand Similarity coefficient
1 ALA ARG 0.9258
2 PCX 0.8700
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: 1
This union binding pocket(no: 1) in the query (biounit: 4pow.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 3VV5 SLZ 48.0769
Pocket No.: 2; Query (leader) PDB : 4POW; Ligand: OP1; Similar sites found with APoc: 8
This union binding pocket(no: 2) in the query (biounit: 4pow.bio2) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 7A99 ARG 38.9706
2 7A99 ARG 38.9706
3 2Q2A ARG 39.2453
4 2Q2A ARG 39.2453
5 2Q2A ARG 39.2453
6 2Q2A ARG 39.2453
7 3VV5 SLZ 48.0769
8 3VV5 SLZ 48.0769
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