Receptor
PDB id Resolution Class Description Source Keywords
5OT9 2.45 Å NON-ENZYME: BINDING STRUCTURE OF THE PERIPLASMIC BINDING PROTEIN (PBP) NOCT FROM A.TUMEFACIENS C58 IN COMPLEX WITH HISTOPINE. AGROBACTERIUM FABRUM STR. C58 AGROBACTERIUM TUMEFACIENS ARGININE BACTERIAL PROTEINS DNABACTERIAL GENE EXPRESSION REGULATION GENES LIGANDS PLANPLASMIDS PROTEIN BINDING
Ref.: STRUCTURAL BASIS FOR HIGH SPECIFICITY OF OCTOPINE B THE PLANT PATHOGEN AGROBACTERIUM TUMEFACIENS. SCI REP V. 7 18033 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AOZ B:301;
A:303;
Valid;
Valid;
none;
none;
Kd = 84.4 uM
227.217 C9 H13 N3 O4 CC(C(...
EDO A:302;
A:304;
A:305;
A:301;
A:306;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
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: AOZ; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 AOZ 1 1
2 8UX 0.678571 0.840909
3 8V0 0.517241 0.68
4 AVI 0.490566 0.673913
5 ALA HIS HIS 0.430769 0.795455
6 ALA HIS ALA 0.424242 0.727273
7 ALA HIS HIS ALA 0.411765 0.733333
Similar Ligands (3D)
Ligand no: 1; Ligand: AOZ; Similar ligands found: 28
No: Ligand Similarity coefficient
1 DY8 0.9213
2 PHY 0.8949
3 AVO 0.8943
4 7QD 0.8934
5 BZS 0.8929
6 AQQ 0.8921
7 HCA 0.8901
8 ALA DGL 0.8897
9 GVQ 0.8876
10 NLQ 0.8840
11 DG2 0.8811
12 0UT 0.8798
13 87L 0.8748
14 1PC 0.8731
15 NLG 0.8729
16 AQK 0.8707
17 2QE 0.8702
18 G01 0.8698
19 HCT 0.8698
20 G88 0.8661
21 M5B 0.8634
22 NZ3 0.8611
23 CIT 0.8606
24 KDO 0.8590
25 2OR 0.8571
26 GLY LEU 0.8570
27 PA5 0.8556
28 FLC 0.8526
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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