Receptor
PDB id Resolution Class Description Source Keywords
5OTC 2.2 Å NON-ENZYME: BINDING STRUCTURE OF THE PERIPLASMIC BINDING PROTEIN (PBP) NOCT FROM AGROBACTERIUM TUMEFACIENS C58 IN COMPLEX WITH NOROCTOPINIC AGROBACTERIUM FABRUM (STRAIN C58 / ATCORGANISM_TAXID: 176299 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
CL A:315;
A:311;
A:313;
A:312;
A:314;
A:308;
B:302;
A:317;
A:310;
A:316;
A:309;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
35.453 Cl [Cl-]
EDO A:304;
A:307;
A:306;
A:303;
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)...
PGE A:319;
 Invalid;
 none;
 submit data
150.173 C6 H14 O4 C(COC...
AQK A:301;
B:301;
 Valid;
Valid;
 none;
none;
 Kd = 23 uM
190.197 C7 H14 N2 O4 C(C[C...
PEG A:318;
 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: AQK; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 AQK 1 1
2 AOR 0.487805 0.72973
3 AQQ 0.465116 0.823529
4 SUO 0.456522 0.857143
Similar Ligands (3D)
Ligand no: 1; Ligand: AQK; Similar ligands found: 54
No: Ligand Similarity coefficient
1 HCA 0.9434
2 BRR 0.9340
3 NIG 0.9298
4 GLY MET 0.9189
5 NLQ 0.9153
6 ALA GLN 0.9133
7 OKM 0.9108
8 GLY LEU 0.9105
9 NLG 0.9090
10 HJ7 0.9077
11 GPE 0.9057
12 ALA GLU 0.9057
13 0GY 0.9017
14 FLC 0.9015
15 ALA DGL 0.9010
16 G88 0.9001
17 HCT 0.8996
18 EKN 0.8971
19 CIT 0.8960
20 DG2 0.8955
21 ALA LYS 0.8951
22 5XR 0.8936
23 CDT 0.8935
24 ASF 0.8915
25 ALA LEU 0.8912
26 692 0.8900
27 C26 0.8898
28 G01 0.8891
29 AME 0.8865
30 ALA ZGL 0.8857
31 NFQ 0.8848
32 JAA 0.8842
33 1X7 0.8831
34 NQM 0.8829
35 X1R 0.8811
36 IN2 0.8809
37 ICT 0.8800
38 VPR 0.8792
39 RSM 0.8771
40 M1C 0.8769
41 CIL 0.8739
42 7QD 0.8724
43 TNG 0.8721
44 AOZ 0.8707
45 TRA 0.8704
46 AVO 0.8698
47 DY8 0.8693
48 P4B 0.8678
49 TRC 0.8674
50 1AL 0.8635
51 3MF 0.8634
52 3S6 0.8615
53 AE5 0.8552
54 0CG 0.8546
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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