Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:306;
A:301;
B:302;
A:304;
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)...
OP1 A:303;
B:301;
Valid;
Valid;
none;
none;
Kd = 0.57 uM
286.284 C11 H18 N4 O5 [H]/N...
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 (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 473 families.
1 4POW Kd = 0.57 uM OP1 C11 H18 N4 O5 [H]/N=C(N)....
2 5ITO Kd = 68.9 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
3 5ITP Kd = 6.1 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
4 4POX Kd = 3.7 uM 2W2 C11 H20 N4 O6 [H]/N=C(/N....
5 4PP0 - OP1 C11 H18 N4 O5 [H]/N=C(N)....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 355 families.
1 4POW Kd = 0.57 uM OP1 C11 H18 N4 O5 [H]/N=C(N)....
2 5ITO Kd = 68.9 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
3 5ITP Kd = 6.1 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
4 4POX Kd = 3.7 uM 2W2 C11 H20 N4 O6 [H]/N=C(/N....
5 4PP0 - OP1 C11 H18 N4 O5 [H]/N=C(N)....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 272 families.
1 4POW Kd = 0.57 uM OP1 C11 H18 N4 O5 [H]/N=C(N)....
2 5ITO Kd = 68.9 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
3 4PP0 - OP1 C11 H18 N4 O5 [H]/N=C(N)....
4 1LAH Kd = 30 nM ORN C5 H12 N2 O2 C(C[C@@H](....
5 1HPB Kd = 0.03 uM HIS C6 H10 N3 O2 c1c([nH+]c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: OP1; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 OP1 1 1
2 PCX 0.532258 0.875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4POW; Ligand: OP1; Similar sites found: 40
This union binding pocket(no: 1) in the query (biounit: 4pow.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1U9L ASN ARG PRO ILE LEU SER LEU 0.03463 0.40074 None
2 4GYW UDP 0.01183 0.40183 1.13208
3 5BNW 12V 0.01265 0.4017 1.13208
4 1O9U ADZ 0.005878 0.42037 1.88679
5 4MDB RLT 0.02685 0.40235 2.22222
6 1XFF GLU 0.008415 0.41491 2.5
7 3LE7 ADE 0.02725 0.40202 2.68199
8 3L4N GSH 0.01931 0.41169 3.14961
9 1NC4 DOF 0.0319 0.40102 3.61991
10 4REP FAD 0.006502 0.421 6.41509
11 2PR5 FMN 0.006233 0.406 6.81818
12 1GPE FAD 0.02313 0.4013 7.16981
13 4WXJ GLU 0.00004024 0.42997 8.30189
14 5WSY 7UC 0.0175 0.40758 12.4528
15 3FV1 DYH 0.00001817 0.51403 12.8906
16 4IO2 GLU 0.00001816 0.47331 13.7097
17 2PYY GLU 0.000002218 0.47806 14.9123
18 5O4F 8VE 0.0002978 0.43213 21.8868
19 2RC8 DSN 0.0002479 0.5004 22.2642
20 4KQP GLN 0.000001304 0.46467 23.2759
21 5CMK GLU 0.0001334 0.47328 23.9382
22 2YJP CYS 0.00007897 0.53712 27.9245
23 4DZ1 DAL 0.0000218 0.57106 31.6602
24 3OEN GLU 0.0005318 0.41122 32.8302
25 2Q89 6CS 0.0000293 0.44899 36.965
26 1XT8 CYS 0.0001451 0.40265 37.3585
27 5DEX GLY 0.000000827 0.47171 38.1132
28 2VHA GLU 0.00005015 0.44648 38.1132
29 5DEX 5E0 0.002071 0.42475 38.1132
30 2Q2A ARG 0.00000003139 0.55738 39.2453
31 1M5B BN1 0.00004726 0.56195 39.5437
32 5L9O GOP 0.0000007081 0.56394 39.6226
33 5IKB KAI 0.0001742 0.43291 40.856
34 5AA4 6X4 0.000001539 0.57009 41.1321
35 1II5 GLU 0.00009731 0.40655 42.0601
36 4G4P GLN 0.000004586 0.46109 42.623
37 4YMX ARG 0.000001306 0.49599 43.4615
38 2YLN CYS 0.001237 0.47591 43.7736
39 3N26 ARG 0.0000002527 0.51982 47.561
40 3VV5 SLZ 0.000000001216 0.75228 48.0769
Pocket No.: 2; Query (leader) PDB : 4POW; Ligand: OP1; Similar sites found: 2
This union binding pocket(no: 2) in the query (biounit: 4pow.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5SWI BMA 0.01007 0.40593 2.26415
2 2WA4 069 0.01653 0.40251 3.39623
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