Receptor
PDB id Resolution Class Description Source Keywords
3VHM 2 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF NPC-BIOTIN-AVIDIN COMPLEX GALLUS GALLUS BETA BARREL BIOTIN-BINDING PROTEIN
Ref.: RATIONAL DEVELOPMENT OF CAGED-BIOTIN PROTEIN-LABELI AND SOME APPLICATIONS IN LIVE CELLS CHEM.BIOL. V. 18 1261 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG A:1125;
B:1125;
C:1125;
D:1125;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
221.208 C8 H15 N O6 CC(=O...
NPK A:1124;
B:1124;
C:1124;
D:1124;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 Ka = 15000 M^-1
481.476 C20 H23 N3 O9 S C[C@H...
SO4 A:1126;
A:1127;
B:1126;
B:1127;
C:1127;
D:1126;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3VHH 2.26 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF DIME-BIOTIN-AVIDIN COMPLEX GALLUS GALLUS BETA BARREL BIOTIN-BINDING PROTEIN
Ref.: RATIONAL DEVELOPMENT OF CAGED-BIOTIN PROTEIN-LABELI AND SOME APPLICATIONS IN LIVE CELLS CHEM.BIOL. V. 18 1261 2011
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 552 families.
1 3VHH Ka = 400000000 M^-1 VHH C12 H20 N2 O3 S CN1[C@H]2C....
2 2A5B Kd = 117 uM 8HG C10 H13 N5 O5 C1[C@@H]([....
3 3VHM Ka = 15000 M^-1 NPK C20 H23 N3 O9 S C[C@H](c1c....
4 5IRU - B9P C26 H24 N2 O2 S c1cc2ccc3c....
5 1LDO - SNR C9 H14 N2 O3 S C1[C@H]2[C....
6 2A5C Kd = 24 uM 8DA C10 H15 N5 O4 C1[C@H]([C....
7 3VGW Ka = 200000 M^-1 NVZ C12 H18 N2 O4 S CC(=O)N1[C....
8 1IJ8 - BNI C16 H20 N4 O4 S c1cc(ccc1N....
9 3VHI Ka = 2300000 M^-1 VHI C18 H22 N2 O5 S c1ccc(cc1)....
10 2A8G Kd = 205 uM GNG C10 H13 N5 O4 c1nc2c(n1[....
11 4I60 Kd = 1.87 uM B1R C20 H16 N2 O2 Ru S C1[C@H]2[C....
12 5IRW - D9P C26 H26 N2 O2 C[C@H]1[C@....
70% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 426 families.
1 1Y55 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
2 1Y52 Kd = 0.000000064 M BTN C10 H16 N2 O3 S C1[C@H]2[C....
3 2FHN - BNI C16 H20 N4 O4 S c1cc(ccc1N....
4 2OF8 - BNI C16 H20 N4 O4 S c1cc(ccc1N....
5 2FHL - BNI C16 H20 N4 O4 S c1cc(ccc1N....
6 2OFB - BNI C16 H20 N4 O4 S c1cc(ccc1N....
7 1WBI - BTN C10 H16 N2 O3 S C1[C@H]2[C....
8 3VHH Ka = 400000000 M^-1 VHH C12 H20 N2 O3 S CN1[C@H]2C....
9 2A5B Kd = 117 uM 8HG C10 H13 N5 O5 C1[C@@H]([....
10 3VHM Ka = 15000 M^-1 NPK C20 H23 N3 O9 S C[C@H](c1c....
11 5IRU - B9P C26 H24 N2 O2 S c1cc2ccc3c....
12 1LDO - SNR C9 H14 N2 O3 S C1[C@H]2[C....
13 2A5C Kd = 24 uM 8DA C10 H15 N5 O4 C1[C@H]([C....
14 3VGW Ka = 200000 M^-1 NVZ C12 H18 N2 O4 S CC(=O)N1[C....
15 1IJ8 - BNI C16 H20 N4 O4 S c1cc(ccc1N....
16 3VHI Ka = 2300000 M^-1 VHI C18 H22 N2 O5 S c1ccc(cc1)....
17 2A8G Kd = 205 uM GNG C10 H13 N5 O4 c1nc2c(n1[....
18 4I60 Kd = 1.87 uM B1R C20 H16 N2 O2 Ru S C1[C@H]2[C....
19 5IRW - D9P C26 H26 N2 O2 C[C@H]1[C@....
20 2C1S - BSO C10 H16 N2 O4 S C1[C@H]2[C....
21 2C1Q Kd ~ 0.1 pM BTN C10 H16 N2 O3 S C1[C@H]2[C....
22 2UYW - BTN C10 H16 N2 O3 S C1[C@H]2[C....
23 2UZ2 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
24 4BCS Kd = 103 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 322 families.
1 1RXJ - BNI C16 H20 N4 O4 S c1cc(ccc1N....
2 1SWK Ka = 100000000000000 M^-1 BTN C10 H16 N2 O3 S C1[C@H]2[C....
3 2RTR - IMI C10 H17 N3 O2 S C1[C@H]2[C....
4 4CPI - LH4 C36 H44 N6 O8 S3 c1cc(c(c(c....
5 2RTD - BTN C10 H16 N2 O3 S C1[C@H]2[C....
6 3WYQ - BTN C10 H16 N2 O3 S C1[C@H]2[C....
7 2RTK - GLL C4 H6 N4 O2 C12C(NC(=O....
8 1LCZ - BH7 C16 H27 N3 O4 S C1[C@H]2[C....
9 6VJK Kd = 0.000000064 M BTN C10 H16 N2 O3 S C1[C@H]2[C....
10 1SWN Ka = 100000000000000 M^-1 BTN C10 H16 N2 O3 S C1[C@H]2[C....
11 1RST Kd = 37 uM ALA TRP ARG HIS PRO GLN PHE GLY GLY n/a n/a
12 2RTG - BTN C10 H16 N2 O3 S C1[C@H]2[C....
13 1Y55 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
14 1Y52 Kd = 0.000000064 M BTN C10 H16 N2 O3 S C1[C@H]2[C....
15 2FHN - BNI C16 H20 N4 O4 S c1cc(ccc1N....
16 1WBI - BTN C10 H16 N2 O3 S C1[C@H]2[C....
17 3WZQ Kd = 0.000000064 M ZOF C16 H28 N4 O3 S [H]/N=C/1N....
18 3VHH Ka = 400000000 M^-1 VHH C12 H20 N2 O3 S CN1[C@H]2C....
19 2A5B Kd = 117 uM 8HG C10 H13 N5 O5 C1[C@@H]([....
20 3VHM Ka = 15000 M^-1 NPK C20 H23 N3 O9 S C[C@H](c1c....
21 5IRU - B9P C26 H24 N2 O2 S c1cc2ccc3c....
22 1LDO - SNR C9 H14 N2 O3 S C1[C@H]2[C....
23 2QCB - KYS C24 H31 Cl N5 O4 Ru S2 c1cc(ccc1N....
24 5IRA - 9RU C31 H41 Cl2 N5 O2 Ru S Cc1cc(c(c(....
25 2C1S - BSO C10 H16 N2 O4 S C1[C@H]2[C....
26 2C1Q Kd ~ 0.1 pM BTN C10 H16 N2 O3 S C1[C@H]2[C....
27 4BJ8 Kd = 5.13 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NPK; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 NPK 1 1
2 NVZ 0.494845 0.682927
3 VHI 0.472727 0.7625
4 Y7Y 0.423077 0.666667
Similar Ligands (3D)
Ligand no: 1; Ligand: NPK; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3VHH; Ligand: VHH; 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: 3vhh.bio1) has 54 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3VHH; Ligand: VHH; 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: 3vhh.bio1) has 51 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3VHH; Ligand: VHH; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3vhh.bio1) has 54 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3VHH; Ligand: VHH; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3vhh.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
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