Receptor
PDB id Resolution Class Description Source Keywords
3VGW 1.6 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF MONOAC-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;
E:1125;
F:1125;
G:1125;
H:1125;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NVZ A:1124;
B:1124;
C:1124;
D:1124;
E:1124;
F:1124;
G:1124;
H:1124;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
Ka = 200000 M^-1
286.347 C12 H18 N2 O4 S CC(=O...
SO4 A:1126;
A:1127;
B:1126;
C:1126;
C:1127;
D:1126;
E:1126;
E:1127;
F:1126;
G:1126;
G:1127;
H:1126;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
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 473 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 355 families.
1 1Y55 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
2 1Y52 Kd = 0.00000145 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 (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 272 families.
1 2JGS Kd = 10 fM BTN C10 H16 N2 O3 S C1[C@H]2[C....
2 1WBI - BTN C10 H16 N2 O3 S C1[C@H]2[C....
3 2A5C Kd = 24 uM 8DA C10 H15 N5 O4 C1[C@H]([C....
4 3VGW Ka = 200000 M^-1 NVZ C12 H18 N2 O4 S CC(=O)N1[C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NVZ; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 NVZ 1 1
2 VHI 0.582278 0.859375
3 Y7Y 0.56338 0.84375
4 NPK 0.494845 0.682927
5 BTQ 0.457143 0.75
6 BTN 0.457143 0.75
7 IMI 0.430556 0.609375
8 VHH 0.424658 0.854839
9 SHM 0.405405 0.75
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3VHH; Ligand: VHH; Similar sites found: 22
This union binding pocket(no: 1) in the query (biounit: 3vhh.bio1) has 54 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1O4T OXL 0.01102 0.45092 None
2 4IAW LIZ 0.0102 0.44844 None
3 4J25 OGA 0.004465 0.4792 1.31004
4 2OVD DAO 0.01861 0.44532 1.62602
5 3A16 PXO 0.03734 0.40379 1.62602
6 1TE2 PGA 0.03934 0.42612 4.06504
7 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.01252 0.42576 4.42478
8 5C3R AKG 0.02594 0.41322 4.87805
9 5C3R HMU 0.02594 0.41322 4.87805
10 5WSY 7UC 0.04211 0.41861 6.50407
11 4Y3O OGA 0.03053 0.431 7.31707
12 1OPB RET 0.03298 0.4052 7.31707
13 3UBQ SIA GAL 0.04116 0.40903 8.13008
14 1QIN GIP 0.007135 0.40793 9.7561
15 1N5S ADL 0.003187 0.46232 9.82143
16 5T96 79J 0.04783 0.41809 11.3821
17 2BOS GLA GAL GLC 0.01425 0.439 11.7647
18 2BOS GLA GAL 0.01293 0.43801 11.7647
19 1LFO OLA 0.03693 0.40278 13.0081
20 5BQS 4VN 0.03316 0.40789 13.8211
21 3H7J PPY 0.03446 0.41307 17.0732
22 4FFG LBS 0.02718 0.4062 20.3252
Pocket No.: 2; Query (leader) PDB : 3VHH; Ligand: VHH; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3VHH; Ligand: VHH; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3VHH; Ligand: VHH; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
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