Receptor
PDB id Resolution Class Description Source Keywords
1LDO 2.2 Å NON-ENZYME: BINDING AVIDIN-NORBIOITN COMPLEX GALLUS GALLUS AVIDIN STREPTAVIDIN BIOTIN HIGH AFFINITY SYSTEMS LIGAND UNKNOWN FUNCTION
Ref.: LIGAND EXCHANGE BETWEEN PROTEINS: EXCHANGE OF BIOTI BIOTIN DERIVATIVES BETWEEN AVIDIN AND STREPTAVIDIN J.BIOL.CHEM. V. 277 30892 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SNR A:150;
B:350;
 Valid;
Valid;
 none;
none;
 submit data
230.284 C9 H14 N2 O3 S C1[C@...
NAG A:151;
B:352;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
221.208 C8 H15 N O6 CC(=O...
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: SNR; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 SNR 1 1
2 BTQ 0.807692 1
3 BTN 0.807692 1
4 SHM 0.777778 1
5 BH7 0.626866 0.921569
6 BTI 0.586207 0.914894
7 BYT 0.513158 0.87037
8 IMI 0.507937 0.803922
9 B1R 0.506849 0.632353
10 BNI 0.486842 0.656716
11 41M 0.486842 0.830189
12 B9P 0.440476 0.796296
13 LUV 0.420455 0.745763
14 ZOF 0.410256 0.833333
15 LH3 0.402174 0.666667
Similar Ligands (3D)
Ligand no: 1; Ligand: SNR; Similar ligands found: 65
No: Ligand Similarity coefficient
1 BSO 0.9415
2 DTB 0.9239
3 VHH 0.9093
4 SN0 0.9080
5 ZIP 0.8973
6 WA2 0.8903
7 C9M 0.8887
8 H35 0.8879
9 ARG 0.8875
10 ZZU 0.8834
11 FER 0.8827
12 EXY 0.8826
13 4FE 0.8825
14 SAZ 0.8794
15 ZEA 0.8785
16 3IP 0.8778
17 IJ6 0.8778
18 YIP 0.8774
19 0OP 0.8770
20 FSA 0.8767
21 ZEZ 0.8757
22 NFZ 0.8753
23 8BD 0.8736
24 SB9 0.8734
25 6HN 0.8733
26 F6P 0.8716
27 BSA 0.8713
28 12R 0.8703
29 PAU 0.8699
30 HWH 0.8697
31 N7I 0.8689
32 EMU 0.8684
33 NPI 0.8683
34 6C9 0.8680
35 FB6 0.8676
36 0QA 0.8671
37 CIR 0.8670
38 GJK 0.8668
39 5WN 0.8668
40 A18 0.8662
41 S2C 0.8661
42 GHQ 0.8655
43 4U7 0.8651
44 ASE 0.8647
45 G3M 0.8643
46 MPP 0.8637
47 4Z9 0.8636
48 I2E 0.8634
49 58X 0.8631
50 QUB 0.8627
51 14W 0.8616
52 4ZF 0.8612
53 CIY 0.8611
54 250 0.8602
55 QR4 0.8601
56 LPA 0.8600
57 6C5 0.8600
58 MBP 0.8580
59 HAR 0.8574
60 LAH 0.8565
61 6Q3 0.8564
62 G30 0.8546
63 HRG 0.8545
64 NAL 0.8513
65 2OR 0.8506
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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