Receptor
PDB id Resolution Class Description Source Keywords
1IJ8 2 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF LITE AVIDIN-BNI COMPLEX GALLUS GALLUS AVIDIN STREPTAVIDIN PSEUDO ENZYMATIC ACTIVITY UNKNOWN FUN
Ref.: CHICKEN AVIDIN EXHIBITS PSEUDO-CATALYTIC PROPERTIES BIOCHEMICAL, STRUCTURAL, AND ELECTROSTATIC CONSEQUE J.BIOL.CHEM. V. 276 32031 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BNI A:501;
B:502;
Valid;
Valid;
none;
none;
submit data
364.419 C16 H20 N4 O4 S c1cc(...
NAG A:401;
B:402;
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 544 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 420 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 (118)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 319 families.
1 2G5L - FME ASP VAL GLU ALA TRP LEU n/a n/a
2 3WZO - ZOE C16 H27 N3 O5 S C1[C@H]2[C....
3 2RTM - IMI C10 H17 N3 O2 S C1[C@H]2[C....
4 4Y59 Kd = 5.8 uM T21 C14 H8 F3 N O2 c1cc(cc(c1....
5 1NQM - BTN C10 H16 N2 O3 S C1[C@H]2[C....
6 1VWQ - HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
7 1NC9 - IMI C10 H17 N3 O2 S C1[C@H]2[C....
8 2RTI - GLL C4 H6 N4 O2 C12C(NC(=O....
9 5B5G Kd = 5.6 uM 6FX C14 H10 N2 O4 COC(=O)c1c....
10 4Y5D Kd = 1.2 uM MT6 C15 H11 N O4 COC(=O)c1c....
11 1SRJ - NAB C17 H12 N2 O3 c1ccc2c(c1....
12 4CPF - LH3 C32 H34 N4 O6 S COC(=O)c1c....
13 1NDJ - BTN C10 H16 N2 O3 S C1[C@H]2[C....
14 2IZL Kd = 1 uM IMI C10 H17 N3 O2 S C1[C@H]2[C....
15 2RTJ - GLL C4 H6 N4 O2 C12C(NC(=O....
16 1SWR Kd = 0.12 uM BTN C10 H16 N2 O3 S C1[C@H]2[C....
17 1SWE - BTN C10 H16 N2 O3 S C1[C@H]2[C....
18 1SRF - MTB C17 H18 N2 O3 CC(C)(C)c1....
19 1VWF Kd = 2200 nM ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
20 2RTO - IMI C10 H17 N3 O2 S C1[C@H]2[C....
21 1SWT - BTN C10 H16 N2 O3 S C1[C@H]2[C....
22 1SWP Ka = 100000000 M^-1 BTN C10 H16 N2 O3 S C1[C@H]2[C....
23 1VWG - ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
24 6M9B - BTN C10 H16 N2 O3 S C1[C@H]2[C....
25 2RTF - BTN C10 H16 N2 O3 S C1[C@H]2[C....
26 1VWC - ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
27 1STS Kd = 10 uM PHE CYS HIS PRO GLN ASN THR NH2 n/a n/a
28 2IZI - BTN C10 H16 N2 O3 S C1[C@H]2[C....
29 1VWN Kd = 1500 nM ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
30 2IZF - BTN C10 H16 N2 O3 S C1[C@H]2[C....
31 1SWD - BTN C10 H16 N2 O3 S C1[C@H]2[C....
32 1LCW - SHM C11 H18 N2 O3 S C1[C@H]2[C....
33 1RXK - BNI C16 H20 N4 O4 S c1cc(ccc1N....
34 1SRG Ka = 200000 M^-1 MHB C14 H12 N2 O3 Cc1cc(ccc1....
35 1I9H - BNI C16 H20 N4 O4 S c1cc(ccc1N....
36 1VWR - HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
37 2IZH - BTN C10 H16 N2 O3 S C1[C@H]2[C....
38 2RTP - IMI C10 H17 N3 O2 S C1[C@H]2[C....
39 1SLD Kd = 270 nM ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
40 1KL3 Kd = 1.37 uM ASN TRP SER HIS PRO GLN PHE GLU LYS n/a n/a
41 1DF8 Kd = 0.2 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
42 3T6F - BTN C10 H16 N2 O3 S C1[C@H]2[C....
43 1VWO - ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
44 1VWK - HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
45 1SLG Kd = 125 uM PHE SER HIS PRO GLN ASN THR n/a n/a
46 2RTQ - IMI C10 H17 N3 O2 S C1[C@H]2[C....
47 1N43 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
48 3WZN - BTN C10 H16 N2 O3 S C1[C@H]2[C....
49 1VWD - ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
50 2Y3F - BTN C10 H16 N2 O3 S C1[C@H]2[C....
51 1VWL Kd = 2.33 uM HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
52 1VWA - PHE SER HIS PRO GLN ASN THR n/a n/a
53 2IZG - BTN C10 H16 N2 O3 S C1[C@H]2[C....
54 3MG5 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
55 1SRI Ka = 1200000 M^-1 DMB C15 H14 N2 O3 Cc1cc(cc(c....
56 1KL5 Kd = 1.02 uM ASN TRP SER HIS PRO GLN PHE GLU LYS n/a n/a
57 1VWH - ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
58 1PTS - PHE SER HIS PRO GLN ASN THR n/a n/a
59 1MK5 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
60 1LUQ - BTN C10 H16 N2 O3 S C1[C@H]2[C....
61 1VWB - ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
62 2IZK - GLL C4 H6 N4 O2 C12C(NC(=O....
63 1VWE - ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
64 2RTN - IMI C10 H17 N3 O2 S C1[C@H]2[C....
65 1MEP - BTN C10 H16 N2 O3 S C1[C@H]2[C....
66 3WYP - BTN C10 H16 N2 O3 S C1[C@H]2[C....
67 2RTL - IMI C10 H17 N3 O2 S C1[C@H]2[C....
68 1N9M - BTN C10 H16 N2 O3 S C1[C@H]2[C....
69 1VWI - HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
70 2IZJ - BTN C10 H16 N2 O3 S C1[C@H]2[C....
71 1STR Kd = 17 uM ACE CYS HIS PRO GLN ASN THR NH2 n/a n/a
72 1VWP - ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
73 1VWJ - HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
74 1LCV - SNR C9 H14 N2 O3 S C1[C@H]2[C....
75 1RSU Kd = 72 uM SER ASN TRP SER HIS PRO GLN PHE GLU LYS n/a n/a
76 2RTH - GLL C4 H6 N4 O2 C12C(NC(=O....
77 5B5F Kd = 5.6 uM 6F3 C14 H12 N2 O4 S CNS(=O)(=O....
78 2F01 Kd ~ 0.1 pM BTN C10 H16 N2 O3 S C1[C@H]2[C....
79 1VWM - ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
80 2GH7 Kd ~ 0.1 pM BTN C10 H16 N2 O3 S C1[C@H]2[C....
81 4JNJ - BTN C10 H16 N2 O3 S C1[C@H]2[C....
82 2JGS Kd = 0.000000064 M BTN C10 H16 N2 O3 S C1[C@H]2[C....
83 3SZJ - BTN C10 H16 N2 O3 S C1[C@H]2[C....
84 3T2W Kd = 0.000000064 M BTN C10 H16 N2 O3 S C1[C@H]2[C....
85 3RDQ Kd = 0.49 nM DTB C10 H18 N2 O3 C[C@H]1[C@....
86 3RDO Kd = 0.14 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
87 3RDM Kd = 0.14 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
88 2OF8 - BNI C16 H20 N4 O4 S c1cc(ccc1N....
89 2FHL - BNI C16 H20 N4 O4 S c1cc(ccc1N....
90 2OFB - BNI C16 H20 N4 O4 S c1cc(ccc1N....
91 3X00 Kd = 0.83 nM ZOF ZOF EDN n/a n/a
92 2A5C Kd = 24 uM 8DA C10 H15 N5 O4 C1[C@H]([C....
93 3VGW Ka = 200000 M^-1 NVZ C12 H18 N2 O4 S CC(=O)N1[C....
94 1IJ8 - BNI C16 H20 N4 O4 S c1cc(ccc1N....
95 3VHI Ka = 2300000 M^-1 VHI C18 H22 N2 O5 S c1ccc(cc1)....
96 2A8G Kd = 205 uM GNG C10 H13 N5 O4 c1nc2c(n1[....
97 4I60 Kd = 1.87 uM B1R C20 H16 N2 O2 Ru S C1[C@H]2[C....
98 5IRW - D9P C26 H26 N2 O2 C[C@H]1[C@....
99 5F2B - 9RU C31 H41 Cl2 N5 O2 Ru S Cc1cc(c(c(....
100 4OKA - 5IR C18 H26 Ir N5 O4 S2 c1cc(ccc1N....
101 6AUL - BTN C10 H16 N2 O3 S C1[C@H]2[C....
102 4GJV - 0OD C21 H32 Cl3 N3 O2 Rh S CC12=C3([R....
103 6ESU Ki = 249.3 mM 6IR C18 H27 N5 O4 S2 c1cc(ccc1N....
104 4GJS - 0OD C21 H32 Cl3 N3 O2 Rh S CC12=C3([R....
105 2WPU Kd < 60 nM KYT C24 H39 Cl N5 O2 Ru S CC1=[CH]2C....
106 3PK2 - 4IR C28 H45 Cl Ir N5 O4 S2 C[CH]12[CH....
107 6ESS - 4IR C28 H45 Cl Ir N5 O4 S2 C[CH]12[CH....
108 2ZSC - BTN C10 H16 N2 O3 S C1[C@H]2[C....
109 3EW2 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
110 5N99 Kd = 61.3 uM ASN GLN DPR TRP GLN n/a n/a
111 4GGZ Kd = 0.066 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
112 2UYW - BTN C10 H16 N2 O3 S C1[C@H]2[C....
113 2UZ2 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
114 4GDA - BTN C10 H16 N2 O3 S C1[C@H]2[C....
115 1SWG Kd = 43.9 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
116 4GD9 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
117 4BCS Kd = 103 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
118 4EKV Kd = 0.00000145 M BTN C10 H16 N2 O3 S C1[C@H]2[C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BNI; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 BNI 1 1
2 6IR 0.651163 0.7
3 5IR 0.633333 0.694118
4 BTN 0.554054 0.656716
5 BTQ 0.554054 0.656716
6 SHM 0.519481 0.656716
7 BH7 0.511628 0.666667
8 BYT 0.494505 0.661972
9 41M 0.488889 0.676471
10 BTI 0.486842 0.671875
11 SNR 0.486842 0.656716
12 LUV 0.46 0.690141
13 LH3 0.442308 0.670886
14 B9P 0.434343 0.701493
15 LH4 0.410714 0.619565
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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