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 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 (123)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 322 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 1SLE Kd = 670 nM ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
20 4CPE - LUV C31 H34 N4 O3 S c1ccc(cc1)....
21 2RTE - BTN C10 H16 N2 O3 S C1[C@H]2[C....
22 3WZP - ZOF C16 H28 N4 O3 S [H]/N=C/1N....
23 1VWF Kd = 2200 nM ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
24 2RTO - IMI C10 H17 N3 O2 S C1[C@H]2[C....
25 1SWT - BTN C10 H16 N2 O3 S C1[C@H]2[C....
26 1SWP Ka = 100000000 M^-1 BTN C10 H16 N2 O3 S C1[C@H]2[C....
27 1VWG - ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
28 6M9B - BTN C10 H16 N2 O3 S C1[C@H]2[C....
29 2RTF - BTN C10 H16 N2 O3 S C1[C@H]2[C....
30 1VWC - ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
31 1STS Kd = 10 uM PHE CYS HIS PRO GLN ASN THR NH2 n/a n/a
32 2IZI - BTN C10 H16 N2 O3 S C1[C@H]2[C....
33 1VWN Kd = 1500 nM ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
34 2IZF - BTN C10 H16 N2 O3 S C1[C@H]2[C....
35 1SWD - BTN C10 H16 N2 O3 S C1[C@H]2[C....
36 1LCW - SHM C11 H18 N2 O3 S C1[C@H]2[C....
37 1RXK - BNI C16 H20 N4 O4 S c1cc(ccc1N....
38 1SRG Ka = 200000 M^-1 MHB C14 H12 N2 O3 Cc1cc(ccc1....
39 1I9H - BNI C16 H20 N4 O4 S c1cc(ccc1N....
40 1VWR - HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
41 2IZH - BTN C10 H16 N2 O3 S C1[C@H]2[C....
42 2RTP - IMI C10 H17 N3 O2 S C1[C@H]2[C....
43 1SLD Kd = 270 nM ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
44 1KL3 Kd = 1.37 uM ASN TRP SER HIS PRO GLN PHE GLU LYS n/a n/a
45 1DF8 Kd = 0.2 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
46 3T6F - BTN C10 H16 N2 O3 S C1[C@H]2[C....
47 1VWO - ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
48 1VWK - HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
49 1SLG Kd = 125 uM PHE SER HIS PRO GLN ASN THR n/a n/a
50 2RTQ - IMI C10 H17 N3 O2 S C1[C@H]2[C....
51 1N43 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
52 3WZN - BTN C10 H16 N2 O3 S C1[C@H]2[C....
53 1VWD - ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
54 2Y3F - BTN C10 H16 N2 O3 S C1[C@H]2[C....
55 1VWL Kd = 2.33 uM HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
56 1VWA - PHE SER HIS PRO GLN ASN THR n/a n/a
57 2IZG - BTN C10 H16 N2 O3 S C1[C@H]2[C....
58 3MG5 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
59 1SRI Ka = 1200000 M^-1 DMB C15 H14 N2 O3 Cc1cc(cc(c....
60 1KL5 Kd = 1.02 uM ASN TRP SER HIS PRO GLN PHE GLU LYS n/a n/a
61 1VWH - ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
62 1PTS - PHE SER HIS PRO GLN ASN THR n/a n/a
63 1MK5 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
64 1LUQ - BTN C10 H16 N2 O3 S C1[C@H]2[C....
65 1VWB - ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
66 2IZK - GLL C4 H6 N4 O2 C12C(NC(=O....
67 1VWE - ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
68 2RTN - IMI C10 H17 N3 O2 S C1[C@H]2[C....
69 1MEP - BTN C10 H16 N2 O3 S C1[C@H]2[C....
70 3WYP - BTN C10 H16 N2 O3 S C1[C@H]2[C....
71 2RTL - IMI C10 H17 N3 O2 S C1[C@H]2[C....
72 1N9M - BTN C10 H16 N2 O3 S C1[C@H]2[C....
73 1VWI - HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
74 2IZJ - BTN C10 H16 N2 O3 S C1[C@H]2[C....
75 1STR Kd = 17 uM ACE CYS HIS PRO GLN ASN THR NH2 n/a n/a
76 1VWP - ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
77 1VWJ - HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
78 1LCV - SNR C9 H14 N2 O3 S C1[C@H]2[C....
79 1RSU Kd = 72 uM SER ASN TRP SER HIS PRO GLN PHE GLU LYS n/a n/a
80 2RTH - GLL C4 H6 N4 O2 C12C(NC(=O....
81 5B5F Kd = 5.6 uM 6F3 C14 H12 N2 O4 S CNS(=O)(=O....
82 2F01 Kd ~ 0.1 pM BTN C10 H16 N2 O3 S C1[C@H]2[C....
83 1VWM - ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
84 2GH7 Kd ~ 0.1 pM BTN C10 H16 N2 O3 S C1[C@H]2[C....
85 4JNJ - BTN C10 H16 N2 O3 S C1[C@H]2[C....
86 2JGS Kd = 0.000000064 M BTN C10 H16 N2 O3 S C1[C@H]2[C....
87 3SZJ - BTN C10 H16 N2 O3 S C1[C@H]2[C....
88 3T2W Kd = 0.000000064 M BTN C10 H16 N2 O3 S C1[C@H]2[C....
89 3RDQ Kd = 0.49 nM DTB C10 H18 N2 O3 C[C@H]1[C@....
90 3RDO Kd = 0.14 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
91 3RDM Kd = 0.14 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
92 2OF8 - BNI C16 H20 N4 O4 S c1cc(ccc1N....
93 2FHL - BNI C16 H20 N4 O4 S c1cc(ccc1N....
94 2OFB - BNI C16 H20 N4 O4 S c1cc(ccc1N....
95 3X00 Kd = 0.83 nM ZOF ZOF EDN n/a n/a
96 2A5C Kd = 24 uM 8DA C10 H15 N5 O4 C1[C@H]([C....
97 3VGW Ka = 200000 M^-1 NVZ C12 H18 N2 O4 S CC(=O)N1[C....
98 1IJ8 - BNI C16 H20 N4 O4 S c1cc(ccc1N....
99 3VHI Ka = 2300000 M^-1 VHI C18 H22 N2 O5 S c1ccc(cc1)....
100 2A8G Kd = 205 uM GNG C10 H13 N5 O4 c1nc2c(n1[....
101 4I60 Kd = 1.87 uM B1R C20 H16 N2 O2 Ru S C1[C@H]2[C....
102 5IRW - D9P C26 H26 N2 O2 C[C@H]1[C@....
103 5F2B - 9RU C31 H41 Cl2 N5 O2 Ru S Cc1cc(c(c(....
104 4OKA - 5IR C18 H26 Ir N5 O4 S2 c1cc(ccc1N....
105 6AUL - BTN C10 H16 N2 O3 S C1[C@H]2[C....
106 4GJV - 0OD C21 H32 Cl3 N3 O2 Rh S CC12=C3([R....
107 6ESU Ki = 249.3 mM 6IR C18 H27 N5 O4 S2 c1cc(ccc1N....
108 4GJS - 0OD C21 H32 Cl3 N3 O2 Rh S CC12=C3([R....
109 2WPU Kd < 60 nM KYT C24 H39 Cl N5 O2 Ru S CC1=[CH]2C....
110 3PK2 - 4IR C28 H45 Cl Ir N5 O4 S2 C[CH]12[CH....
111 6VJL Kd = 0.000000064 M BTN C10 H16 N2 O3 S C1[C@H]2[C....
112 6ESS - 4IR C28 H45 Cl Ir N5 O4 S2 C[CH]12[CH....
113 2ZSC - BTN C10 H16 N2 O3 S C1[C@H]2[C....
114 3EW2 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
115 5N99 Kd = 61.3 uM ASN GLN DPR TRP GLN n/a n/a
116 4GGZ Kd = 0.066 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
117 2UYW - BTN C10 H16 N2 O3 S C1[C@H]2[C....
118 2UZ2 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
119 4GDA - BTN C10 H16 N2 O3 S C1[C@H]2[C....
120 1SWG Kd = 43.9 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
121 4GD9 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
122 4BCS Kd = 103 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
123 4EKV Kd = 0.000000064 M BTN C10 H16 N2 O3 S C1[C@H]2[C....
Polypharmacology
Similar Ligands (2D)
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 BTN 0.457143 0.75
6 BTQ 0.457143 0.75
7 IMI 0.430556 0.609375
8 VHH 0.424658 0.854839
9 SHM 0.405405 0.75
Similar Ligands (3D)
Ligand no: 1; Ligand: NVZ; Similar ligands found: 8
No: Ligand Similarity coefficient
1 ALJ 0.8789
2 KWK 0.8758
3 1UA 0.8705
4 BSO 0.8681
5 5HG 0.8653
6 6XR 0.8610
7 DTB 0.8561
8 00G 0.8535
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
APoc FAQ
Feedback