Receptor
PDB id Resolution Class Description Source Keywords
4I60 2.5 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF AVIDIN - BIOTINYLRUTHENOCENE COMPLEX GALLUS GALLUS BETA BARREL BIOTIN-BINDING PROTEIN BIOTINYLRUTHENOCENE GLYCOPROTEIN HEN EGG WHITE
Ref.: STRUCTURAL INVESTIGATION OF THE INTERACTIONS OF BIOTINYLRUTHENOCENE WITH AVIDIN. CHEM.BIOL.INTERACT V. 204 6 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
B1R A:203;
Valid;
none;
Kd = 1.87 uM
449.488 C20 H16 N2 O2 Ru S C1[C@...
NAG NAG A:201;
Invalid;
none;
submit data
408.404 n/a O=C(N...
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 (139)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 272 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 1RXJ - BNI C16 H20 N4 O4 S c1cc(ccc1N....
20 1SWK Ka ~ 1000000000000 M^-1 BTN C10 H16 N2 O3 S C1[C@H]2[C....
21 2RTR - IMI C10 H17 N3 O2 S C1[C@H]2[C....
22 4CPI - LH4 C36 H44 N6 O8 S3 c1cc(c(c(c....
23 2RTD - BTN C10 H16 N2 O3 S C1[C@H]2[C....
24 3WYQ - BTN C10 H16 N2 O3 S C1[C@H]2[C....
25 2RTK - GLL C4 H6 N4 O2 C12C(NC(=O....
26 1LCZ - BH7 C16 H27 N3 O4 S C1[C@H]2[C....
27 1SWN Ka ~ 1000000000000 M^-1 BTN C10 H16 N2 O3 S C1[C@H]2[C....
28 1RST Kd = 37 uM ALA TRP ARG HIS PRO GLN PHE GLY GLY n/a n/a
29 2RTG - BTN C10 H16 N2 O3 S C1[C@H]2[C....
30 1SLE Kd = 670 nM ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
31 4CPE - LUV C31 H34 N4 O3 S c1ccc(cc1)....
32 2RTE - BTN C10 H16 N2 O3 S C1[C@H]2[C....
33 3WZP - ZOF C16 H28 N4 O3 S [H]/N=C/1N....
34 1VWF Kd ~ 2200 nM ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
35 2RTO - IMI C10 H17 N3 O2 S C1[C@H]2[C....
36 1SWT - BTN C10 H16 N2 O3 S C1[C@H]2[C....
37 1SWP Ka = 100000000 M^-1 BTN C10 H16 N2 O3 S C1[C@H]2[C....
38 1VWG - ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
39 2RTF - BTN C10 H16 N2 O3 S C1[C@H]2[C....
40 1VWC - ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
41 1STS Ki = 10 uM PHE CYS HIS PRO GLN ASN THR NH2 n/a n/a
42 2IZI - BTN C10 H16 N2 O3 S C1[C@H]2[C....
43 1VWN Kd ~ 1500 nM ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
44 2IZF - BTN C10 H16 N2 O3 S C1[C@H]2[C....
45 1SWD - BTN C10 H16 N2 O3 S C1[C@H]2[C....
46 1LCW - SHM C11 H18 N2 O3 S C1[C@H]2[C....
47 1RXK - BNI C16 H20 N4 O4 S c1cc(ccc1N....
48 1SRG Ki = 5 uM MHB C14 H12 N2 O3 Cc1cc(ccc1....
49 1I9H - BNI C16 H20 N4 O4 S c1cc(ccc1N....
50 1VWR - HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
51 2IZH - BTN C10 H16 N2 O3 S C1[C@H]2[C....
52 2RTP - IMI C10 H17 N3 O2 S C1[C@H]2[C....
53 1SLD Kd = 270 nM ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
54 1KL3 Kd = 1.37 uM ASN TRP SER HIS PRO GLN PHE GLU LYS n/a n/a
55 1DF8 Kd = 0.2 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
56 3T6F - BTN C10 H16 N2 O3 S C1[C@H]2[C....
57 1VWO - ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
58 1VWK - HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
59 1SLG Kd = 125 uM PHE SER HIS PRO GLN ASN THR n/a n/a
60 2RTQ - IMI C10 H17 N3 O2 S C1[C@H]2[C....
61 1N43 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
62 3WZN - BTN C10 H16 N2 O3 S C1[C@H]2[C....
63 1VWD - ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
64 2Y3F - BTN C10 H16 N2 O3 S C1[C@H]2[C....
65 1VWL Kd = 2.33 uM HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
66 1VWA - PHE SER HIS PRO GLN ASN THR n/a n/a
67 2IZG - BTN C10 H16 N2 O3 S C1[C@H]2[C....
68 3MG5 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
69 1SRI Ki = 0.83 uM DMB C15 H14 N2 O3 Cc1cc(cc(c....
70 1KL5 Kd = 1 uM ASN TRP SER HIS PRO GLN PHE GLU LYS n/a n/a
71 1VWH - ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
72 1PTS - PHE SER HIS PRO GLN ASN THR n/a n/a
73 1MK5 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
74 1LUQ - BTN C10 H16 N2 O3 S C1[C@H]2[C....
75 1VWB - ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
76 2IZK - GLL C4 H6 N4 O2 C12C(NC(=O....
77 1VWE - ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
78 2RTN - IMI C10 H17 N3 O2 S C1[C@H]2[C....
79 1MEP - BTN C10 H16 N2 O3 S C1[C@H]2[C....
80 3WYP - BTN C10 H16 N2 O3 S C1[C@H]2[C....
81 2RTL - IMI C10 H17 N3 O2 S C1[C@H]2[C....
82 1N9M - BTN C10 H16 N2 O3 S C1[C@H]2[C....
83 1VWI - HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
84 2IZJ - BTN C10 H16 N2 O3 S C1[C@H]2[C....
85 1STR Ki = 17 uM ACE CYS HIS PRO GLN ASN THR NH2 n/a n/a
86 1VWP - ACE CYS HIS PRO GLN GLY PRO PRO CYS NH2 n/a n/a
87 1VWJ - HIS PRO GLN GLY PRO PRO CYS LYS NH2 LEA n/a n/a
88 1LCV - SNR C9 H14 N2 O3 S C1[C@H]2[C....
89 1RSU Kd = 72 uM SER ASN TRP SER HIS PRO GLN PHE GLU LYS n/a n/a
90 2RTH - GLL C4 H6 N4 O2 C12C(NC(=O....
91 5B5F Kd = 5.6 uM 6F3 C14 H12 N2 O4 S CNS(=O)(=O....
92 2F01 Kd ~ 0.1 pM BTN C10 H16 N2 O3 S C1[C@H]2[C....
93 1VWM - ACE CYS HIS PRO GLN PHE CYS NH2 n/a n/a
94 2GH7 Kd ~ 0.1 pM BTN C10 H16 N2 O3 S C1[C@H]2[C....
95 4JNJ - BTN C10 H16 N2 O3 S C1[C@H]2[C....
96 3SZJ - BTN C10 H16 N2 O3 S C1[C@H]2[C....
97 3T2W Kd = 0.00000145 M BTN C10 H16 N2 O3 S C1[C@H]2[C....
98 3RDQ Kd = 0.49 nM DTB C10 H18 N2 O3 C[C@H]1[C@....
99 3RDO Kd = 0.14 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
100 3RDM Kd = 0.14 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
101 1Y55 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
102 1Y52 Kd = 0.00000145 M BTN C10 H16 N2 O3 S C1[C@H]2[C....
103 2FHN - BNI C16 H20 N4 O4 S c1cc(ccc1N....
104 2OF8 - BNI C16 H20 N4 O4 S c1cc(ccc1N....
105 2FHL - BNI C16 H20 N4 O4 S c1cc(ccc1N....
106 2OFB - BNI C16 H20 N4 O4 S c1cc(ccc1N....
107 3WZQ Kd = 0.00000145 M ZOF C16 H28 N4 O3 S [H]/N=C/1N....
108 3X00 Kd = 0.83 nM ZOF ZOF EDN n/a n/a
109 3VHH Ka = 400000000 M^-1 VHH C12 H20 N2 O3 S CN1[C@H]2C....
110 2A5B Kd = 117 uM 8HG C10 H13 N5 O5 C1[C@@H]([....
111 3VHM Ka = 15000 M^-1 NPK C20 H23 N3 O9 S C[C@H](c1c....
112 5IRU - B9P C26 H24 N2 O2 S c1cc2ccc3c....
113 1LDO - SNR C9 H14 N2 O3 S C1[C@H]2[C....
114 1IJ8 - BNI C16 H20 N4 O4 S c1cc(ccc1N....
115 3VHI Ka = 2300000 M^-1 VHI C18 H22 N2 O5 S c1ccc(cc1)....
116 2A8G Kd = 205 uM GNG C10 H13 N5 O4 c1nc2c(n1[....
117 4I60 Kd = 1.87 uM B1R C20 H16 N2 O2 Ru S C1[C@H]2[C....
118 5IRW - D9P C26 H26 N2 O2 C[C@H]1[C@....
119 2QCB - KYS C24 H31 Cl N5 O4 Ru S2 c1cc(ccc1N....
120 5IRA - 9RU C31 H41 Cl2 N5 O2 Ru S Cc1cc(c(c(....
121 5F2B - 9RU C31 H41 Cl2 N5 O2 Ru S Cc1cc(c(c(....
122 4OKA - 5IR C18 H26 Ir N5 O4 S2 c1cc(ccc1N....
123 4GJV - 0OD C21 H32 Cl3 N3 O2 Rh S CC12=C3([R....
124 4GJS - 0OD C21 H32 Cl3 N3 O2 Rh S CC12=C3([R....
125 2WPU Kd < 60 nM KYT C24 H39 Cl N5 O2 Ru S CC1=[CH]2C....
126 3PK2 - 4IR C28 H45 Cl Ir N5 O4 S2 C[CH]12[CH....
127 2ZSC - BTN C10 H16 N2 O3 S C1[C@H]2[C....
128 3EW2 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
129 2C1S - BSO C10 H16 N2 O4 S C1[C@H]2[C....
130 2C1Q Kd ~ 0.1 pM BTN C10 H16 N2 O3 S C1[C@H]2[C....
131 4GGZ Kd = 0.066 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
132 4BJ8 Kd = 3.745 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
133 2UYW - BTN C10 H16 N2 O3 S C1[C@H]2[C....
134 2UZ2 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
135 4GDA - BTN C10 H16 N2 O3 S C1[C@H]2[C....
136 1SWG Kd = 43.9 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
137 4GD9 - BTN C10 H16 N2 O3 S C1[C@H]2[C....
138 4BCS Kd = 103 nM BTN C10 H16 N2 O3 S C1[C@H]2[C....
139 4EKV Kd = 0.00000145 M BTN C10 H16 N2 O3 S C1[C@H]2[C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: B1R; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 B1R 1 1
2 BTN 0.6 0.632353
3 BTQ 0.6 0.632353
4 SHM 0.540541 0.632353
5 SNR 0.506849 0.632353
6 BTI 0.486486 0.671875
7 BH7 0.476744 0.619718
8 0OD 0.456522 0.777778
9 41M 0.455556 0.628571
10 BYT 0.445652 0.616438
11 B9P 0.418367 0.727273
12 LUV 0.415842 0.643836
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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