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Receptor
PDB id Resolution Class Description Source Keywords
3E6J 1.67 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF VARIABLE LYMPHOCYTE RECEPTOR (VLR) RBC3 COMPLEX WITH H-TRISACCHARIDE PETROMYZON MARINUS VARIABLE LYMPHOCYTE RECEPTORS VLR LEUCINE-RICH REPEAT LRRADAPTIVE IMMUNITY IMMUNE SYSTEM SEA LAMPREY JAWLESS FISHRECEPTOR
Ref.: ANTIGEN RECOGNITION BY VARIABLE LYMPHOCYTE RECEPTOR SCIENCE V. 321 1834 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DR2 A:300;
Valid;
none;
submit data
529.49 C20 H35 N O15 C[C@H...
GOL A:306;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:301;
A:302;
A:303;
A:304;
A:305;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
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
5UFF 2.14 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF VARIABLE LYMPHOCYTE RECEPTOR (VLR) RBC3 FUCOSE(ALPHA-1-2)LACTOSE BOUND PETROMYZON MARINUS VARIABLE LYMPHOCYTE RECEPTORS VLR LEUCINE-RICH REPEAT LRRADAPTIVE IMMUNITY IMMUNE SYSTEM SEA LAMPREY JAWLESS FISHRECEPTOR GLYCAN BINDING GLYCAN RECEPTOR
Ref.: STRUCTURAL INSIGHTS INTO VLR FINE SPECIFICITY FOR B GROUP CARBOHYDRATES. STRUCTURE V. 25 1667 2017
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 286 families.
1 3E6J - DR2 C20 H35 N O15 C[C@H]1[C@....
2 5UFF Kd = 57.1 uM 8B7 C18 H32 O15 C[C@H]1[C@....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 5UF1 Kd = 2.6 uM FUC GAL NAG n/a n/a
2 5UF4 Kd = 160 uM GLC GAL NAG GAL n/a n/a
3 3E6J - DR2 C20 H35 N O15 C[C@H]1[C@....
4 5UFF Kd = 57.1 uM 8B7 C18 H32 O15 C[C@H]1[C@....
5 4K5U Ka = 9600 M^-1 GAL C6 H12 O6 C([C@@H]1[....
6 4K79 Ka = 22100 M^-1 GAL A2G n/a n/a
7 5UFC Kd = 6.9 uM DR2 C20 H35 N O15 C[C@H]1[C@....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 5UF1 Kd = 2.6 uM FUC GAL NAG n/a n/a
2 5UF4 Kd = 160 uM GLC GAL NAG GAL n/a n/a
3 3E6J - DR2 C20 H35 N O15 C[C@H]1[C@....
4 5UFF Kd = 57.1 uM 8B7 C18 H32 O15 C[C@H]1[C@....
5 4K5U Ka = 9600 M^-1 GAL C6 H12 O6 C([C@@H]1[....
6 4K79 Ka = 22100 M^-1 GAL A2G n/a n/a
7 5UFC Kd = 6.9 uM DR2 C20 H35 N O15 C[C@H]1[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DR2; Similar ligands found: 170
No: Ligand ECFP6 Tc MDL keys Tc
1 FUC GAL NDG 1 1
2 GAL NAG FUC 1 1
3 FUL GAL NAG 1 1
4 DR2 1 1
5 FUC GAL NAG 1 1
6 NDG GAL FUC 1 1
7 NAG GAL FUC 1 1
8 NAG FUC 0.809524 0.956522
9 BDZ 0.739726 0.978723
10 FUC GAL NAG FUC 0.739726 0.978723
11 FUC NDG GAL FUC 0.739726 0.978723
12 FUC NAG GAL FUC 0.739726 0.978723
13 BCW 0.739726 0.978723
14 FUC GAL NDG FUC 0.739726 0.978723
15 GAL NDG FUC FUC 0.739726 0.978723
16 GAL NAG FUC FUC 0.739726 0.978723
17 DR3 0.712329 1
18 A2G GAL NAG FUC 0.703704 0.938776
19 FUC GAL NAG A2G 0.703704 0.938776
20 8B7 0.695652 0.73913
21 LAT FUC 0.695652 0.73913
22 BGC GAL FUC 0.695652 0.73913
23 GLC GAL FUC 0.695652 0.73913
24 FUC GAL GLC 0.695652 0.73913
25 NLC 0.671642 0.978261
26 GAL NDG 0.671642 0.978261
27 NDG GAL 0.671642 0.978261
28 FUC GAL NAG GAL BGC 0.62069 1
29 GLC NAG GAL GAL FUC 0.62069 1
30 GAL GLC NAG GAL FUC 0.62069 1
31 FUC GAL NAG GAL FUC 0.619048 0.978723
32 GAL NDG FUC 0.597403 1
33 FUC NDG GAL 0.597403 1
34 NAG GDL 0.597222 0.958333
35 CBS 0.597222 0.958333
36 CBS CBS 0.597222 0.958333
37 NDG NAG 0.597222 0.958333
38 BGC GAL NAG GAL FUC FUC 0.593407 0.978723
39 GLC GAL NAG GAL FUC FUC 0.593407 0.978723
40 GLA GAL NAG 0.592105 0.978261
41 MAN BMA NAG 0.592105 0.978261
42 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.576087 0.978261
43 A2G GAL BGC FUC 0.568182 1
44 NDG NAG NAG NAG 0.565789 0.938776
45 NAG NAG NDG 0.565789 0.938776
46 NAG NAG NAG NDG 0.565789 0.938776
47 CTO 0.565789 0.938776
48 NDG NAG NAG 0.565789 0.938776
49 NAG NAG NAG NAG NDG 0.565789 0.938776
50 NAG NAG NAG NAG NAG NAG 0.565789 0.938776
51 NDG NAG NAG NDG 0.565789 0.938776
52 NAG NAG NAG NAG NAG NAG NAG NAG 0.565789 0.938776
53 NAG NAG NDG NAG 0.565789 0.938776
54 NAG NAG NAG NAG NAG 0.565789 0.938776
55 XYS GAL FUC 0.551282 0.723404
56 G6S NAG 0.55 0.714286
57 MAN BMA NAG NAG MAN NAG GAL GAL 0.541667 0.938776
58 NAG MAN MAN MAN NAG GAL NAG GAL 0.541667 0.938776
59 NAG GAL NAG 0.536585 0.958333
60 GAL NAG GAL NAG GAL NAG 0.535714 0.938776
61 NAG GAL GAL NAG 0.535714 0.958333
62 FUC GAL NAG NON FUC 0.531915 0.836364
63 GAL BGC NAG GAL 0.53012 0.978261
64 FUC GAL A2G 0.52439 1
65 BGC GLA GAL FUC 0.52439 0.73913
66 A2G GLA FUC 0.52439 1
67 NGA GAL FUC 0.52439 1
68 FUC GLA A2G 0.52439 1
69 A2G GAL FUC 0.52439 1
70 FUC GAL NAG A2G FUC 0.521739 0.938776
71 NAG GAL FUC FUC A2G 0.521739 0.938776
72 NAG BMA NAG MAN MAN NAG NAG 0.520408 0.938776
73 MAG FUC GAL 0.518519 0.958333
74 NAG MAN BMA NDG MAN NAG GAL 0.514852 0.938776
75 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.514563 0.958333
76 FUC GAL 0.514286 0.717391
77 FUC NAG 0.512821 0.9
78 TCG 0.511905 0.793103
79 NAG NAG BMA MAN MAN NAG GAL NAG 0.509804 0.938776
80 M5G 0.509804 0.958333
81 BGC FUC GAL FUC A2G 0.505495 0.978723
82 GLC FUC GAL FUC A2G 0.505495 0.978723
83 GLA GAL NAG FUC GAL GLC 0.505155 1
84 HS2 0.5 0.86
85 GAL NAG GAL FUC 0.5 1
86 GLA NAG GAL FUC 0.5 1
87 FUC BGC GAL NAG GAL 0.494737 1
88 BHE 0.493827 0.648148
89 FUC BGC GAL 0.493506 0.73913
90 UNU GAL NAG 0.488636 0.9
91 FUC NAG GAL 0.488095 0.92
92 BHG FUC 0.4875 0.648148
93 FUC BHG 0.4875 0.648148
94 4YA 0.4875 0.648148
95 NAG MAN BMA 0.481928 0.978261
96 GAL NAG MAN 0.481928 0.978261
97 GLC GAL NAG GAL FUC A2G 0.480392 0.938776
98 A2G GAL NAG FUC GAL GLC 0.480392 0.938776
99 NAG BMA MAN MAN MAN MAN 0.478723 0.978261
100 FUC BGC GAL NAG 0.478261 1
101 8VZ 0.473684 0.938776
102 SN5 SN5 0.468354 0.823529
103 ASG 0.465753 0.650794
104 NAG NAG BMA MAN MAN 0.463918 0.958333
105 FUC NAG GLA GAL 0.462366 0.978723
106 GAL GAL FUC 0.461538 0.73913
107 GLA GLA FUC 0.461538 0.73913
108 FUC GAL GLA 0.461538 0.73913
109 GLA GAL FUC 0.461538 0.73913
110 FUC GLA GLA 0.461538 0.73913
111 MAN MAN BMA 0.459459 0.717391
112 BMA BMA MAN 0.459459 0.717391
113 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.459184 0.92
114 GCS GCS NAG 0.455556 0.9
115 GAL A2G 0.454545 0.978261
116 GAL NGA 0.454545 0.978261
117 A2G GAL 0.454545 0.978261
118 NGA GAL BGC 0.452381 0.978261
119 FUC NAG TA5 0.451613 0.671642
120 MAN MAN NAG 0.448276 0.9375
121 GLC GAL NAG GAL 0.444444 0.978261
122 LAT NAG GAL 0.444444 0.978261
123 BEK GAL NAG 0.443299 0.807018
124 NAG MAN MMA 0.44186 0.978723
125 NAG MAN BMA MAN NAG GAL 0.441176 0.958333
126 NAG MAN MAN MAN NAG 0.44086 0.958333
127 G4S MAG FUC 0.44086 0.692308
128 GAL NAG GAL GLC 0.438202 0.978261
129 BGC GAL NAG GAL 0.438202 0.978261
130 FUC NAG T45 0.4375 0.671642
131 BMA MAN MAN MAN 0.435897 0.717391
132 FUC C4W NAG BMA 0.434343 0.884615
133 BGA 0.43299 0.836364
134 KPM 0.431579 0.865385
135 NAG MAN MAN 0.426966 0.978261
136 A2G 0.426471 0.869565
137 NDG 0.426471 0.869565
138 NAG 0.426471 0.869565
139 HSQ 0.426471 0.869565
140 BM3 0.426471 0.869565
141 NGA 0.426471 0.869565
142 4U1 0.424528 0.884615
143 NAG GAL SIA 0.424528 0.867925
144 SGA MAG FUC 0.421053 0.692308
145 FUC C4W NAG BMA MAN NAG 0.419643 0.884615
146 GAL NGA GLA BGC GAL 0.419355 0.978261
147 FUC C4W NAG BMA MAN MAN NAG NAG 0.418803 0.884615
148 GAL MGC 0.417722 0.978723
149 NAG GAL GAL NAG GAL 0.417582 0.958333
150 NAG GAL BGC 0.41573 0.978261
151 A2G MBG 0.414634 0.978723
152 MAN MAN MAN GLC 0.414634 0.717391
153 MBG A2G 0.414634 0.978723
154 NAG NAG FUL BMA MAN MAN NAG GAL 0.413793 0.867925
155 NAG GCU NAG GCD 0.411215 0.851852
156 GAL NAG GAL 0.411111 0.9375
157 NGA GLA GAL BGC 0.408602 0.978261
158 NAG AMU 0.406593 0.92
159 NAG NAG BMA 0.406593 0.884615
160 NAG MUB 0.406593 0.92
161 NAG NDG BMA 0.406593 0.884615
162 GLA MBG 0.402778 0.723404
163 NAG BMA 0.402439 0.88
164 NAG A2G 0.402439 0.958333
165 NAG NGA 0.402439 0.958333
166 BMA MAN MAN MAN MAN 0.402299 0.717391
167 MMA MAN NAG MAN NAG NAG 0.402062 0.92
168 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.401869 0.9
169 GAL NAG GAL BGC 0.4 0.9375
170 4U2 0.4 0.901961
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5UFF; Ligand: 8B7; Similar sites found with APoc: 30
This union binding pocket(no: 1) in the query (biounit: 5uff.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5T2Y 753 1.51515
2 3MQG ACO 1.5625
3 3MQG UDP 1.5625
4 2PO3 T4K 2.77778
5 1HV9 COA 2.77778
6 6F05 GTS 2.7907
7 4EA7 COA 3.24074
8 4EA7 JB2 3.24074
9 6CB2 OLC 3.24074
10 1DKF BMS 3.24074
11 1FCZ 156 3.24074
12 2G50 PYR 3.7037
13 2V1O COA 3.97351
14 5DEP UD1 4.16667
15 3NJ4 NAD 4.16667
16 1SG4 CO8 4.16667
17 3DR4 G4M 4.16667
18 5WS9 OXL 4.16667
19 5LYR MAN MNM 4.16667
20 4URF NAD 4.62963
21 3PG7 PTY 5.09259
22 1IY8 NAD 5.09259
23 6DO3 PRO PRO PRO MET ALA GLY GLY 5.55556
24 5UCD NAP 5.55556
25 1PI5 SM2 6.01852
26 3V4S ADP 6.94444
27 4AZC NGW 9.25926
28 1G72 PQQ 10.1449
29 3FS8 TDR 12.963
30 2D0V PQQ 14.8148
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