Receptor
PDB id Resolution Class Description Source Keywords
2DVA 2.2 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF PEANUT LECTIN GAL-BETA-1,3-GALNAC-ALPHA (METHYL-T-ANTIGEN) COMPLEX ARACHIS HYPOGAEA LEGUME LECTIN AGGLUTININ OPEN QUATERNARY STRUCTURE CARBOHSPECIFICITY SUGAR BINDING PROTEIN
Ref.: STRUCTURAL STUDIES ON PEANUT LECTIN COMPLEXED WITH DISACCHARIDES INVOLVING DIFFERENT LINKAGES: FURTHER INTO THE STRUCTURE AND INTERACTIONS OF THE LECTIN ACTA CRYSTALLOGR.,SECT.D V. 62 1413 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:237;
B:237;
C:237;
D:237;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
40.078 Ca [Ca+2...
MN A:238;
B:238;
C:238;
D:238;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
54.938 Mn [Mn+2...
SO4 B:2236;
C:1236;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
MGC GAL F:1;
E:1;
G:1;
H:1;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
397.377 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6VGF 1.83 Å NON-ENZYME: BINDING PEANUT LECTIN COMPLEXED WITH DIVALENT S-BETA-D-THIOGALACTOPY BETA-D-GLUCOPYRANOSIDE DERIVATIVE (DISTGD) ARACHIS HYPOGAEA BETA-GALACTOSYLAMIDES BETA-THIOGALACTOSIDES PEANUT AGGLUTIGLYCOMIMETICS SUGAR BINDING PROTEIN
Ref.: CRYSTAL STRUCTURES OF PEANUT LECTIN IN THE PRESENCE SYNTHETIC BETA-N- AND BETA-S-GALACTOSIDES DISCLOSE FOR THE RECOGNITION OF DIFFERENT GLYCOMIMETIC LIGAN ACTA CRYSTALLOGR D STRUCT V. 76 1080 2020 BIOL
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 552 families.
1 2DVA - MGC GAL n/a n/a
2 6VC4 Kd = 360 uM QWG C22 H37 N3 O14 S2 CO[C@@H]1[....
3 6VGF Kd = 180 uM WA3 C42 H68 N6 O27 S4 c1c(nnn1C[....
4 2DV9 - GAL GAL n/a n/a
5 1V6K - GLC GAL n/a n/a
6 1V6L - BGC GAL n/a n/a
7 2DVD - GAL GAL n/a n/a
8 6VC3 Kd = 482 uM QWJ C15 H24 O9 S2 C#CCSC[C@@....
9 2TEP - NGA GAL n/a n/a
10 6V95 Kd = 495 uM QSG C32 H48 N10 O20 c1c(nnn1[C....
11 6VAV Kd = 690 uM QTY C32 H48 N10 O16 c1c(nnn1[C....
12 2DVB - GAL C6 H12 O6 C([C@@H]1[....
13 1V6I - GLC GAL n/a n/a
14 6VAW Kd = 1563 uM S3W C20 H33 N5 O12 CO[C@@H]1[....
15 2PEL Ki = 1.37 mM BGC GAL n/a n/a
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 426 families.
1 2DVA - MGC GAL n/a n/a
2 6VC4 Kd = 360 uM QWG C22 H37 N3 O14 S2 CO[C@@H]1[....
3 6VGF Kd = 180 uM WA3 C42 H68 N6 O27 S4 c1c(nnn1C[....
4 2DV9 - GAL GAL n/a n/a
5 1V6K - GLC GAL n/a n/a
6 1V6L - BGC GAL n/a n/a
7 2DVD - GAL GAL n/a n/a
8 6VC3 Kd = 482 uM QWJ C15 H24 O9 S2 C#CCSC[C@@....
9 2TEP - NGA GAL n/a n/a
10 6V95 Kd = 495 uM QSG C32 H48 N10 O20 c1c(nnn1[C....
11 6VAV Kd = 690 uM QTY C32 H48 N10 O16 c1c(nnn1[C....
12 2DVB - GAL C6 H12 O6 C([C@@H]1[....
13 1V6I - GLC GAL n/a n/a
14 6VAW Kd = 1563 uM S3W C20 H33 N5 O12 CO[C@@H]1[....
15 2PEL Ki = 1.37 mM BGC GAL n/a n/a
50% Homology Family (67)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 322 families.
1 5T55 Kd = 0.68 nM BGC GAL GLA NGA n/a n/a
2 5T54 Kd = 0.87 nM GLA FUC A2G n/a n/a
3 5T5J Kd = 0.73 nM ACA SER SER VAL GLY A2G n/a n/a
4 5T52 Kd = 0.54 nM NGA C8 H15 N O6 CC(=O)N[C@....
5 5T5L Kd = 0.73 nM ACE SER SER VAL GLY A2G n/a n/a
6 5T5P Kd = 0.71 nM ACE SER THR VAL GLY A2G n/a n/a
7 1FNZ - A2G C8 H15 N O6 CC(=O)N[C@....
8 1S1A - MMA MAN n/a n/a
9 2ARB Ka = 26000 M^-1 MAN NAG n/a n/a
10 1N3Q - FRU GLC n/a n/a
11 2AR6 Ka = 63000 M^-1 MAN MAN MAN NAG NAG n/a n/a
12 1N3O - GYP C7 H14 O6 CO[C@@H]1[....
13 1N3P - GLC FRU n/a n/a
14 2ARX - MAN MAN n/a n/a
15 2ARE Ka = 1900 M^-1 MAN C6 H12 O6 C([C@@H]1[....
16 1LED - MAG GAL FUC FUC n/a n/a
17 1GSL - MAG FUC GAL FUC n/a n/a
18 1V00 - BGC GAL n/a n/a
19 3N3H - CIT C6 H8 O7 C(C(=O)O)C....
20 3N36 - GLA C6 H12 O6 C([C@@H]1[....
21 1AX0 Ka = 1340 M^-1 A2G C8 H15 N O6 CC(=O)N[C@....
22 1UZY - BGC GAL n/a n/a
23 1LTE - BGC GAL n/a n/a
24 1AX1 Ka = 1940 M^-1 BGC GAL n/a n/a
25 1AX2 Ka = 9730 M^-1 NDG GAL n/a n/a
26 1GZC Kd = 0.32 mM BGC GAL n/a n/a
27 3N35 - A2G C8 H15 N O6 CC(=O)N[C@....
28 1AXZ Ka = 1570 M^-1 GAL C6 H12 O6 C([C@@H]1[....
29 1GZ9 Kd = 0.31 mM BGC GAL FUC n/a n/a
30 3ZYR Kd = 4.6 uM NAG ASN NAG BMA MAN MAN NAG NAG n/a n/a
31 3ZVX - MAN MAN MAN n/a n/a
32 5U38 - MMA MAN n/a n/a
33 5KXE Kd = 5.45 uM 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
34 5KXB - NGA C8 H15 N O6 CC(=O)N[C@....
35 5KXC - 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
36 5KXD - 6Y2 C22 H31 N3 O13 CC(=O)N[C@....
37 4WV8 - GLC GAL n/a n/a
38 4U2A - A2G C8 H15 N O6 CC(=O)N[C@....
39 4U36 - SER A2G n/a n/a
40 1JXN - MFU C7 H14 O5 C[C@H]1[C@....
41 3WCS - MAN NAG GAL n/a n/a
42 3WOG - MAN NAG n/a n/a
43 5EYX - MMA MAN n/a n/a
44 5EYY - MMA MAN n/a n/a
45 2BQP - GLC C6 H12 O6 C([C@@H]1[....
46 5T7P - XMM C14 H15 Br Cl N O6 c1cc(c(c2c....
47 2DVA - MGC GAL n/a n/a
48 6VC4 Kd = 360 uM QWG C22 H37 N3 O14 S2 CO[C@@H]1[....
49 6VGF Kd = 180 uM WA3 C42 H68 N6 O27 S4 c1c(nnn1C[....
50 2DV9 - GAL GAL n/a n/a
51 1V6K - GLC GAL n/a n/a
52 1V6L - BGC GAL n/a n/a
53 2DVD - GAL GAL n/a n/a
54 6VC3 Kd = 482 uM QWJ C15 H24 O9 S2 C#CCSC[C@@....
55 2TEP - NGA GAL n/a n/a
56 6V95 Kd = 495 uM QSG C32 H48 N10 O20 c1c(nnn1[C....
57 6VAV Kd = 690 uM QTY C32 H48 N10 O16 c1c(nnn1[C....
58 2DVB - GAL C6 H12 O6 C([C@@H]1[....
59 1V6I - GLC GAL n/a n/a
60 6VAW Kd = 1563 uM S3W C20 H33 N5 O12 CO[C@@H]1[....
61 2PEL Ki = 1.37 mM BGC GAL n/a n/a
62 1G9F - GAL NAG GAL NAG GAL n/a n/a
63 2DTW - 2GS C7 H14 O6 CO[C@@H]1[....
64 1WBL - AMG C7 H14 O6 CO[C@@H]1[....
65 2ZMK - EGA GLA n/a n/a
66 2D3S - SER A2G n/a n/a
67 2FMD - MAN MAN n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: MGC GAL; Similar ligands found: 126
No: Ligand ECFP6 Tc MDL keys Tc
1 MGC GAL 1 1
2 A2G GAL 0.666667 0.957447
3 A2G THR GAL 0.628571 0.884615
4 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.617284 0.94
5 A2G SER GAL 0.614286 0.849057
6 BGC GAL NGA GAL 0.605634 0.957447
7 GAL A2G MBN 0.597222 0.9
8 A2G MBN GAL 0.597222 0.918367
9 A2G NPO GAL 0.594595 0.692308
10 BGC GAL NAG GAL 0.589041 0.957447
11 MAG 0.578947 0.93617
12 2F8 0.578947 0.93617
13 NAG GAL 0.5625 0.957447
14 TVD GAL 0.5625 0.92
15 MBG GAL 0.559322 0.744681
16 BGC GAL GLA NGA GAL 0.558442 0.957447
17 NAG GAL GAL 0.535211 0.957447
18 MBG GLA 0.534483 0.744681
19 NAG BMA 0.514706 0.862745
20 MBG NAG 0.514706 1
21 LOG GAL 0.514286 0.775862
22 MAG FUC GAL FUC 0.513158 0.979167
23 MAG GAL FUC FUC 0.513158 0.979167
24 MGL GAL 0.508197 0.744681
25 A2G GAL NAG 0.506494 0.938776
26 BQZ 0.5 0.638298
27 NAG FUC GAL 0.5 0.978723
28 NAG FUC 0.5 0.957447
29 1GN ACY GAL 1GN BGC ACY GAL BGC 0.494118 0.938776
30 GAL NAG GAL 0.493333 0.957447
31 GAL NGA A2G 0.493151 0.938776
32 NOK GAL 0.486111 0.77193
33 MBG A2G 0.485714 1
34 MAG FUC SGA 0.481928 0.707692
35 GAL NAG FUC GAL 0.481481 0.978723
36 NAG GAL NAG GAL NAG GAL 0.481013 0.92
37 NAG GAL NAG GAL 0.481013 0.938776
38 GAL NAG GAL NAG GAL 0.481013 0.938776
39 MAN NAG GAL 0.48 0.957447
40 NGA THR GAL NAG 0.477273 0.884615
41 NAG GAL FUC GLA 0.47561 0.978723
42 A2G NAG 0.471429 0.938776
43 NAG BDP NAG BDP NAG BDP NAG 0.470588 0.901961
44 FUC GAL 0.46875 0.702128
45 NAG GAL FUC 0.467532 0.978723
46 A2G THR GAL NAG 0.465909 0.884615
47 GLA NAG GAL FUC 0.463415 0.978723
48 MMA 0.462963 0.680851
49 MBG 0.462963 0.680851
50 GYP 0.462963 0.680851
51 AMG 0.462963 0.680851
52 GLC U8V 0.461538 0.729167
53 NM9 NAG 0.461538 0.921569
54 GAL GC2 0.461538 0.666667
55 GLC GAL NAG GAL FUC GLA 0.456522 0.978723
56 NAG GAL BGC GAL 0.455696 0.957447
57 MMA MAN NAG 0.454545 1
58 MAG FUC G4S 0.452381 0.707692
59 NAG BDP 0.452055 0.88
60 GAL GLA 0.451613 0.702128
61 MMA MAN MAN 0.450704 0.744681
62 NAG NAG BMA 0.45 0.867925
63 BGC GAL NAG GAL FUC 0.449438 0.978723
64 GAL NAG GAL FUC 0.447059 0.938776
65 BGC GAL NAG 0.443038 0.957447
66 GLA NAG FUC GAL 0.44186 0.958333
67 GCU BGC 0.441176 0.6875
68 LEC NGA 0.440476 0.707692
69 BGC BGC BGC BGC BGC BGC BGC 0.439394 0.702128
70 BGC BGC BGC BGC BGC BGC 0.439394 0.702128
71 BGC BGC BGC 0.439394 0.702128
72 BGC BGC BGC BGC BGC 0.439394 0.702128
73 GLC BGC BGC BGC 0.439394 0.702128
74 NAG NAG BMA MAN 0.436782 0.867925
75 GAL FUC GAL 0.43662 0.723404
76 BGC GLA GAL 0.435484 0.702128
77 MMA GLA ABE 0.434211 0.734694
78 BGC GAL GLA NGA 0.433735 0.957447
79 BGC FUC GAL 0.430556 0.723404
80 GLC BGC FUC GAL 0.430556 0.723404
81 BMA MAN NAG 0.43038 0.957447
82 GAL FUC A2G 0.43038 0.978723
83 BGC GAL NGA 0.428571 0.957447
84 BGC FUC GAL NAG GAL 0.428571 0.978723
85 MAN MNM 0.426471 0.807692
86 NAG GAL NAG 0.425 0.938776
87 NG1 0.424242 0.724138
88 GN1 0.424242 0.724138
89 MAN NAG 0.422535 0.957447
90 GAL SIA NGA GAL 0.421569 0.851852
91 SIA GAL NGA GAL 0.421569 0.867925
92 GAL NGA 0.418919 0.897959
93 FRU BMA 0.41791 0.615385
94 NAG GAL FUC A2G 0.417722 0.978723
95 NAG G6S 0.417722 0.703125
96 MAN NAG PO4 NGA PO4 0.416667 0.793103
97 8VW 0.41573 0.886792
98 H1M MAN MAN 0.415584 0.7
99 RZM 0.415385 0.698113
100 BGC GAL GLA 0.414286 0.702128
101 IFM BGC 0.411765 0.685185
102 NAG BMA MAN MAN MAN MAN 0.411111 0.957447
103 GDL NAG 0.410959 0.938776
104 NAG GC4 0.410256 0.88
105 RR7 GLC 0.409091 0.673469
106 AMV NAG AMU NAG 0.409091 0.921569
107 BGC FUC GAL NAG 0.409091 0.978723
108 BGC 5VQ GAL GLA 0.408451 0.68
109 AHR FUB 0.40678 0.612245
110 GLC DMJ 0.405797 0.703704
111 491 0.405405 0.706897
112 BMA MAN MAN MAN 0.405063 0.765957
113 GLC GAL NAG GAL FUC A2G 0.40404 0.92
114 GLC GLC GLC GLC BGC GLC GLC 0.402985 0.702128
115 MAN BMA BMA BMA BMA BMA BMA 0.402985 0.702128
116 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.402985 0.702128
117 NDG FUC GAL FUC 0.402439 0.958333
118 NAG GAL FUC FUC 0.402439 0.958333
119 NAG GAL GLC NAG GLC RAM 0.402299 0.938776
120 YZ0 MAN MAN NAG MAN 0.402174 1
121 NBG 0.4 0.851064
122 MAN MAN 0.4 0.666667
123 BGC GAL FUC A2G 0.4 0.978723
124 ABL 0.4 0.843137
125 BGC GAL NAG GAL FUC FUC 0.4 0.958333
126 NDG NAG 0.4 0.92
Similar Ligands (3D)
Ligand no: 1; Ligand: MGC GAL; Similar ligands found: 13
No: Ligand Similarity coefficient
1 NGA GAL 0.9539
2 NGA GCD 0.9125
3 NDG GAD 0.9078
4 NDG GAL 0.9038
5 BGC GAL 0.8842
6 GAL NGT 0.8829
7 NGT GAL 0.8829
8 GAL GAL 0.8824
9 NAG GCD 0.8764
10 GLC GAL 0.8761
11 BGC BGC 0.8660
12 BMA GAL 0.8606
13 FRU GAL 0.8600
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6VGF; Ligand: WA3; 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: 6vgf.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6VGF; Ligand: WA3; 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: 6vgf.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6VGF; Ligand: WA3; 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: 6vgf.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6VGF; Ligand: WA3; 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: 6vgf.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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