Receptor
PDB id Resolution Class Description Source Keywords
2DT0 2.45 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE COMPLEX OF GOAT SIGNALLING PROTEIN TRIMER OF N-ACETYLGLUCOSAMINE AT 2.45A RESOLUTION CAPRA HIRCUS SPG-40 TRISACCHARIDE COMPLEX SIGNALING PROTEIN
Ref.: CARBOHYDRATE-BINDING PROPERTIES OF GOAT SECRETORY GLYCOPROTEIN (SPG-40) AND ITS FUNCTIONAL IMPLICATIO STRUCTURES OF THE NATIVE GLYCOPROTEIN AND ITS FOUR WITH CHITIN-LIKE OLIGOSACCHARIDES ACTA CRYSTALLOGR.,SECT.D V. 63 437 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG NAG NAG C:1;
B:1;
Part of Protein;
Valid;
none;
none;
submit data
611.598 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2DT3 2.28 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN GOAT SIGNALL PROTEIN AND THE HEXASACCHARIDE AT 2.28 A RESOLUTION CAPRA HIRCUS TIM BARREL SIGNALLING INVOLUTION MAMMARY GLAND SIGNALING
Ref.: CARBOHYDRATE-BINDING PROPERTIES OF GOAT SECRETORY GLYCOPROTEIN (SPG-40) AND ITS FUNCTIONAL IMPLICATIO STRUCTURES OF THE NATIVE GLYCOPROTEIN AND ITS FOUR WITH CHITIN-LIKE OLIGOSACCHARIDES ACTA CRYSTALLOGR.,SECT.D V. 63 437 2007
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 289 families.
1 1ZB5 - TRP PRO TRP n/a n/a
2 2DSU - NDG NAG NAG n/a n/a
3 1ZBC - TRP PRO TRP n/a n/a
4 2DT0 - NAG NAG NAG n/a n/a
5 2DT1 - NAG NAG NAG NAG n/a n/a
6 2DT3 Kd = 18 uM NAG NAG NAG NAG NAG NAG n/a n/a
70% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 1NWT - NAG NAG NAG NAG NDG NAG n/a n/a
2 1NWU - NAG NAG NAG NDG n/a n/a
3 1HJW - NAG NAG NAG NAG NAG n/a n/a
4 1ZBC - TRP PRO TRP n/a n/a
5 2DT0 - NAG NAG NAG n/a n/a
6 2DT1 - NAG NAG NAG NAG n/a n/a
7 1WAW ic50 = 0.013 uM 0AR DPR HSE HIS UN1 n/a n/a
8 1WB0 ic50 = 4.5 uM VR0 MEA IAS IAS DAL n/a n/a
9 4WKH - NAG NAG n/a n/a
10 1HKK ic50 = 40 nM NAA AMI NAA n/a n/a
11 4WK9 - NAG NAG n/a n/a
12 5NRF ic50 = 163 nM 95Q C22 H27 Cl N6 c1ccc(cc1)....
13 4WKF - NAG NAG n/a n/a
14 6JK6 Kd = 1.12 uM BV0 C24 H25 N6 O3 CC1=CC=CN2....
15 6ZE8 ic50 = 23 nM QGB C19 H27 Cl N6 O C[C@H]1CN(....
16 5NR8 ic50 = 175 nM 95N C16 H23 Br N6 CN(CCc1ccc....
17 5NRA ic50 = 123 nM 95K C19 H29 Br N6 CC(C)CN(CC....
18 6JJR Ki = 0.049 uM BU0 C27 H25 N5 O2 C[C@@H](c1....
19 2YBT ic50 = 20 uM DW0 C17 H20 N8 O4 Cn1cnc2c1C....
20 3RM4 Kd = 1.69 uM 3RM C14 H19 Br N6 O c1cc(ccc1O....
21 3RM9 Kd = 17 uM 613 C11 H15 Cl N4 [H]/N=C(N)....
22 2YBU Ki = 0.42 uM CX9 C16 H18 N8 O4 Cn1cnc2c1C....
23 3RME ic50 = 22 uM RME C17 H22 N6 O3 Cc1ccnc(c1....
24 3FY1 - NAA AMI NA1 n/a n/a
25 4P8V Kd = 204 uM NAG NAG n/a n/a
26 4AY1 - NAG NAG NAG NAG n/a n/a
27 4P8X Kd = 0.04 uM NAG NAG NAG NAG NAG NAG n/a n/a
50% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 223 families.
1 5Y2B - NAG NAG NAG NAG NAG NAG NAG n/a n/a
2 6JAW Ki = 2.18 uM BBO C19 H20 N2 O3 c1cc2cccc3....
3 6JAX - GCS GCS GCS GCS GCS GCS GCS GCS n/a n/a
4 6JAV Ki = 1.72 uM BC0 C20 H19 Cl N4 S2 CN1Cc2c(c3....
5 6JAY Ki = 1.99 uM JUK C22 H22 N5 O4 c1cc(oc1)C....
6 1NWT - NAG NAG NAG NAG NDG NAG n/a n/a
7 1NWU - NAG NAG NAG NDG n/a n/a
8 1HJW - NAG NAG NAG NAG NAG n/a n/a
9 3WQV Kd = 6.2 uM GCS GCS GCS GCS GCS n/a n/a
10 3WQW - GCS GCS GCS GCS GCS n/a n/a
11 1WNO - NAG C8 H15 N O6 CC(=O)N[C@....
12 2A3C Kd = 43 uM PNX C13 H18 N4 O3 CC(=O)CCCC....
13 2A3A ic50 = 1500 uM TEP C7 H8 N4 O2 CN1c2c([nH....
14 1W9U Kd = 0.81 uM 0AR DPR HSE HIS UN1 n/a n/a
15 6KXN - NAG NAG n/a n/a
16 6KXL - NAG C8 H15 N O6 CC(=O)N[C@....
17 6KXM - NAG NAG n/a n/a
18 1ZB5 - TRP PRO TRP n/a n/a
19 2DSU - NDG NAG NAG n/a n/a
20 1ZBC - TRP PRO TRP n/a n/a
21 2DT0 - NAG NAG NAG n/a n/a
22 2DT1 - NAG NAG NAG NAG n/a n/a
23 2DT3 Kd = 18 uM NAG NAG NAG NAG NAG NAG n/a n/a
24 1WAW ic50 = 0.013 uM 0AR DPR HSE HIS UN1 n/a n/a
25 1WB0 ic50 = 4.5 uM VR0 MEA IAS IAS DAL n/a n/a
26 5Y2C - NAG NAG NAG NAG NAG n/a n/a
27 4WKH - NAG NAG n/a n/a
28 1HKK ic50 = 40 nM NAA AMI NAA n/a n/a
29 4WK9 - NAG NAG n/a n/a
30 5NRF ic50 = 163 nM 95Q C22 H27 Cl N6 c1ccc(cc1)....
31 4WKF - NAG NAG n/a n/a
32 6JK6 Kd = 1.12 uM BV0 C24 H25 N6 O3 CC1=CC=CN2....
33 6ZE8 ic50 = 23 nM QGB C19 H27 Cl N6 O C[C@H]1CN(....
34 5NR8 ic50 = 175 nM 95N C16 H23 Br N6 CN(CCc1ccc....
35 5NRA ic50 = 123 nM 95K C19 H29 Br N6 CC(C)CN(CC....
36 6JJR Ki = 0.049 uM BU0 C27 H25 N5 O2 C[C@@H](c1....
37 3RM8 ic50 = 0.7 uM RM8 C19 H22 N4 Cc1c(c2ccc....
38 2YBT ic50 = 20 uM DW0 C17 H20 N8 O4 Cn1cnc2c1C....
39 3RM4 Kd = 1.69 uM 3RM C14 H19 Br N6 O c1cc(ccc1O....
40 3RM9 Kd = 17 uM 613 C11 H15 Cl N4 [H]/N=C(N)....
41 2YBU Ki = 0.42 uM CX9 C16 H18 N8 O4 Cn1cnc2c1C....
42 3RME ic50 = 22 uM RME C17 H22 N6 O3 Cc1ccnc(c1....
43 3FY1 - NAA AMI NA1 n/a n/a
44 4P8V Kd = 204 uM NAG NAG n/a n/a
45 4AY1 - NAG NAG NAG NAG n/a n/a
46 4P8X Kd = 0.04 uM NAG NAG NAG NAG NAG NAG n/a n/a
47 4R5E Kd = 0.000000064 M AO3 C25 H42 N4 O14 CC(=O)N[C@....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NAG NAG NAG; Similar ligands found: 97
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG NAG NAG 1 1
2 NAG NAG NAG NAG NAG NAG NAG 1 1
3 NAG NAG NAG NAG 1 1
4 NAG NAG BMA 0.830986 0.981132
5 NAG NAG BMA MAN 0.7375 0.981132
6 NAG NAG BMA BMA 0.730769 0.981481
7 NAG NAG BMA MAN MAN NAG NAG 0.680851 1
8 NAG NAG NAG NAG NAG NAG NAG NAG 0.680556 0.924528
9 NDG NAG NAG NAG NAG 0.680556 0.924528
10 NAG NAG NAG NAG NAG NAG 0.680556 0.924528
11 NAG NAG NAG NAG NAG 0.680556 0.924528
12 NAG BMA 0.647887 0.90566
13 NAG NOJ NAG 0.62963 0.894737
14 Z4S NAG NAG 0.62963 0.859649
15 NAG NOJ NAG NAG 0.62963 0.912281
16 GDL NAG 0.625 0.90566
17 NAG NAG BMA MAN MAN MAN MAN 0.584158 0.981132
18 MBG A2G 0.573333 0.851852
19 GAL NGA 0.565789 0.867925
20 NAG NGT NAG 0.551724 0.777778
21 BGC GAL NGA 0.55 0.849057
22 BMA MAN NAG 0.548781 0.849057
23 Z3Q NGA 0.547619 0.777778
24 GAL NAG GAL 0.536585 0.849057
25 AMV NAG AMU NAG 0.533333 0.890909
26 MAN NAG 0.533333 0.849057
27 NAG NAG BMA MAN NAG 0.532609 0.924528
28 3QL 0.530864 0.842105
29 MAN NAG GAL 0.52439 0.849057
30 NAG GAL NAG 0.52381 0.90566
31 MAN MAN NAG 0.52381 0.886792
32 A2G NAG 0.519481 0.90566
33 NAG NAG NAG TMX 0.517647 0.790323
34 6Y2 0.516854 0.720588
35 NAA AMI NAA 0.516129 0.710145
36 AO3 0.516129 0.710145
37 NAG NGO 0.511905 0.79661
38 NDG NAG 0.506329 0.924528
39 GAL NAG GAL NAG GAL 0.505747 0.90566
40 GAL NGA A2G 0.5 0.90566
41 MBG NAG 0.5 0.851852
42 NAG NAG FUL BMA MAN MAN NAG GAL 0.495495 1
43 UMG 0.494845 0.816667
44 BMA MAN MAN NAG GAL NAG 0.49 0.90566
45 NAG GAL NAG GAL NAG GAL 0.488636 0.924528
46 NAG GAL NAG GAL 0.488636 0.90566
47 BGC GAL NAG 0.488372 0.849057
48 NGT NAG 0.482759 0.761905
49 BGC GAL GLA NGA 0.477778 0.849057
50 AH0 NAG 0.477273 0.844828
51 SN5 SN5 0.475 0.754386
52 GUM 0.474227 0.816667
53 MMA MAN NAG 0.465116 0.851852
54 2F8 0.464789 0.796296
55 MAG 0.464789 0.796296
56 MAN MAN MAN NAG NAG 0.462366 0.90566
57 AMU NAG 0.460674 0.907407
58 GAL FUC A2G 0.45977 0.867925
59 GN1 0.459459 0.709677
60 NG1 0.459459 0.709677
61 NAG NAG BMA MAN MAN NAG GAL NAG 0.457944 0.924528
62 NM9 NAG 0.454545 0.890909
63 FHY 0.452632 0.859649
64 NAG AH0 0.451613 0.844828
65 NAA AMI NA1 0.45098 0.7
66 NDG BMA MAN MAN NAG GAL NAG 0.448598 0.924528
67 JXD 0.447619 0.728571
68 NAG GAL 0.443038 0.849057
69 NAG NAG MAN MAN MAN 0.44 0.90566
70 BGC FUC GAL NAG GAL 0.44 0.867925
71 BDP NPO NDG BDP NDG 0.439252 0.720588
72 MMA MAN NAG MAN NAG NAG 0.4375 0.907407
73 BGC FUC GAL NAG 0.4375 0.867925
74 BMA Z4Y NAG 0.43617 0.833333
75 BGC FUC GAL FUC A2G 0.43299 0.886792
76 GYU 0.432099 0.813559
77 BGC GAL FUC A2G 0.428571 0.867925
78 BGC GAL NAG NAG GAL GAL 0.425743 0.90566
79 C4W NAG FUC BMA 0.425743 0.875
80 TVD GAL 0.425 0.888889
81 C4W NAG FUC BMA MAN NAG 0.424779 0.875
82 SN5 NGT SN5 0.421053 0.6875
83 NAG GAL GLC NAG GLC RAM 0.416667 0.90566
84 3YW 0.4125 0.811321
85 ALA ASN LYS NAG NAG BMA MAN MAN NAG NAG 0.40678 0.910714
86 NAG ASN NAG BMA MAN MAN NAG NAG 0.40678 0.894737
87 BGC GAL NGA GAL 0.406593 0.849057
88 LEC NGA 0.40625 0.720588
89 NAG FUC GAL FUC A2G 0.405941 0.924528
90 NAG GAL FUC FUC A2G 0.405941 0.924528
91 GAL NAG 0.404762 0.849057
92 NAG BDP NAG BDP NAG BDP NAG 0.40404 0.907407
93 NAG NAG 0.402299 0.924528
94 NAG BMA MAN MAN NAG GAL NAG GAL 0.401869 0.924528
95 ALA NAG AH0 DAL 0.4 0.830508
96 MA8 0.4 0.821429
97 C4W NAG FUC BMA MAN MAN NAG NAG 0.4 0.875
Similar Ligands (3D)
Ligand no: 1; Ligand: NAG NAG NAG; Similar ligands found: 2
No: Ligand Similarity coefficient
1 NDG NAG NAG 0.9395
2 NAG NAG MAN 0.8511
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2DT3; Ligand: NAG NAG NAG NAG NAG NAG; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 2dt3.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 6JMN BV0 39.8892
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