Receptor
PDB id Resolution Class Description Source Keywords
3EE5 2.2 Å EC: 2.4.1.22 CRYSTAL STRUCTURE OF HUMAN M340H-BETA1,4-GALACTOSYLTRANSFERA (M340H-B4GAL-T1) IN COMPLEX WITH GLCNAC-BETA1,3-GAL-BETA- N APHTHALENEMETHANOL HOMO SAPIENS CLOSED CONFORMATION CARBOHYDRATE ACCEPTOR BINDING ALTERNATINITIATION CELL MEMBRANE CONGENITAL DISORDER OF GLYCOSYLAGLYCOPROTEIN GLYCOSYLTRANSFERASE GOLGI APPARATUS MANGANEMEMBRANE METAL-BINDING SECRETED SIGNAL-ANCHOR TRANSFERATRANSMEMBRANE
Ref.: DEOXYGENATED DISACCHARIDE ANALOGS AS SPECIFIC INHIB {BETA}1-4-GALACTOSYLTRANSFERASE 1 AND SELECTIN-MEDI TUMOR METASTASIS J.BIOL.CHEM. V. 284 4952 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DIO C:435;
Invalid;
none;
submit data
88.105 C4 H8 O2 C1COC...
GOL A:417;
A:420;
B:414;
B:415;
B:416;
B:419;
C:418;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MES C:436;
Invalid;
none;
submit data
195.237 C6 H13 N O4 S C1COC...
MN A:611;
B:400;
C:400;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
NAG GAL 2NA A:400;
B:1400;
C:2400;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
525.551 n/a O=C(N...
SO4 A:602;
A:604;
A:607;
A:609;
A:610;
B:601;
B:603;
B:605;
B:606;
B:611;
B:613;
B:614;
C:608;
C:612;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
UDH A:399;
B:1399;
C:2399;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
503.335 C15 H27 N3 O12 P2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2AGD 1.9 Å EC: 2.4.1.22 CRYSTAL STRUCTURE OF HUMAN M340H-BETA-1,4-GALACTOSYLTRANSFER I(M340H-B4GAL-T1) IN COMPLEX WITH GLCNAC-BETA1,4-MAN-ALPHA1B ETA-OR HOMO SAPIENS BETA14-GALACTOSYLTRANSFERASE-I; TRISACCHARIDE; CLOSED CONFOMUTANT TRANSFERASE
Ref.: OLIGOSACCHARIDE PREFERENCES OF BETA1,4-GALACTOSYLTRANSFERASE-I: CRYSTAL STRUCTURES MET340HIS MUTANT OF HUMAN BETA1,4-GALACTOSYLTRANSFE WITH A PENTASACCHARIDE AND TRISACCHARIDES OF THE N-MOIETY J.MOL.BIOL. V. 353 53 2005
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2AGD - NAG MAN BMA n/a n/a
2 2AE7 - NAG MAN n/a n/a
3 2AEC - NAG MAN BMA n/a n/a
4 2AES - NAG MAN BMA n/a n/a
5 2FYB - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
6 1TVY - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
7 2AH9 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
8 3EE5 - NAG GAL 2NA n/a n/a
9 1O0R - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
10 1FR8 - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
11 4KRV - NGS C8 H15 N O9 S CC(=O)N[C@....
12 1TW1 - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
13 1TW5 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2AGD - NAG MAN BMA n/a n/a
2 2AE7 - NAG MAN n/a n/a
3 2AEC - NAG MAN BMA n/a n/a
4 2AES - NAG MAN BMA n/a n/a
5 2FYB - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
6 1TVY - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
7 2AH9 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
8 3EE5 - NAG GAL 2NA n/a n/a
9 1O0R - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
10 1FR8 - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
11 4KRV - NGS C8 H15 N O9 S CC(=O)N[C@....
12 1TW1 - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
13 1TW5 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
14 1FGX - U5P C9 H13 N2 O9 P C1=CN(C(=O....
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2AGD - NAG MAN BMA n/a n/a
2 2AE7 - NAG MAN n/a n/a
3 2AEC - NAG MAN BMA n/a n/a
4 2AES - NAG MAN BMA n/a n/a
5 2FYB - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
6 1TVY - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
7 2AH9 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
8 3EE5 - NAG GAL 2NA n/a n/a
9 1O0R - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
10 1FR8 - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
11 4KRV - NGS C8 H15 N O9 S CC(=O)N[C@....
12 1TW1 - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
13 1TW5 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
14 1FGX - U5P C9 H13 N2 O9 P C1=CN(C(=O....
15 4LW3 - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
16 4LW6 - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
17 3LW6 - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
18 4M4K - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
19 4IRP - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAG GAL 2NA; Similar ligands found: 21
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG GAL 2NA 1 1
2 GAL NAG 0.505495 0.882353
3 NAG GAL 0.505495 0.882353
4 NGA GAL 0.505495 0.882353
5 NAG MBG 0.5 0.849057
6 NAG GAL BGC 0.460784 0.882353
7 NAG MAN MMA 0.455446 0.849057
8 NAG GAL NAG 0.446602 0.833333
9 NAG MAN MAN MAN NAG 0.440367 0.833333
10 NGA GLA GAL BGC 0.439252 0.882353
11 FUC BGC GAL NAG 0.432432 0.865385
12 NAG MAN BMA 0.428571 0.882353
13 NAG MAN MAN 0.428571 0.882353
14 WZ5 0.426087 0.849057
15 NAG NGA 0.408163 0.833333
16 NAG A2G 0.408163 0.833333
17 NAG GAL GAL NAG GAL 0.407407 0.833333
18 NAG NAG 0.405941 0.758621
19 MAN MAN NAG 0.40566 0.849057
20 M5G 0.404762 0.833333
21 MAN NAG 0.402062 0.882353
Ligand no: 2; Ligand: UDH; Similar ligands found: 82
No: Ligand ECFP6 Tc MDL keys Tc
1 UDH 1 1
2 UDP 0.705128 0.864865
3 UTP 0.7 0.864865
4 UNP 0.654762 0.842105
5 UPP 0.640449 0.842105
6 U5P 0.628205 0.851351
7 UPG 0.615385 0.866667
8 GUD 0.615385 0.866667
9 GDU 0.615385 0.866667
10 UFM 0.615385 0.866667
11 44P 0.604938 0.88
12 UPU 0.602273 0.864865
13 URM 0.597826 0.905405
14 660 0.597826 0.905405
15 UDX 0.595745 0.866667
16 UAD 0.595745 0.866667
17 U2F 0.595745 0.822785
18 UPF 0.595745 0.822785
19 UFG 0.595745 0.822785
20 G3N 0.59375 0.893333
21 UGA 0.583333 0.853333
22 UDP UDP 0.583333 0.837838
23 USQ 0.583333 0.764706
24 UGB 0.583333 0.853333
25 2KH 0.574713 0.842105
26 3UC 0.571429 0.822785
27 UD4 0.552381 0.844156
28 UD2 0.543689 0.855263
29 UD1 0.543689 0.855263
30 MJZ 0.542857 0.844156
31 UDM 0.539216 0.893333
32 HP7 0.533333 0.842105
33 UD7 0.533333 0.831169
34 Y6W 0.525773 0.945946
35 12V 0.523364 0.833333
36 HWU 0.523364 0.833333
37 UP5 0.518182 0.792683
38 IUG 0.513761 0.735632
39 UDZ 0.504505 0.814815
40 EEB 0.504425 0.833333
41 U 0.5 0.794521
42 UDP GAL 0.5 0.842105
43 URI 0.5 0.794521
44 4TC 0.495575 0.795181
45 EPZ 0.495575 0.844156
46 EPU 0.491228 0.833333
47 U U 0.49 0.828947
48 U20 0.472 0.864198
49 U22 0.472 0.865854
50 U21 0.472 0.864198
51 UMA 0.471074 0.844156
52 CSQ 0.46729 0.8125
53 CSV 0.46729 0.8125
54 CJB 0.463415 0.756757
55 CTP 0.452632 0.844156
56 CDP 0.451613 0.844156
57 CH 0.449438 0.794872
58 UA3 0.448276 0.837838
59 U3P 0.448276 0.837838
60 2QR 0.44186 0.831325
61 DUT 0.4375 0.891892
62 C2G 0.435644 0.881579
63 4RA 0.42963 0.752941
64 A U 0.428571 0.771084
65 DUD 0.425532 0.891892
66 C5G 0.424528 0.846154
67 U4S 0.422222 0.813333
68 UML 0.42069 0.935897
69 7XL 0.42 0.894737
70 CDC 0.419048 0.788235
71 UAG 0.416058 0.871795
72 1AA 0.415929 0.814815
73 U2P 0.41573 0.851351
74 PUP 0.415094 0.891892
75 CDM 0.415094 0.85
76 U2S 0.413043 0.826667
77 U3S 0.413043 0.813333
78 UD0 0.413043 0.744186
79 5GW 0.411765 0.820513
80 U1S 0.405941 0.807692
81 U U U U 0.403846 0.815789
82 UTP U U U 0.4 0.8
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2AGD; Ligand: NAG MAN BMA; Similar sites found: 8
This union binding pocket(no: 1) in the query (biounit: 2agd.bio3) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3JSZ UPG 0.005385 0.41296 1.74216
2 1YQC GLV 0.02192 0.4053 1.76471
3 5TZJ UD1 0.0006147 0.42952 3.48432
4 5FV9 Y6W 0.002728 0.41919 6.96864
5 5FV9 UDP 0.002728 0.41919 6.96864
6 1A0T SUC 0.04701 0.40384 6.96864
7 1O7Q UDP 0.003045 0.40568 7.31707
8 1O7Q GAL NAG 0.003045 0.40568 7.31707
Pocket No.: 2; Query (leader) PDB : 2AGD; Ligand: UDH; Similar sites found: 9
This union binding pocket(no: 2) in the query (biounit: 2agd.bio3) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3JSZ UPG 0.00578 0.41296 1.74216
2 1YQC GLV 0.0229 0.4053 1.76471
3 5TZJ UD1 0.0006772 0.42318 3.48432
4 5FV9 Y6W 0.002946 0.41919 6.96864
5 5FV9 UDP 0.002946 0.41919 6.96864
6 1A0T SUC 0.04918 0.40384 6.96864
7 1O7Q UDP 0.003304 0.40568 7.31707
8 1O7Q GAL NAG 0.003304 0.40568 7.31707
9 4GK9 MAN BMA MAN MAN MAN 0.02154 0.425 10.0358
Pocket No.: 3; Query (leader) PDB : 2AGD; Ligand: UDH; Similar sites found: 2
This union binding pocket(no: 3) in the query (biounit: 2agd.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4NYT PC 0.02397 0.40361 9.21659
2 2Y2B AH0 0.03969 0.40618 10.1604
Pocket No.: 4; Query (leader) PDB : 2AGD; Ligand: UDH; Similar sites found: 2
This union binding pocket(no: 4) in the query (biounit: 2agd.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2OVW CBI 0.008505 0.43515 2.78746
2 2D7I UDP 0.004145 0.44193 5.92335
Feedback