Receptor
PDB id Resolution Class Description Source Keywords
3ee5 2.2 Å EC: 2.4.1.90 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...
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...
GAL 2NA NAG F:1;
E:1;
D:1;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
525.551 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2AGD 1.9 Å EC: 2.4.1.90 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 BETA1 4-GALACTOSYLTRANSFERASE-I; TRISACCHARIDE; CLOSED CONFMUTANT 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 1 families.
1 2AGD - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
2 2AE7 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
3 2AEC - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
4 2AES - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
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 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
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 1 families.
1 2AGD - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
2 2AE7 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
3 2AEC - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
4 2AES - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
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 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
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 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
2 2AE7 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
3 2AEC - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
4 2AES - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
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 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
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 (2D)
Ligand no: 1; Ligand: UDH; Similar ligands found: 88
No: Ligand ECFP6 Tc MDL keys Tc
1 UDH 1 1
2 UDP 0.705128 0.864865
3 UTP 0.7 0.864865
4 U5F 0.691358 0.864865
5 UNP 0.654762 0.842105
6 UPP 0.640449 0.842105
7 U 0.628205 0.851351
8 U5P 0.628205 0.851351
9 UFM 0.615385 0.866667
10 UPG 0.615385 0.866667
11 GDU 0.615385 0.866667
12 AWU 0.608696 0.842105
13 44P 0.604938 0.88
14 UPU 0.602273 0.864865
15 URM 0.597826 0.905405
16 660 0.597826 0.905405
17 UPF 0.595745 0.822785
18 UFG 0.595745 0.822785
19 UDX 0.595745 0.866667
20 UAD 0.595745 0.866667
21 U2F 0.595745 0.822785
22 G3N 0.59375 0.893333
23 USQ 0.583333 0.764706
24 UDP UDP 0.583333 0.837838
25 UGA 0.583333 0.853333
26 UGB 0.583333 0.853333
27 UGF 0.57732 0.810127
28 2KH 0.574713 0.842105
29 3UC 0.571429 0.822785
30 F5P 0.552381 0.844156
31 UD4 0.552381 0.844156
32 UD1 0.543689 0.855263
33 UD2 0.543689 0.855263
34 MJZ 0.542857 0.844156
35 UDM 0.539216 0.893333
36 F5G 0.537736 0.831169
37 HP7 0.533333 0.842105
38 UD7 0.533333 0.831169
39 Y6W 0.525773 0.945946
40 HWU 0.523364 0.833333
41 12V 0.523364 0.833333
42 UP5 0.518182 0.792683
43 IUG 0.513761 0.735632
44 UDZ 0.504505 0.814815
45 EEB 0.504425 0.833333
46 URI 0.5 0.794521
47 UDP GAL 0.5 0.842105
48 4TC 0.495575 0.795181
49 EPZ 0.495575 0.844156
50 EPU 0.491228 0.833333
51 U20 0.472 0.864198
52 U21 0.472 0.864198
53 U22 0.472 0.865854
54 UMA 0.471074 0.844156
55 CSQ 0.46729 0.8125
56 CSV 0.46729 0.8125
57 CJB 0.463415 0.756757
58 FZK 0.459184 0.788235
59 CTP 0.452632 0.844156
60 HF4 0.452632 0.844156
61 CDP 0.451613 0.844156
62 0RC 0.44898 0.921053
63 U3P 0.448276 0.837838
64 UA3 0.448276 0.837838
65 BUP 0.447917 0.810127
66 2QR 0.44186 0.831325
67 LSU 0.441176 0.730337
68 DUT 0.4375 0.891892
69 C2G 0.435644 0.881579
70 4RA 0.42963 0.752941
71 YSU 0.425926 0.738636
72 DUD 0.425532 0.891892
73 C5G 0.424528 0.846154
74 U4S 0.422222 0.813333
75 UML 0.42069 0.935897
76 7XL 0.42 0.894737
77 CDC 0.419048 0.788235
78 UAG 0.416058 0.871795
79 1AA 0.415929 0.814815
80 U2P 0.41573 0.851351
81 PUP 0.415094 0.891892
82 CDM 0.415094 0.85
83 UD0 0.413043 0.744186
84 U2S 0.413043 0.826667
85 U3S 0.413043 0.813333
86 5GW 0.411765 0.820513
87 U1S 0.405941 0.807692
88 UTP U U U 0.4 0.8
Ligand no: 2; Ligand: GAL 2NA NAG; Similar ligands found: 17
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL 2NA NAG 1 1
2 MBG NAG 0.5 0.849057
3 GAL NGA A2G 0.484536 0.833333
4 BGC GAL NAG 0.460784 0.882353
5 MMA MAN NAG 0.455446 0.849057
6 NAG GAL NAG 0.446602 0.833333
7 MAN MAN MAN NAG NAG 0.440367 0.833333
8 BGC GAL GLA NGA 0.439252 0.882353
9 BMA MAN NAG 0.436893 0.882353
10 BGC FUC GAL NAG 0.432432 0.865385
11 GAL NGA 0.428571 0.830189
12 YZ0 MAN MAN NAG MAN 0.426087 0.849057
13 A2G NAG 0.408163 0.833333
14 GAL NAG GAL NAG GAL 0.407407 0.833333
15 MAN MAN NAG 0.40566 0.849057
16 NDG BMA MAN MAN NAG MAN MAN 0.404762 0.833333
17 MAN NAG 0.402062 0.882353
Similar Ligands (3D)
Ligand no: 1; Ligand: UDH; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: GAL 2NA NAG; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2AGD; Ligand: BMA MAN NAG; 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: 2agd.bio3) has 30 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2AGD; Ligand: UDH; 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: 2agd.bio3) has 31 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2AGD; Ligand: UDH; 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: 2agd.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2AGD; Ligand: UDH; 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: 2agd.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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