Receptor
PDB id Resolution Class Description Source Keywords
1TW1 2.3 Å EC: 2.4.1.22 BETA-1,4-GALACTOSYLTRANSFERASE MUTANT MET344HIS (M344H-GAL- T1) COMPLEX WITH UDP-GALACTOSE AND MAGNESIUM BOS TAURUS MET344HIS MUTATION; CLOSED CONFORMATION; MN BINDING TRANSFERASE
Ref.: EFFECT OF THE MET344HIS MUTATION ON THE CONFORMATIONAL DYNAMICS OF BOVINE BETA-1,4-GALACTOSYLTRANSFERASE: CRYSTAL STRUCTURE OF THE MET344HIS MUTANT IN COMPLEX WITH CHITOBIOSE BIOCHEMISTRY V. 43 12513 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DIO A:860;
A:861;
Invalid;
Invalid;
none;
none;
submit data
88.105 C4 H8 O2 C1COC...
GDU A:2;
B:404;
Valid;
Valid;
none;
none;
submit data
566.302 C15 H24 N2 O17 P2 C1=CN...
MES B:870;
Invalid;
none;
submit data
195.237 C6 H13 N O4 S C1COC...
MG A:1;
B:403;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
SO4 A:858;
A:859;
B:855;
B:856;
B:857;
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
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 (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 1TVY - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
4 2AEC - NAG MAN BMA n/a n/a
5 2AH9 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
6 3EE5 - NAG GAL 2NA n/a n/a
7 1O0R - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
8 1FR8 - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
9 4KRV - NGS C8 H15 N O9 S CC(=O)NC1C....
10 1TW1 - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
11 2AES - NAG MAN BMA n/a n/a
12 1FGX - U5P C9 H13 N2 O9 P C1=CN(C(=O....
13 1TW5 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
14 2FYB - UDP C9 H14 N2 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 1TVY - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
4 2AEC - NAG MAN BMA n/a n/a
5 2AH9 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
6 3EE5 - NAG GAL 2NA n/a n/a
7 1O0R - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
8 1FR8 - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
9 4KRV - NGS C8 H15 N O9 S CC(=O)NC1C....
10 1TW1 - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
11 2AES - NAG MAN BMA n/a n/a
12 1FGX - U5P C9 H13 N2 O9 P C1=CN(C(=O....
13 1TW5 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
14 2FYB - UDP C9 H14 N2 O12 P2 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 4LW6 - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 3LW6 - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
3 4LW3 - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
4 4M4K - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
5 4IRP - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
6 2AGD - NAG MAN BMA n/a n/a
7 2AE7 - NAG MAN n/a n/a
8 1TVY - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
9 2AEC - NAG MAN BMA n/a n/a
10 2AH9 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
11 3EE5 - NAG GAL 2NA n/a n/a
12 1O0R - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
13 1FR8 - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
14 4KRV - NGS C8 H15 N O9 S CC(=O)NC1C....
15 1TW1 - GDU C15 H24 N2 O17 P2 C1=CN(C(=O....
16 2AES - NAG MAN BMA n/a n/a
17 1FGX - U5P C9 H13 N2 O9 P C1=CN(C(=O....
18 1TW5 - UDH C15 H27 N3 O12 P2 C1=CN(C(=O....
19 2FYB - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GDU; Similar ligands found: 85
No: Ligand ECFP6 Tc MDL keys Tc
1 GDU 1 1
2 UPG 1 1
3 GUD 1 1
4 UFM 1 1
5 USQ 0.8 0.846154
6 UPF 0.797619 0.943662
7 U2F 0.797619 0.943662
8 UFG 0.797619 0.943662
9 UD1 0.73913 0.985294
10 UD2 0.73913 0.985294
11 UGA 0.738636 0.985075
12 UGB 0.738636 0.985075
13 UDP 0.717949 0.941176
14 UAD 0.715909 0.970588
15 UDP GAL 0.715909 0.970588
16 UDX 0.715909 0.970588
17 UTP 0.7125 0.941176
18 IUG 0.693878 0.835443
19 C5G 0.688889 0.943662
20 UPU 0.670588 0.970149
21 EPZ 0.650485 0.971014
22 UNP 0.647059 0.914286
23 EPU 0.644231 0.957143
24 EEB 0.644231 0.957143
25 U 0.641026 0.926471
26 U5P 0.641026 0.926471
27 HP7 0.636364 0.970588
28 UD7 0.636364 0.956522
29 2GW 0.632653 0.957143
30 MJZ 0.63 0.942857
31 UD4 0.623762 0.942857
32 UDZ 0.615385 0.88
33 UPP 0.615385 0.942029
34 UDH 0.615385 0.866667
35 UMA 0.598214 0.971014
36 44P 0.597561 0.901408
37 UDM 0.59596 0.942857
38 12V 0.592233 0.929577
39 HWU 0.592233 0.929577
40 1GW 0.590476 0.917808
41 2KH 0.586207 0.914286
42 UDP UDP 0.576471 0.911765
43 U20 0.567797 0.858974
44 U21 0.567797 0.858974
45 U22 0.567797 0.8375
46 URI 0.552632 0.865672
47 CJB 0.551282 0.850746
48 UP5 0.527273 0.855263
49 UAG 0.523438 0.917808
50 2QR 0.520325 0.848101
51 DAU 0.519608 0.891892
52 U3P 0.511905 0.911765
53 UA3 0.511905 0.911765
54 CSQ 0.504762 0.878378
55 CSV 0.504762 0.878378
56 4TC 0.504425 0.833333
57 U U 0.5 0.927536
58 UD0 0.484848 0.846154
59 PUP 0.480392 0.887324
60 UML 0.478571 0.858974
61 U2P 0.476744 0.926471
62 CXY 0.471154 0.916667
63 GKE 0.463636 0.8
64 GDD 0.463636 0.8
65 GDC 0.463636 0.8
66 A U 0.461538 0.831169
67 CTP 0.447917 0.888889
68 CDP 0.446809 0.888889
69 ADQ 0.443396 0.828947
70 DKX 0.44186 0.774648
71 U2S 0.43956 0.77027
72 UMF 0.438202 0.833333
73 U4S 0.433333 0.733333
74 DUT 0.43299 0.861111
75 U3S 0.423913 0.756757
76 5GW 0.421569 0.915493
77 DUD 0.421053 0.861111
78 5FU 0.417582 0.863014
79 C2G 0.417476 0.902778
80 UPA 0.416667 0.868421
81 U1S 0.415842 0.776316
82 2TU 0.411765 0.777778
83 UTP U U U 0.409524 0.897059
84 139 0.406504 0.835443
85 APU 0.401639 0.831169
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2AGD; Ligand: UDH; Similar sites found: 15
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)
1 2D7I UDP 0.003468 0.44438
2 4AMF ACP 0.01269 0.4347
3 4D0Z HWU 0.001073 0.42942
4 2OVW CBI 0.01061 0.42889
5 4D0Z HWU 0.002703 0.42592
6 4GK9 MAN BMA MAN MAN MAN 0.02055 0.425
7 4D0Z HWU 0.001839 0.42002
8 4D0Z HWU 0.001556 0.41991
9 3JSZ UPG 0.005385 0.41296
10 4D0Z HWU 0.002004 0.40998
11 4D0Z HWU 0.004631 0.40671
12 1YQC GLV 0.02192 0.4053
13 1A0T SUC 0.04701 0.40384
14 1O7Q GAL NAG 0.004266 0.4
15 1O7Q UDP 0.004266 0.4
Pocket No.: 2; Query (leader) PDB : 2AGD; Ligand: UDH; Similar sites found: 15
This union binding pocket(no: 2) in the query (biounit: 2agd.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 2D7I UDP 0.003938 0.44167
2 2OVW CBI 0.009718 0.43086
3 4D0Z HWU 0.001275 0.42641
4 4D0Z HWU 0.002961 0.42421
5 4D0Z HWU 0.001652 0.41889
6 4D0Z HWU 0.002106 0.41766
7 3JSZ UPG 0.00481 0.41509
8 4D0Z HWU 0.002154 0.40878
9 2Y2B AH0 0.04169 0.40618
10 1A0T SUC 0.04621 0.40448
11 4NYT PC 0.02503 0.40361
12 1O7Q GAL NAG 0.003602 0.40285
13 1O7Q UDP 0.003602 0.40285
14 2Q2Y MKR 0.02466 0.4001
15 2Q2Y ADP 0.02466 0.4001
Pocket No.: 3; Query (leader) PDB : 2AGD; Ligand: NAG MAN BMA; Similar sites found: 14
This union binding pocket(no: 3) in the query (biounit: 2agd.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 2D7I UDP 0.004145 0.44193
2 2OVW CBI 0.008505 0.43515
3 2OVW CBI 0.008754 0.4345
4 4D0Z HWU 0.001572 0.42419
5 4D0Z HWU 0.003344 0.4233
6 4D0Z HWU 0.00222 0.41523
7 4D0Z HWU 0.002634 0.41516
8 3JSZ UPG 0.005539 0.41377
9 1A0T SUC 0.03864 0.4114
10 1O7Q GAL NAG 0.002558 0.41001
11 1O7Q UDP 0.002558 0.41001
12 4D0Z HWU 0.005938 0.40362
13 4D0Z HWU 0.003266 0.40327
14 4AOI 4K0 0.02158 0.40297
Pocket No.: 4; Query (leader) PDB : 2AGD; Ligand: UDH; Similar sites found: 14
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)
1 2D7I UDP 0.004145 0.44193
2 2OVW CBI 0.008505 0.43515
3 2OVW CBI 0.008754 0.4345
4 4D0Z HWU 0.001572 0.42419
5 4D0Z HWU 0.003344 0.4233
6 4D0Z HWU 0.00222 0.41523
7 4D0Z HWU 0.002634 0.41516
8 3JSZ UPG 0.005539 0.41377
9 1A0T SUC 0.03864 0.4114
10 1O7Q GAL NAG 0.002558 0.41001
11 1O7Q UDP 0.002558 0.41001
12 4D0Z HWU 0.005938 0.40362
13 4D0Z HWU 0.003266 0.40327
14 4AOI 4K0 0.02158 0.40297
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