Receptor
PDB id Resolution Class Description Source Keywords
2AE7 2 Å EC: 2.4.1.22 CRYSTAL STRUCTURE OF HUMAN M340H-BETA1,4-GALACTOSYLTRANSFERA (M340H-B4GAL-T1) IN COMPLEX WITH PENTASACCHARIDE HOMO SAPIENS BETA14-GALACTOSYLTRANSFERASE-I; PENTASACCHARIDE; CLOSED CONFORMATION; MUTANT 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DIO C:433;
Invalid;
none;
submit data
88.105 C4 H8 O2 C1COC...
GOL A:415;
B:412;
B:413;
B:414;
B:417;
B:418;
C:416;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MN A:400;
B:402;
C:404;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
NAG MAN A:405;
C:410;
Valid;
Valid;
none;
none;
submit data
383.35 n/a O=C(N...
NAG MAN MAN B:407;
Valid;
none;
submit data
545.491 n/a O=C(N...
SO4 A:419;
A:420;
A:421;
A:429;
B:422;
B:424;
B:425;
B:428;
B:430;
B:432;
C:423;
C:426;
C:427;
C:431;
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:401;
C:403;
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 MAN; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG MAN 1 1
2 5AX 0.660714 0.862745
3 FUC GAL NAG A2G 0.414894 0.875
Ligand no: 2; Ligand: NAG MAN MAN; Similar ligands found: 164
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG MAN MAN 1 1
2 NAG MAN BMA 1 1
3 NAG MAN MAN MAN NAG 0.779221 0.9375
4 MMA MAN NAG MAN NAG NAG 0.635294 0.9
5 NAG MAN GAL MAN MAN NAG GAL 0.629214 0.9375
6 NAG BMA NAG MAN MAN NAG NAG 0.617021 0.918367
7 NAG NAG BMA MAN NAG 0.617021 0.849057
8 NAG MAN BMA NDG MAN NAG GAL 0.608247 0.918367
9 MAN NAG 0.589041 1
10 WZ5 0.582418 0.957447
11 NGA GAL BGC 0.5625 1
12 MAN MAN MAN BMA MAN 0.560976 0.733333
13 NGA GAL 0.56 1
14 NAG GAL 0.56 1
15 GAL NAG 0.56 1
16 NAG NAG BMA MAN MAN NAG NAG 0.558824 0.849057
17 NAG MAN GAL BMA NDG MAN NAG GAL 0.556701 0.918367
18 NAG MAN MAN MAN NAG GAL NAG GAL 0.556701 0.918367
19 NAG MAN GAL BMA NAG MAN NAG GAL 0.556701 0.918367
20 MAN BMA NAG NAG MAN NAG GAL GAL 0.556701 0.918367
21 3PV 0.555556 0.9
22 M5G 0.554455 0.9375
23 MAN MAN NAG 0.554217 0.957447
24 NAG NGA 0.552632 0.9375
25 CBS CBS 0.552632 0.9375
26 NAG A2G 0.552632 0.9375
27 NAG GDL 0.552632 0.9375
28 CBS 0.552632 0.9375
29 NAG NDG 0.552632 0.9375
30 NAG MAN MMA 0.548781 0.957447
31 NAG GAL BGC 0.535714 1
32 CTO 0.525 0.918367
33 NAG NAG NAG NAG NDG NAG 0.525 0.918367
34 NDG NAG NAG NDG 0.525 0.918367
35 NAG NAG NAG NAG NAG NAG NAG NAG 0.525 0.918367
36 NAG NAG NAG NDG 0.525 0.918367
37 NAG NAG NAG 0.525 0.918367
38 NAG NAG NAG NAG NAG NAG 0.525 0.918367
39 NDG NAG NAG NDG NAG 0.525 0.918367
40 NDG NAG NAG 0.525 0.918367
41 NAG NAG NAG NAG NDG 0.525 0.918367
42 NDG NAG NAG NAG 0.525 0.918367
43 NAG NAG NAG NAG 0.525 0.918367
44 NAG NAG NDG 0.525 0.918367
45 NAG NAG NAG NAG NAG 0.525 0.918367
46 NDG NAG 0.518987 0.918367
47 MAN MAN MAN BMA MAN MAN MAN 0.516484 0.73913
48 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.514286 0.9375
49 MBG A2G 0.506329 0.957447
50 A2G MBG 0.506329 0.957447
51 NGA GLA GAL BGC 0.505618 1
52 ASN NAG NAG BMA MAN MAN NAG NAG 0.5 0.833333
53 NAG MBG 0.493671 0.957447
54 WZ4 0.490566 0.9
55 NAG AMU 0.488636 0.9
56 NAG MUB 0.488636 0.9
57 FUC GL0 A2G 0.488372 0.978261
58 FUC GAL A2G 0.488372 0.978261
59 A2G GLA FUC 0.488372 0.978261
60 NGA GAL FUC 0.488372 0.978261
61 FUC GLA A2G 0.488372 0.978261
62 A2G GAL FUC 0.488372 0.978261
63 NAG NAG 0.487805 0.846154
64 A2G GAL BGC FUC 0.484211 0.978261
65 NAG GAL NAG 0.482759 0.9375
66 GAL GAL 0.472222 0.733333
67 GLA GLC 0.472222 0.733333
68 GLA BMA 0.472222 0.733333
69 BMA GLA 0.472222 0.733333
70 LAK 0.472222 0.733333
71 MAN BMA 0.472222 0.733333
72 GLA BGC 0.472222 0.733333
73 MLB 0.472222 0.733333
74 BGC GLA 0.472222 0.733333
75 MAN NAG GAL 0.465116 1
76 GAL NAG MAN 0.465116 1
77 GLC GLC GLC GLC GLC GLC 0.463415 0.733333
78 RAM GLC GAL NAG NAG GLC 0.461538 0.865385
79 NGT NAG 0.460674 0.775862
80 MAN MAN MAN 0.459459 0.733333
81 GLC GLC GLC GLC BGC 0.459459 0.733333
82 GLC GLC GLC 0.459459 0.733333
83 GLC GLC GLC GLC GLC BGC 0.459459 0.733333
84 MAG 0.458333 0.893617
85 2F8 0.458333 0.893617
86 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.457143 0.918367
87 AH0 NAG 0.455556 0.833333
88 3QL 0.453488 0.865385
89 GN1 0.453333 0.75
90 NG1 0.453333 0.75
91 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.45098 1
92 DLD 0.450549 0.775862
93 MAN MAN NAG MAN NAG 0.45 0.9375
94 NAG NAG BMA MAN MAN 0.45 0.9375
95 NAG NGO 0.448276 0.865385
96 FUC BGC GAL NAG 0.447917 0.978261
97 NAG NAG NGT 0.446809 0.762712
98 GLC GAL NAG GAL 0.445652 1
99 NOJ NAG NAG NAG 0.445652 0.818182
100 NOJ NAG NAG 0.445652 0.833333
101 GAL BGC NAG GAL 0.444444 1
102 BGC FUC GAL FUC A2G 0.443299 0.957447
103 GLC FUC GAL FUC A2G 0.443299 0.957447
104 NAG NAG NAG NAG NAG NAG NAG 0.442105 0.833333
105 MAN MAN MAN MAN 0.440476 0.733333
106 MAN MAN BMA MAN 0.440476 0.733333
107 A2G GAL NAG FUC 0.438776 0.918367
108 NAG NAG BMA MAN MAN MAN MAN 0.4375 0.865385
109 1GN ACY GAL ACY 1GN BGC GAL BGC 0.434343 0.9375
110 BGA 0.434343 0.818182
111 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.434343 0.9375
112 NAG NM9 0.433333 0.882353
113 NAG AMU NAG AMV 0.43299 0.882353
114 NAG AH0 0.431579 0.833333
115 6Y2 0.431579 0.703125
116 LEC NGA 0.431579 0.703125
117 NAG GAL FUC FUC A2G 0.43 0.918367
118 FUC GAL NAG A2G FUC 0.43 0.918367
119 NAG BDP NAG BDP NAG BDP NAG 0.428571 0.9
120 MA8 0.428571 0.843137
121 NAG GAL 2NA 0.428571 0.882353
122 NAG GCU NAG GCU NAG GCU 5AX 0.428571 0.9
123 FUC GAL NAG 0.426966 0.978261
124 FUL GAL NAG 0.426966 0.978261
125 FUC GAL NDG 0.426966 0.978261
126 DR2 0.426966 0.978261
127 NDG GAL FUC 0.426966 0.978261
128 GLC GAL NAG GAL FUC A2G 0.425926 0.918367
129 A2G GAL NAG FUC GAL GLC 0.425926 0.918367
130 3YW 0.425 0.913043
131 GAL NDG 0.419753 1
132 NLC 0.419753 1
133 NDG GAL 0.419753 1
134 NAG GAL GAL NAG GAL 0.419355 0.9375
135 NAG BMA MAN MAN MAN MAN 0.418367 1
136 SN5 SN5 0.416667 0.803922
137 BDZ 0.413043 0.957447
138 FUC NDG GAL FUC 0.413043 0.957447
139 FUC GAL NDG FUC 0.413043 0.957447
140 GAL NDG FUC FUC 0.413043 0.957447
141 GAL NAG FUC FUC 0.413043 0.957447
142 FUC GAL NAG FUC 0.413043 0.957447
143 FUC NAG GAL FUC 0.413043 0.957447
144 BCW 0.413043 0.957447
145 FUC GAL NAG GAL BGC 0.411765 0.978261
146 TNR 0.409639 0.86
147 LAT NAG GAL 0.408602 1
148 BGC GAL NAG GAL 0.408602 1
149 GAL NAG GAL BGC 0.408602 1
150 NAG GAL FUC 0.406593 0.978261
151 DR3 0.406593 0.978261
152 AO3 0.405941 0.692308
153 FUB AHR AHR 0.405405 0.638298
154 AHR AHR AHR 0.405405 0.638298
155 GLC GLC GLC GLC 0.404762 0.733333
156 NAG GAL GAL NAG 0.404255 0.9375
157 GAL NAG GAL NAG GAL NAG 0.404255 0.918367
158 FUB AHR 0.402778 0.638298
159 AHR AHR 0.402778 0.638298
160 GAL NGA 0.402439 1
161 A2G GAL 0.402439 1
162 GAL A2G 0.402439 1
163 GAL NGA A2G 0.402299 0.918367
164 GLC GLC GLC BGC 0.402299 0.733333
Ligand no: 3; 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
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