Receptor
PDB id Resolution Class Description Source Keywords
4IRP 2.1 Å EC: 2.4.1.133 CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF HUMAN BETA1,4- GALACTOSYLTRANSFERASE-7 IN OPEN CONFORMATION WITH MANGANSES HOMO SAPIENS GT-A FOLD OPEN CONFORMATION MANGANESE AND UDP COMPLEX GLYCOSYLTRANSFERASE GOLGI TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF BETA-1,4-GALACTOSYLTRANSFERAS ENZYME REVEAL CONFORMATIONAL CHANGES AND SUBSTRATE J.BIOL.CHEM. V. 288 31963 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT B:404;
A:406;
A:404;
B:403;
A:403;
A:405;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
UDP B:401;
A:401;
Valid;
Valid;
none;
none;
submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
MN A:402;
B:402;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
IMD A:407;
Invalid;
none;
submit data
69.085 C3 H5 N2 c1c[n...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4IRP 2.1 Å EC: 2.4.1.133 CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF HUMAN BETA1,4- GALACTOSYLTRANSFERASE-7 IN OPEN CONFORMATION WITH MANGANSES HOMO SAPIENS GT-A FOLD OPEN CONFORMATION MANGANESE AND UDP COMPLEX GLYCOSYLTRANSFERASE GOLGI TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF BETA-1,4-GALACTOSYLTRANSFERAS ENZYME REVEAL CONFORMATIONAL CHANGES AND SUBSTRATE J.BIOL.CHEM. V. 288 31963 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4IRP - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4IRP - 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 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: UDP; Similar ligands found: 116
No: Ligand ECFP6 Tc MDL keys Tc
1 UDP 1 1
2 UTP 0.892308 1
3 UNP 0.8 0.970149
4 U5P 0.78125 0.984615
5 UPU 0.72973 0.940298
6 2KH 0.722222 0.970149
7 44P 0.720588 0.955882
8 URM 0.717949 0.927536
9 GUD 0.717949 0.941176
10 GDU 0.717949 0.941176
11 UFM 0.717949 0.941176
12 UPG 0.717949 0.941176
13 660 0.717949 0.927536
14 UDP UDP 0.714286 0.939394
15 UDH 0.705128 0.864865
16 UPP 0.705128 0.941176
17 UPF 0.691358 0.888889
18 U2F 0.691358 0.888889
19 UFG 0.691358 0.888889
20 UDX 0.670732 0.941176
21 UAD 0.670732 0.941176
22 3UC 0.658824 0.888889
23 USQ 0.654762 0.820513
24 UGB 0.654762 0.955224
25 UGA 0.654762 0.955224
26 G3N 0.647059 0.914286
27 UDM 0.636364 0.914286
28 URI 0.625 0.863636
29 U 0.625 0.863636
30 UD1 0.622222 0.927536
31 UD2 0.622222 0.927536
32 UDP GAL 0.611765 0.913043
33 Y6W 0.607143 0.888889
34 CDP 0.605263 0.942029
35 UD7 0.591398 0.927536
36 HP7 0.591398 0.941176
37 MJZ 0.585106 0.914286
38 IUG 0.583333 0.810127
39 12V 0.578947 0.901408
40 HWU 0.578947 0.901408
41 UD4 0.578947 0.914286
42 CJB 0.573529 0.820895
43 UDZ 0.571429 0.853333
44 DUD 0.571429 0.913043
45 UP5 0.571429 0.853333
46 U U 0.563218 0.955224
47 EPZ 0.56 0.914286
48 5GW 0.559524 0.942029
49 EPU 0.554455 0.901408
50 EEB 0.554455 0.901408
51 UA3 0.547945 0.939394
52 U3P 0.547945 0.939394
53 CH 0.546667 0.913043
54 4TC 0.544554 0.831169
55 CTP 0.54321 0.942029
56 CSV 0.531915 0.851351
57 CSQ 0.531915 0.851351
58 DUT 0.52439 0.913043
59 4GW 0.516484 0.915493
60 UMA 0.513761 0.914286
61 U4S 0.513158 0.753425
62 U2P 0.506667 0.954545
63 U2S 0.5 0.767123
64 U3S 0.5 0.753425
65 PUP 0.48913 0.913043
66 U22 0.486957 0.790123
67 U21 0.486957 0.810127
68 U20 0.486957 0.810127
69 DKX 0.486486 0.746479
70 U1S 0.482759 0.75
71 A U 0.481132 0.805195
72 2QR 0.478632 0.822785
73 5FU 0.474359 0.914286
74 8OD 0.47191 0.851351
75 C5G 0.468085 0.888889
76 7XL 0.465909 0.888889
77 U U U U 0.461538 0.940298
78 UMF 0.461538 0.857143
79 G8D 0.460674 0.855263
80 UTP U U U 0.456522 0.895522
81 2TU 0.452055 0.774648
82 4RA 0.451613 0.855263
83 C2G 0.450549 0.901408
84 DU 0.45 0.898551
85 CAR 0.45 0.927536
86 C 0.45 0.927536
87 C5P 0.45 0.927536
88 UMP 0.45 0.898551
89 UAG 0.448 0.864865
90 CDC 0.446809 0.777778
91 UD0 0.444444 0.844156
92 5BU 0.444444 0.914286
93 N3E 0.440476 0.733333
94 UC5 0.440476 0.9
95 UUA 0.438356 0.772727
96 DUP 0.431818 0.887324
97 2GW 0.431373 0.901408
98 M7G 0.430108 0.780488
99 CNU 0.428571 0.927536
100 CDM 0.427083 0.842105
101 H6Y 0.425532 0.851351
102 16B 0.421687 0.888889
103 S5P 0.419753 0.915493
104 8GT 0.419355 0.855263
105 CXY 0.418367 0.888889
106 UPA 0.418182 0.842105
107 CDP MG 0.413793 0.849315
108 U2G 0.410714 0.822785
109 U A A U 0.409836 0.842105
110 UML 0.408759 0.810127
111 UP6 0.407407 0.871429
112 M7M 0.40625 0.771084
113 PMP UD1 0.404762 0.794872
114 1GW 0.40367 0.864865
115 BMP 0.402439 0.970149
116 APU 0.401786 0.828947
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4IRP; Ligand: UDP; Similar sites found: 57
This union binding pocket(no: 1) in the query (biounit: 4irp.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3OJF NDP 0.04718 0.40676 None
2 1EYR CDP 0.005787 0.43286 1.31579
3 1UZN NAP 0.01529 0.41053 1.61943
4 4MIX UD1 0.0108 0.41685 1.99203
5 4CNK FAD 0.04287 0.41297 1.99203
6 1KQP ADJ 0.04957 0.41243 1.99203
7 2VT3 ATP 0.01603 0.40425 2.32558
8 1OMZ UD2 0.002938 0.45251 2.39044
9 2VL8 CTS 0.00736 0.4309 2.39044
10 3ZF8 GDP 0.006064 0.42313 2.39044
11 2VL8 UDP 0.01097 0.42265 2.39044
12 1S4M LUM 0.02721 0.41217 2.39044
13 1NJR XYL 0.03355 0.40644 2.39044
14 4CFP NAG AMU NAG AMV 0.03657 0.40282 2.39044
15 1H7F C5P 0.0229 0.40116 2.44898
16 4MAF ADX 0.002929 0.44857 2.78884
17 2X3F APC 0.04371 0.40114 2.78884
18 3OIG NAD 0.02753 0.41182 3.00752
19 1V84 UDP 0.0008082 0.46567 3.18725
20 3IOI 1GW 0.009424 0.44082 3.18725
21 5X8G S0N 0.04241 0.4206 3.18725
22 2WZF UDP 0.009524 0.41653 3.18725
23 1BXK NAD 0.0412 0.40426 3.58566
24 1H5Q NAP 0.02383 0.41899 3.98406
25 3CU0 GAL GAL SO4 0.001958 0.48032 4.38247
26 3CU0 UDP 0.001079 0.47447 4.38247
27 1V47 ADX 0.008757 0.42777 4.38247
28 2Q1S NAI 0.0357 0.41971 4.38247
29 1LTH NAD 0.03745 0.40098 4.38247
30 2FFU UDP 0.001712 0.45933 4.78088
31 3QWI CUE 0.03322 0.42097 4.78088
32 5AJP UDP 0.0007688 0.4081 4.78088
33 3OJO NAD 0.02676 0.40753 4.78088
34 2GKS ADP 0.008458 0.43031 5.57769
35 4CQM NAP 0.03651 0.40803 5.57769
36 3EVG SAH 0.0212 0.40694 5.9761
37 4MP8 NAD 0.04152 0.41142 6.3745
38 2RGO FAD 0.04427 0.411 6.3745
39 3L6R MLI 0.003284 0.40666 6.3745
40 3V91 UPG 0.00071 0.4878 7.17131
41 4F07 FAD 0.0222 0.40636 7.36842
42 3U2U UDP 0.002114 0.47657 7.56972
43 1F06 NDP 0.02486 0.41825 7.96813
44 1YJQ NAP 0.03721 0.40973 8.36653
45 1E5F PLP 0.0194 0.40359 8.76494
46 1MV8 NAD 0.04113 0.4018 8.76494
47 1CZA G6P 0.01252 0.40801 9.16335
48 2D7I UDP 0.00118 0.41698 9.96016
49 5O4J PJL 0.03907 0.40879 9.96016
50 5O4J 9KH 0.04593 0.40581 9.96016
51 5O4J SAH 0.04593 0.40581 9.96016
52 3QF7 ANP 0.04257 0.40458 12
53 1USF FMN 0.02102 0.41806 13.4831
54 1USF NAP 0.0245 0.41806 13.4831
55 2AKO ADP 0.02214 0.40136 14.741
56 1REO FAD 0.04571 0.41068 15.1394
57 1YRO GDU 0.00000001753 0.40393 43.4263
Pocket No.: 2; Query (leader) PDB : 4IRP; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4irp.bio3) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4IRP; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4irp.bio3) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4IRP; Ligand: UDP; Similar sites found: 18
This union binding pocket(no: 4) in the query (biounit: 4irp.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3OJF IMJ 0.04556 0.41285 None
2 5CUQ NSC 0.04347 0.40633 1.19522
3 2PZ8 APC 0.02645 0.40352 1.99203
4 4HXY NDP 0.04723 0.4032 2.78884
5 4D42 NAP 0.03793 0.42388 3.18725
6 4D42 W0I 0.03793 0.42388 3.18725
7 5L53 NAP 0.02446 0.40773 3.58566
8 1RJD SAM 0.01674 0.41139 3.89222
9 2PWY SAH 0.03509 0.40114 4.26357
10 4RDI ATP 0.02589 0.40134 4.38247
11 1BC5 SAH 0.03571 0.40133 4.38247
12 1UP7 NAD 0.02685 0.40842 4.78088
13 1WMA AB3 0.04736 0.41391 5.17928
14 4USQ FAD 0.04017 0.40895 5.17928
15 1U7T TDT 0.04726 0.41267 6.3745
16 1X87 NAD 0.03238 0.40313 7.17131
17 2ZWA SAH 0.03128 0.40207 7.56972
18 3LCC SAH 0.0193 0.40573 7.65957
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