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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 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....
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: 117
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 U 0.78125 0.984615
6 UPU 0.72973 0.940298
7 2KH 0.722222 0.970149
8 44P 0.720588 0.955882
9 UFM 0.717949 0.941176
10 GDU 0.717949 0.941176
11 URM 0.717949 0.927536
12 660 0.717949 0.927536
13 UPG 0.717949 0.941176
14 GUD 0.717949 0.941176
15 UDP UDP 0.714286 0.939394
16 UPP 0.705128 0.941176
17 UDH 0.705128 0.864865
18 U2F 0.691358 0.888889
19 UFG 0.691358 0.888889
20 UPF 0.691358 0.888889
21 UAD 0.670732 0.941176
22 UDX 0.670732 0.941176
23 3UC 0.658824 0.888889
24 USQ 0.654762 0.820513
25 UGB 0.654762 0.955224
26 UGA 0.654762 0.955224
27 G3N 0.647059 0.914286
28 UDM 0.636364 0.914286
29 URI 0.625 0.863636
30 UD1 0.622222 0.927536
31 UD2 0.622222 0.927536
32 Y6W 0.607143 0.888889
33 CDP 0.605263 0.942029
34 HP7 0.591398 0.941176
35 UD7 0.591398 0.927536
36 MJZ 0.585106 0.914286
37 IUG 0.583333 0.810127
38 F5G 0.578947 0.927536
39 12V 0.578947 0.901408
40 HWU 0.578947 0.901408
41 F5P 0.578947 0.914286
42 UD4 0.578947 0.914286
43 CJB 0.573529 0.820895
44 UDZ 0.571429 0.853333
45 DUD 0.571429 0.913043
46 UP5 0.571429 0.853333
47 U U 0.563218 0.955224
48 EPZ 0.56 0.914286
49 5GW 0.559524 0.942029
50 EPU 0.554455 0.901408
51 EEB 0.554455 0.901408
52 U3P 0.547945 0.939394
53 UA3 0.547945 0.939394
54 4TC 0.544554 0.831169
55 HF4 0.54321 0.942029
56 CTP 0.54321 0.942029
57 CSQ 0.531915 0.851351
58 CSV 0.531915 0.851351
59 DUT 0.52439 0.913043
60 4GW 0.516484 0.915493
61 UMA 0.513761 0.914286
62 U4S 0.513158 0.753425
63 U2P 0.506667 0.954545
64 U2S 0.5 0.767123
65 U3S 0.5 0.753425
66 PUP 0.48913 0.913043
67 U21 0.486957 0.810127
68 U20 0.486957 0.810127
69 U22 0.486957 0.790123
70 DKX 0.486486 0.746479
71 U1S 0.482759 0.75
72 A U 0.481132 0.805195
73 2QR 0.478632 0.822785
74 5FU 0.474359 0.914286
75 G U 0.472222 0.7875
76 8OD 0.47191 0.851351
77 C5G 0.468085 0.888889
78 7XL 0.465909 0.888889
79 U U U U 0.461538 0.940298
80 UMF 0.461538 0.857143
81 G8D 0.460674 0.855263
82 UTP U U U 0.456522 0.895522
83 2TU 0.452055 0.774648
84 4RA 0.451613 0.855263
85 C2G 0.450549 0.901408
86 DU 0.45 0.898551
87 UMP 0.45 0.898551
88 C 0.45 0.927536
89 CAR 0.45 0.927536
90 C5P 0.45 0.927536
91 UAG 0.448 0.864865
92 CDC 0.446809 0.777778
93 5BU 0.444444 0.914286
94 UD0 0.444444 0.844156
95 N3E 0.440476 0.733333
96 UC5 0.440476 0.9
97 UUA 0.438356 0.772727
98 DUP 0.431818 0.887324
99 2GW 0.431373 0.901408
100 M7G 0.430108 0.780488
101 CNU 0.428571 0.927536
102 CDM 0.427083 0.842105
103 H6Y 0.425532 0.851351
104 16B 0.421687 0.888889
105 S5P 0.419753 0.915493
106 8GT 0.419355 0.855263
107 CXY 0.418367 0.888889
108 UPA 0.418182 0.842105
109 U2G 0.410714 0.822785
110 U A A U 0.409836 0.842105
111 UML 0.408759 0.810127
112 UP6 0.407407 0.871429
113 M7M 0.40625 0.771084
114 1GW 0.40367 0.864865
115 BMP 0.402439 0.970149
116 APU 0.401786 0.828947
117 PMP UD1 0.401575 0.7875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4IRP; Ligand: UDP; Similar sites found with APoc: 126
This union binding pocket(no: 1) in the query (biounit: 4irp.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 3OJF IMJ None
2 3OJF NDP None
3 5ZZ6 NAD 0.961538
4 5ZZ6 ADP 0.961538
5 1YXM ADE 1.19522
6 1EYR CDP 1.31579
7 5O98 NAP 1.59363
8 1UZN NAP 1.61943
9 5JE0 SAH 1.61943
10 5JE0 AZ8 1.61943
11 4HJY NAG NAG NAG 1.94175
12 3AB1 FAD 1.99203
13 3CKJ CIT 1.99203
14 4MIX UD1 1.99203
15 4CNK FAD 1.99203
16 5TS5 FAD 1.99203
17 2VT3 ATP 2.32558
18 1OMZ UD2 2.39044
19 2BVL GLC 2.39044
20 2BVL UDP 2.39044
21 2VL8 CTS 2.39044
22 5UQK U2F 2.39044
23 3ZF8 GDP 2.39044
24 2VL8 UDP 2.39044
25 1S4M LUM 2.39044
26 4UIB GWX 2.39044
27 1NJR XYL 2.39044
28 4CFP NAG AMU NAG AMV 2.39044
29 4DEC UDP 2.39044
30 4DEC 3PG 2.39044
31 1H7F C5P 2.44898
32 4MAF ADX 2.78884
33 1E5Q NDP 2.78884
34 2IVD FAD 2.78884
35 5OVK NDP 2.78884
36 2X3F APC 2.78884
37 3OIG NAD 3.00752
38 1V84 UDP 3.18725
39 3IOI 1GW 3.18725
40 6H21 UD1 3.18725
41 5X8G S0N 3.18725
42 4D42 W0I 3.18725
43 4D42 NAP 3.18725
44 2WYV NAD 3.18725
45 2WZF UDP 3.18725
46 3WXB NDP 3.18725
47 2PD4 NAD 3.58566
48 2PD4 DCN 3.58566
49 4GLL NAD 3.58566
50 5TTJ FAD 3.58566
51 5MW4 5JU 3.58566
52 1BXK NAD 3.58566
53 6FXR UDP 3.58566
54 5TZJ UD1 3.98406
55 2NXE SAM 3.98406
56 1H5Q NAP 3.98406
57 2PI8 NAG NAG NAG NAG NAG NAG 3.98406
58 3WDM ADN 3.98406
59 4NDO ATP 3.98406
60 3CU0 GAL GAL SO4 4.38247
61 3CU0 UDP 4.38247
62 2WZG UPG 4.38247
63 1V47 ADX 4.38247
64 2Q1S NAI 4.38247
65 1E3W NAD 4.38247
66 1E6W NAD 4.38247
67 4RDI ATP 4.38247
68 1LTH NAD 4.38247
69 5AJP UDP 4.78088
70 5NDF LU2 4.78088
71 5NDF UDP 4.78088
72 2FFU UDP 4.78088
73 1GA8 UPF 4.78088
74 1JQ3 AAT 4.78088
75 3QWI CUE 4.78088
76 6F7L FAD 4.78088
77 3OJO NAD 4.78088
78 1UP7 NAD 4.78088
79 2DT5 NAD 5.21327
80 3SJ7 NDP 5.57769
81 2GKS ADP 5.57769
82 4CQM NAP 5.57769
83 3RUV ANP 5.57769
84 3EVG SAH 5.9761
85 5MM0 GDD 6.3745
86 2UUU FAD 6.3745
87 4MP8 NAD 6.3745
88 4MP8 MLI 6.3745
89 2RGO FAD 6.3745
90 3L6R MLI 6.3745
91 2DXU BT5 6.38298
92 3V91 UPG 7.17131
93 1LL2 UPG 7.17131
94 1X87 NAD 7.17131
95 4F07 FAD 7.36842
96 3U2U UDP 7.56972
97 1F06 NDP 7.96813
98 6H0B UDP 8.36653
99 1YJQ NAP 8.36653
100 1O7Q UDP 8.76494
101 1O7Q GAL NAG 8.76494
102 2H8Z 8CM 8.76494
103 3H4V NAP 8.76494
104 1E5F PLP 8.76494
105 1MV8 NAD 8.76494
106 6BSW CE6 9.16335
107 6BSW UDP 9.16335
108 1CZA G6P 9.16335
109 2BO4 FLC 9.56175
110 4OHU 2TK 9.56175
111 4OHU NAD 9.56175
112 2D7I UDP 9.96016
113 5O4J SAH 9.96016
114 5O4J PJL 9.96016
115 5O4J 9KH 9.96016
116 6GKV SAH 11.1554
117 2QTR NXX 11.6402
118 5XLX SAH 11.9522
119 3QF7 ANP 12
120 1USF FMN 13.4831
121 1USF NAP 13.4831
122 6GAS FAD 14.3426
123 2AKO ADP 14.741
124 1REO FAD 15.1394
125 1GUZ NAD 17.9283
126 1YRO GDU 43.4263
Pocket No.: 2; Query (leader) PDB : 4IRP; Ligand: UDP; 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: 4irp.bio3) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4IRP; Ligand: UDP; Similar sites found with APoc: 39
This union binding pocket(no: 3) in the query (biounit: 4irp.bio3) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 5CUQ NSC 1.19522
2 1GV0 NAD 1.59363
3 5ULP KB1 1.86567
4 5KOK SAH 1.99203
5 1HV6 MAW MAV GCU 1.99203
6 2PZ8 APC 1.99203
7 1QG6 NAD 2.39044
8 5LAU AR6 2.40385
9 2WPB ZZI 2.63158
10 5HJM MTA 2.78884
11 4HXY NDP 2.78884
12 2XOC ADP 2.78884
13 3LL5 ATP 3.21285
14 1NJJ GET 3.58566
15 2RH4 EMO 3.58566
16 5THQ NDP 3.58566
17 4C3Y FAD 3.58566
18 4ZRN NAD 3.58566
19 5L53 NAP 3.58566
20 1RJD SAM 3.89222
21 2PWY SAH 4.26357
22 3COW 52H 4.38247
23 4RDH AMP 4.38247
24 1BC5 SAH 4.38247
25 1GA8 DEL 4.78088
26 2I7C AAT 4.78088
27 1WMA AB3 5.17928
28 1WMA NDP 5.17928
29 4USQ FAD 5.17928
30 5JAQ NAI 5.9761
31 1U7T TDT 6.3745
32 1YQZ FAD 6.77291
33 6AIN FAD 6.77291
34 5O0B 9FE 6.79012
35 2ZWA SAH 7.56972
36 3LCC SAH 7.65957
37 6GAR FAD 8.36653
38 1MUU NAD 8.36653
39 3GGO NAI 11.1554
Pocket No.: 4; Query (leader) PDB : 4IRP; Ligand: UDP; 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: 4irp.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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