Receptor
PDB id Resolution Class Description Source Keywords
5FV9 2.07 Å EC: 2.4.1.41 CRYSTAL STRUCTURE OF GALNAC-T2 IN COMPLEX WITH COMPOUND 16D HOMO SAPIENS TRANSFERASE
Ref.: GLYCOMIMETICS TARGETING GLYCOSYLTRANSFERASES: SYNTH COMPUTATIONAL AND STRUCTURAL STUDIES OF LESS-POLAR CONJUGATES. CHEMISTRY V. 22 7215 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO E:1576;
F:1575;
E:1574;
F:1574;
B:1573;
E:1573;
F:1573;
A:1574;
C:1573;
A:1572;
C:1572;
B:1574;
A:1573;
E:1575;
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
62.068 C2 H6 O2 C(CO)...
MN B:1571;
D:1556;
F:1571;
E:1571;
C:1571;
A:1571;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
GOL F:1577;
F:1576;
C:1574;
A:1576;
A:1575;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
UDP E:1570;
D:1555;
F:1570;
A:1570;
B:1572;
C:1570;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
Y6W B:1570;
E:1572;
F:1572;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 254 uM
512.402 C18 H29 N2 O13 P C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FV9 2.07 Å EC: 2.4.1.41 CRYSTAL STRUCTURE OF GALNAC-T2 IN COMPLEX WITH COMPOUND 16D HOMO SAPIENS TRANSFERASE
Ref.: GLYCOMIMETICS TARGETING GLYCOSYLTRANSFERASES: SYNTH COMPUTATIONAL AND STRUCTURAL STUDIES OF LESS-POLAR CONJUGATES. CHEMISTRY V. 22 7215 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5FV9 Kd = 254 uM Y6W C18 H29 N2 O13 P C1=CN(C(=O....
2 4D0T - ASP SER THR THR PRO ALA PRO THR NGA n/a n/a
3 4D0Z - SER THR CYS PRO ALA ALA n/a n/a
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5FV9 Kd = 254 uM Y6W C18 H29 N2 O13 P C1=CN(C(=O....
2 4D0T - ASP SER THR THR PRO ALA PRO THR NGA n/a n/a
3 4D0Z - SER THR CYS PRO ALA ALA n/a n/a
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5FV9 Kd = 254 uM Y6W C18 H29 N2 O13 P C1=CN(C(=O....
2 4D0T - ASP SER THR THR PRO ALA PRO THR NGA n/a n/a
3 4D0Z - SER THR CYS PRO ALA ALA n/a n/a
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
Ligand no: 2; Ligand: Y6W; Similar ligands found: 68
No: Ligand ECFP6 Tc MDL keys Tc
1 Y6W 1 1
2 660 0.674157 0.957747
3 URM 0.674157 0.957747
4 44P 0.65 0.90411
5 U5P 0.632911 0.875
6 UDP 0.607143 0.888889
7 UPU 0.588889 0.915493
8 UTP 0.586207 0.888889
9 UPG 0.585106 0.916667
10 GUD 0.585106 0.916667
11 UFM 0.585106 0.916667
12 GDU 0.585106 0.916667
13 UDP GAL 0.56701 0.890411
14 2KH 0.561798 0.864865
15 UDM 0.558824 0.944444
16 UDP UDP 0.551724 0.861111
17 UPF 0.55102 0.868421
18 U2F 0.55102 0.868421
19 UNP 0.549451 0.864865
20 U 0.545455 0.816901
21 URI 0.545455 0.816901
22 CJB 0.544304 0.802817
23 UDH 0.525773 0.945946
24 UFG 0.52 0.868421
25 UPP 0.510204 0.890411
26 UGB 0.509804 0.902778
27 USQ 0.509804 0.804878
28 UGA 0.509804 0.902778
29 UD1 0.504673 0.90411
30 UD2 0.504673 0.90411
31 3UC 0.5 0.868421
32 UAD 0.490196 0.916667
33 UDX 0.490196 0.916667
34 U3P 0.488372 0.861111
35 UA3 0.488372 0.861111
36 CSQ 0.485981 0.833333
37 CSV 0.485981 0.833333
38 U U 0.480392 0.876712
39 MJZ 0.477477 0.866667
40 G3N 0.47619 0.891892
41 HP7 0.468468 0.890411
42 IUG 0.464912 0.77381
43 EPZ 0.461538 0.891892
44 12V 0.460177 0.88
45 UD4 0.460177 0.866667
46 HWU 0.460177 0.88
47 EPU 0.457627 0.88
48 EEB 0.457627 0.88
49 UD7 0.455357 0.878378
50 U2P 0.454545 0.875
51 4TC 0.449153 0.814815
52 A U 0.445378 0.790123
53 UDZ 0.444444 0.8125
54 UP5 0.444444 0.8125
55 CH 0.43956 0.815789
56 DKX 0.436782 0.733333
57 U2S 0.434783 0.824324
58 UMA 0.428571 0.891892
59 U4S 0.428571 0.786667
60 PUP 0.420561 0.916667
61 U22 0.419847 0.8875
62 U21 0.419847 0.910256
63 U20 0.419847 0.910256
64 U3S 0.419355 0.810811
65 UMF 0.417582 0.789474
66 UC5 0.416667 0.878378
67 U U U U 0.409524 0.863014
68 UTP U U U 0.40566 0.847222
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FV9; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5fv9.bio3) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5FV9; Ligand: Y6W; 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: 5fv9.bio3) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5FV9; Ligand: Y6W; 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: 5fv9.bio3) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5FV9; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5fv9.bio3) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5FV9; Ligand: UDP; Similar sites found: 15
This union binding pocket(no: 5) in the query (biounit: 5fv9.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5JCM ISD 0.01248 0.41773 2.88248
2 3CU0 UDP 0.0001104 0.44316 3.55872
3 3CU0 GAL GAL SO4 0.000897 0.44017 3.55872
4 3U2U UDP 0.002009 0.42567 3.80228
5 3CKJ CIT 0.01708 0.40708 4.25532
6 4YDD MGD 0.0116 0.42271 5.77933
7 4YDD MD1 0.0116 0.42271 5.77933
8 2BVL GLC 0.003618 0.40208 5.89319
9 2BVL UDP 0.003618 0.40208 5.89319
10 4M4K XYP XYP 0.001494 0.41067 6.62021
11 4M4K GDU 0.001494 0.41067 6.62021
12 1OMZ UD2 0.00003811 0.46472 7.16724
13 2APC UDM 0.001998 0.4029 7.60234
14 5MM0 GDD 0.000432 0.44208 13.1016
15 5TZJ UD1 0.00000559 0.52592 13.587
Pocket No.: 6; Query (leader) PDB : 5FV9; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5fv9.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5FV9; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5fv9.bio4) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5FV9; Ligand: Y6W; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5fv9.bio4) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 5FV9; Ligand: Y6W; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 5fv9.bio4) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 5FV9; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 5fv9.bio4) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 5FV9; Ligand: UDP; Similar sites found: 8
This union binding pocket(no: 11) in the query (biounit: 5fv9.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VL8 CTS 0.001704 0.40437 2.9304
2 2VL8 UDP 0.002223 0.40343 2.9304
3 3OID NDP 0.008984 0.40255 3.87597
4 5UQK U2F 0.004224 0.40375 4.30108
5 2AGD NAG MAN BMA 0.002728 0.41919 6.96864
6 2AGD UDH 0.002946 0.41919 6.96864
7 4DEC UDP 0.01786 0.40867 8.43023
8 4DEC 3PG 0.01786 0.40867 8.43023
Pocket No.: 12; Query (leader) PDB : 5FV9; Ligand: Y6W; Similar sites found: 20
This union binding pocket(no: 12) in the query (biounit: 5fv9.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VL8 CTS 0.001704 0.40437 2.9304
2 2VL8 UDP 0.002223 0.40343 2.9304
3 3CU0 UDP 0.0002669 0.43657 3.55872
4 3CU0 GAL GAL SO4 0.00144 0.43495 3.55872
5 3U2U UDP 0.001107 0.43977 3.80228
6 3OID NDP 0.008984 0.40255 3.87597
7 3CKJ CIT 0.01252 0.4157 4.25532
8 5UQK U2F 0.004224 0.40375 4.30108
9 2BVL UDP 0.002774 0.41116 5.89319
10 2BVL GLC 0.002774 0.41116 5.89319
11 4M4K XYP XYP 0.0009451 0.42279 6.62021
12 4M4K GDU 0.0009451 0.42279 6.62021
13 2AGD NAG MAN BMA 0.002728 0.41919 6.96864
14 2AGD UDH 0.002946 0.41919 6.96864
15 1OMZ UD2 0.00004281 0.47132 7.16724
16 2APC UDM 0.0007151 0.42401 7.60234
17 4DEC UDP 0.01786 0.40867 8.43023
18 4DEC 3PG 0.01786 0.40867 8.43023
19 5MM0 GDD 0.0003503 0.44949 13.1016
20 5TZJ UD1 0.000003119 0.54159 13.587
Pocket No.: 13; Query (leader) PDB : 5FV9; Ligand: UDP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 13) in the query (biounit: 5fv9.bio2) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback