Receptor
PDB id Resolution Class Description Source Keywords
2D7I 2.5 Å EC: 2.4.1.41 CRSYTAL STRUCTURE OF PP-GALNAC-T10 WITH UDP, GALNAC AND MN2+ HOMO SAPIENS BETA TREFOIL ROSSMANN FOLD TRANSFERASE
Ref.: STRUCTURAL BASIS OF CARBOHYDRATE TRANSFER ACTIVITY UDP-GALNAC: POLYPEPTIDE ALPHA-N-ACETYLGALACTOSAMINYLTRANSFERASE (PP-GALNAC- J.MOL.BIOL. V. 359 708 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MN A:706;
Part of Protein;
none;
submit data
54.938 Mn [Mn+2...
NAG A:701;
A:704;
Invalid;
Invalid;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NAG NAG A:700;
Invalid;
none;
submit data
408.404 n/a O=C(N...
NGA A:702;
Valid;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
UDP A:705;
Valid;
none;
submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2D7I 2.5 Å EC: 2.4.1.41 CRSYTAL STRUCTURE OF PP-GALNAC-T10 WITH UDP, GALNAC AND MN2+ HOMO SAPIENS BETA TREFOIL ROSSMANN FOLD TRANSFERASE
Ref.: STRUCTURAL BASIS OF CARBOHYDRATE TRANSFER ACTIVITY UDP-GALNAC: POLYPEPTIDE ALPHA-N-ACETYLGALACTOSAMINYLTRANSFERASE (PP-GALNAC- J.MOL.BIOL. V. 359 708 2006
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2D7I - NGA C8 H15 N O6 CC(=O)N[C@....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2D7I - NGA C8 H15 N O6 CC(=O)N[C@....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2D7I - NGA C8 H15 N O6 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NGA; Similar ligands found: 109
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG 1 1
2 HSQ 1 1
3 NGA 1 1
4 A2G 1 1
5 NDG 1 1
6 BM3 1 1
7 BGN 0.638298 0.888889
8 SIZ 0.630435 0.906977
9 YX1 0.625 0.65
10 GAL NGA A2G 0.614035 0.816327
11 STZ 0.612245 0.65
12 16G 0.591837 0.735849
13 BMX 0.591837 0.735849
14 4QY 0.591837 0.735849
15 SNG 0.5625 0.866667
16 NGS 0.54902 0.661017
17 NAG GDL 0.54386 0.833333
18 CBS 0.54386 0.833333
19 CBS CBS 0.54386 0.833333
20 NAG NDG 0.54386 0.833333
21 ASG 0.538462 0.661017
22 BG8 0.537037 0.906977
23 2F8 0.530612 0.909091
24 MAG 0.530612 0.909091
25 NLC 0.517857 0.888889
26 GAL NDG 0.517857 0.888889
27 NDG GAL 0.517857 0.888889
28 NAG A2G 0.517241 0.833333
29 4V5 0.517241 0.829787
30 NAG NGA 0.517241 0.833333
31 MAN NAG 0.508772 0.888889
32 4UZ 0.508475 0.808511
33 NDG NAG NAG 0.508197 0.816327
34 CTO 0.508197 0.816327
35 NAG NAG NDG 0.508197 0.816327
36 NAG NAG NAG NDG 0.508197 0.816327
37 NAG NAG NAG NAG NAG NAG NAG NAG 0.508197 0.816327
38 NDG NAG NAG NDG 0.508197 0.816327
39 NAG NAG NAG NAG 0.508197 0.816327
40 NAG NAG NAG 0.508197 0.816327
41 NAG NAG NAG NAG NDG NAG 0.508197 0.816327
42 NAG NAG NAG NAG NAG NAG 0.508197 0.816327
43 NDG NAG NAG NDG NAG 0.508197 0.816327
44 NDG NAG NAG NAG 0.508197 0.816327
45 NAG NAG NAG NAG NDG 0.508197 0.816327
46 NAG NAG NAG NAG NAG 0.508197 0.816327
47 NBG 0.5 0.951219
48 MQG 0.5 0.698113
49 A2G GAL 0.491228 0.888889
50 GAL A2G 0.491228 0.888889
51 GAL NGA 0.491228 0.888889
52 AMU 0.490909 0.930233
53 GN1 0.490566 0.754717
54 NG1 0.490566 0.754717
55 NDG NAG 0.47541 0.816327
56 NAG GAL 0.474576 0.888889
57 NGA GAL 0.474576 0.888889
58 NAG FUC 0.474576 0.866667
59 GAL NAG 0.474576 0.888889
60 NAG GAL NAG 0.455882 0.833333
61 FUC NAG 0.45 0.888889
62 3YW 0.448276 0.930233
63 GLA GAL NAG 0.446154 0.888889
64 MAN BMA NAG 0.446154 0.888889
65 NAG GAL GAL 0.446154 0.888889
66 FUL GAL NAG 0.426471 0.869565
67 G6S NAG 0.426471 0.677966
68 DR2 0.426471 0.869565
69 FUC GAL NDG 0.426471 0.869565
70 FUC GAL NAG 0.426471 0.869565
71 NDG GAL FUC 0.426471 0.869565
72 GYU 0.42623 0.740741
73 TNR 0.42623 0.833333
74 NAG BDP 0.421875 0.851064
75 NAG MBG 0.419355 0.851064
76 NGA GAL BGC 0.41791 0.888889
77 NAG NAG 0.415385 0.784314
78 AZC 0.415094 0.795918
79 SN5 SN5 0.412698 0.705882
80 MBG A2G 0.412698 0.851064
81 A2G MBG 0.412698 0.851064
82 HS2 0.411765 0.8125
83 5AX 0.411765 0.866667
84 6ZC 0.409091 0.655738
85 LEC 0.409091 0.655738
86 GAL BGC NAG GAL 0.408451 0.888889
87 TCG 0.408451 0.689655
88 CTO TMX 0.408451 0.689655
89 NAG NAG NAG NAG NAG NAG NAG 0.407895 0.740741
90 BMA 0.404762 0.7
91 WOO 0.404762 0.7
92 ALL 0.404762 0.7
93 GLA 0.404762 0.7
94 MAN 0.404762 0.7
95 GAL 0.404762 0.7
96 GLC 0.404762 0.7
97 GXL 0.404762 0.7
98 GIV 0.404762 0.7
99 BGC 0.404762 0.7
100 NAG AMU 0.402778 0.8
101 NAG MUB 0.402778 0.8
102 A2G GAL FUC 0.4 0.869565
103 DR3 0.4 0.869565
104 NAG GAL FUC 0.4 0.869565
105 FUC GL0 A2G 0.4 0.869565
106 A2G GLA FUC 0.4 0.869565
107 FUC GAL A2G 0.4 0.869565
108 NGA GAL FUC 0.4 0.869565
109 FUC GLA A2G 0.4 0.869565
Ligand no: 2; 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 : 2D7I; Ligand: NGA; Similar sites found: 22
This union binding pocket(no: 1) in the query (biounit: 2d7i.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3N29 GOL 0.01214 0.40296 1.67464
2 4DHY S41 0.02905 0.40498 1.70576
3 1JIL 485 0.0167 0.41129 2.14286
4 4EHU ANP 0.02698 0.40523 2.17391
5 3T31 FAD 0.03245 0.42892 2.746
6 3T31 DCQ 0.03421 0.42892 2.746
7 4ZNO SUC 0.01948 0.40166 4.47761
8 5NJI 8Z2 0.0325 0.40509 7.14286
9 2HYR BGC GLC 0.01137 0.40159 7.37705
10 4M4K GDU 0.01448 0.41617 9.05923
11 4M4K XYP XYP 0.01448 0.41617 9.05923
12 4TXJ THM 0.03636 0.40615 9.45946
13 1VHD NAP 0.03564 0.40887 10.5121
14 1O2D NAP 0.03614 0.40961 10.7817
15 2GN3 MAN 0.01496 0.4027 11.5079
16 2GN3 MMA 0.01412 0.40258 11.5079
17 2GMM MAN MAN 0.01649 0.40211 11.5079
18 1Q8Q MAN MMA 0.01569 0.40167 11.5079
19 1VG8 GNP 0.03239 0.40385 11.5942
20 1ZC3 GNP 0.02245 0.41228 14.1593
21 1R4A GNP 0.03187 0.40144 21.5686
22 2C49 ANP 0.02901 0.40054 25.8278
Pocket No.: 2; Query (leader) PDB : 2D7I; Ligand: UDP; Similar sites found: 61
This union binding pocket(no: 2) in the query (biounit: 2d7i.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3LAD FAD 0.03273 0.40928 1.2605
2 1OMZ UD2 0.0005202 0.47038 1.36519
3 1MXH DHF 0.03904 0.4018 1.44928
4 4M52 FAD 0.03517 0.40766 1.50215
5 3BMN NAP 0.01036 0.42227 1.73611
6 3JQ8 NAP 0.01144 0.42015 1.73611
7 4CM9 NAP 0.01269 0.41791 1.73611
8 3JQ9 NAP 0.01555 0.41353 1.73611
9 5K6A NAP 0.01562 0.41343 1.73611
10 4CNK FAD 0.01254 0.42703 2.30179
11 3V91 UPG 0.01597 0.40322 2.4055
12 1HV9 UD1 0.01923 0.40772 2.41228
13 3JUK UPG 0.01586 0.40924 2.4911
14 2APC UDM 0.004515 0.42597 2.63158
15 3U2U UDP 0.01176 0.42198 2.6616
16 1H7F C5P 0.01268 0.40101 2.85714
17 3NRR D16 0.02804 0.41602 2.91262
18 5MSO NAP 0.0239 0.40049 2.98246
19 3OID NDP 0.01297 0.421 3.10078
20 5A07 GDP 0.0009189 0.45236 3.22581
21 4JD0 1KH 0.01358 0.40782 3.33333
22 2NUN ADP 0.0123 0.40359 3.40557
23 2X1L MET 0.007819 0.42222 3.43511
24 1LSS NAD 0.01065 0.41002 3.57143
25 3CU0 UDP 0.001138 0.45223 3.91459
26 3CU0 GAL GAL SO4 0.00364 0.44733 3.91459
27 2P69 PLP 0.01731 0.40378 3.92157
28 1V84 UDP 0.0007511 0.43907 3.95257
29 1S4P GDP 0.004798 0.41414 4.02299
30 2QGI UDP 0.002229 0.40459 4.03226
31 2XWL CTP 0.002195 0.4367 4.03587
32 1DR1 NAP 0.03692 0.40212 4.2328
33 5WRJ A3P 0.01859 0.40005 4.62046
34 2PA4 UPG 0.004029 0.44254 4.95356
35 5KZD RCJ 0.01187 0.40038 5.11945
36 1E7S NAP 0.02535 0.40528 5.29595
37 1EDO NAP 0.01401 0.41818 5.32787
38 2AGD UDH 0.004145 0.44193 5.92335
39 1WVG APR 0.004326 0.43531 6.40669
40 1JYL CDC 0.01423 0.40401 6.69291
41 3L0E G58 0.01486 0.41062 7.11462
42 1I52 CTP 0.006107 0.43362 7.62712
43 1AE1 NAP 0.03253 0.40091 7.69231
44 3OIG NAD 0.01625 0.41006 8.27068
45 4DS0 A2G GAL NAG FUC 0.02195 0.40532 8.58896
46 4M4K XYP XYP 0.003839 0.43116 9.05923
47 4M4K GDU 0.003839 0.43116 9.05923
48 2VDF OCT 0.007376 0.41135 9.09091
49 1JA9 NDP 0.01957 0.41092 9.48905
50 2BO4 FLC 0.000277 0.49137 9.57179
51 4IRP UDP 0.00118 0.41698 9.96016
52 4M7V RAR 0.01601 0.42623 10.2857
53 2F5Z FAD 0.02386 0.41808 10.9375
54 5TZJ UD1 0.00002035 0.42171 11.6848
55 3CKJ CIT 0.00003609 0.41685 14.2857
56 3SJ7 NDP 0.02169 0.40513 14.6825
57 4NYT PC 0.001453 0.44533 14.7465
58 3RNM FAD 0.01954 0.42174 15.5172
59 5MM0 GDD 0.00002824 0.43806 16.0428
60 2CIG 1DG 0.02887 0.41211 19.4969
61 1QGQ UDP 0.0007212 0.44307 22.7451
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