Receptor
PDB id Resolution Class Description Source Keywords
2IV3 2.3 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF AVIGT4, A GLYCOSYLTRANSFERASE INVOLVED IN AVILAMYCIN A BIOSYNTHESIS STREPTOMYCES VIRIDOCHROMOGENES GLYCOSYLTRANSFERASE TRANSFERASE ANTIBIOTICS FAMILY GT-4 AVILAMYCIN A
Ref.: INSIGHTS INTO THE SYNTHESIS OF LIPOPOLYSACCHARIDE A ANTIBIOTICS THROUGH THE STRUCTURES OF TWO RETAINING GLYCOSYLTRANSFERASES FROM FAMILY GT4 CHEM.BIOL. V. 13 1143 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1354;
B:1354;
C:1354;
D:1354;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
UDP A:1353;
B:1353;
C:1353;
D:1353;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
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
2IV3 2.3 Å EC: 2.-.-.- CRYSTAL STRUCTURE OF AVIGT4, A GLYCOSYLTRANSFERASE INVOLVED IN AVILAMYCIN A BIOSYNTHESIS STREPTOMYCES VIRIDOCHROMOGENES GLYCOSYLTRANSFERASE TRANSFERASE ANTIBIOTICS FAMILY GT-4 AVILAMYCIN A
Ref.: INSIGHTS INTO THE SYNTHESIS OF LIPOPOLYSACCHARIDE A ANTIBIOTICS THROUGH THE STRUCTURES OF TWO RETAINING GLYCOSYLTRANSFERASES FROM FAMILY GT4 CHEM.BIOL. V. 13 1143 2006
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 2IV3 - 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 211 families.
1 2IV3 - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 166 families.
1 2IV3 - 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 : 2IV3; Ligand: UDP; Similar sites found: 49
This union binding pocket(no: 1) in the query (biounit: 2iv3.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.02376 0.40407 None
2 2WTX UDP 0.00001196 0.43548 1.16959
3 2WTX VDO 0.0000508 0.42071 1.16959
4 1XV5 UDP 0.0006536 0.45561 1.46199
5 2GMM MAN MAN 0.0159 0.41422 1.5873
6 4IP7 FLC 0.02603 0.40135 1.75439
7 4XJ7 ADE 0.01951 0.40485 1.87266
8 1F6D UDP 0.01563 0.40423 2.33918
9 3RHZ UDP 0.004283 0.41126 2.35988
10 3HBN UDP 0.005061 0.4117 2.48227
11 1C1X HFA 0.007244 0.41624 2.63158
12 1BW9 PPY 0.008125 0.40991 2.63158
13 4PQG UDP 0.000003706 0.53732 2.92398
14 3S2U UD1 0.00101 0.42829 2.92398
15 2XA2 UPG 0.001272 0.4241 2.92398
16 1J39 UPG 0.0002273 0.41883 2.92398
17 1RYD GLC 0.01524 0.41656 2.92398
18 5IFK HPA 0.02862 0.40128 3.20513
19 1RZU ADP 0.00001685 0.54814 3.21637
20 1NLM UD1 0.007633 0.4038 3.21637
21 3CV3 UDP 0.000002341 0.5589 3.50877
22 5A1S FLC 0.006881 0.43194 3.80117
23 2XG5 EC5 0.02103 0.40909 4.04624
24 2XG5 EC2 0.02103 0.40909 4.04624
25 1US5 GLU 0.01214 0.40558 4.14013
26 5EOO CIT 0.02181 0.40881 4.15094
27 4X7R UDP 0.0000002132 0.5971 4.38596
28 4X7R 3YW 0.0000009767 0.51206 4.38596
29 4F97 GDP 0.0001019 0.51028 4.38596
30 4X7R NTO 0.000001681 0.45601 4.38596
31 3HQP OXL 0.02673 0.40332 4.67836
32 2VDF OCT 0.03599 0.41339 5.13834
33 4LOC OXM 0.007643 0.41621 5.26316
34 2G50 PYR 0.03123 0.40209 5.26316
35 1Y4Z PCI 0.01052 0.42643 5.84795
36 1FWV SGA MAG FUC 0.02859 0.40092 5.97015
37 1VBO MAN 0.01936 0.42044 6.04027
38 1TUU AMP 0.01158 0.41488 6.43275
39 5IXB LGA 0.004976 0.41156 12.037
40 4XSU UDP 0.0000001521 0.5412 12.6289
41 4XSU GLC 0.0000006736 0.51819 12.6289
42 3OTH TYD 0.009878 0.40231 12.8641
43 3CYI ATP 0.004921 0.44025 13.6364
44 3OKP GDD 0.00000004783 0.65143 14.2132
45 4X1T UDP 0.0002494 0.4745 14.3275
46 2IW1 U2F 0.0000008517 0.50998 14.6199
47 3OKA GDD 0.0000004538 0.62419 14.6982
48 2WDQ CBE 0.018 0.41084 14.7826
49 3HY2 ATP 0.007598 0.42401 18.1818
Pocket No.: 2; Query (leader) PDB : 2IV3; 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: 2iv3.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2IV3; Ligand: UDP; Similar sites found: 12
This union binding pocket(no: 3) in the query (biounit: 2iv3.bio2) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2GJP MAL 0.01331 0.40904 2.04678
2 3PLN U5P 0.01331 0.41635 2.63158
3 5OFW 9TW 0.02343 0.40531 2.69058
4 3PA8 621 0.01824 0.40932 2.75591
5 3A76 SPD 0.02212 0.40701 3.40909
6 1RL4 BRR 0.02209 0.40503 3.7234
7 5N9X THR 0.001396 0.46789 3.80117
8 4Z7X 3CX 0.01289 0.40136 4.62185
9 5LKC FUC GLA A2G 0.03733 0.40197 4.67836
10 1VBO MAN MAN MAN 0.03297 0.40302 6.04027
11 5CIC 51R 0.02286 0.4051 6.43275
12 1XHL TNE 0.02596 0.40589 6.73401
Pocket No.: 4; Query (leader) PDB : 2IV3; 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: 2iv3.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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