Receptor
PDB id Resolution Class Description Source Keywords
1MP4 2.2 Å EC: 2.7.7.24 W224H VARIANT OF S. ENTERICA RMLA SALMONELLA ENTERICA TRANSFERASE
Ref.: EXPANDING PYRIMIDINE DIPHOSPHOSUGAR LIBRARIES VIA STRUCTURE-BASED NUCLEOTIDYLYLTRANSFERASE ENGINEERIN PROC.NATL.ACAD.SCI.USA V. 99 13397 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UPG A:501;
B:502;
 Valid;
Valid;
 none;
none;
 submit data
566.302 C15 H24 N2 O17 P2 C1=CN...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1IIM 2.1 Å EC: 2.7.7.24 THYMIDYLYLTRANSFERASE COMPLEXED WITH TTP SALMONELLA ENTERICA TRANSFERASE
Ref.: STRUCTURE, MECHANISM AND ENGINEERING OF A NUCLEOTIDYLYLTRANSFERASE AS A FIRST STEP TOWARD GLYCORANDOMIZATION. NAT.STRUCT.BIOL. V. 8 545 2001
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1IIM - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
2 1IIN - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
3 1MP3 - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
4 1MP4 - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
5 3PKQ - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
70% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4ASJ Kd = 0.028 uM N6A C18 H18 N4 O4 S CN(C1=C(N(....
2 1G1L - DAU C16 H26 N2 O16 P2 CC1=CN(C(=....
3 4B42 - 942 C16 H20 N4 O3 CCCCN1C(=C....
4 4B4G ic50 = 0.175 uM KKT C16 H22 N4 O4 S CCCCS(=O)(....
5 4B4B - GJB C12 H12 N2 O3 c1ccc(cc1)....
6 4B4M ic50 = 0.205 uM JWT C18 H17 F N4 O4 S CN(C1=C(N(....
7 3ZLK ic50 = 1.32 uM Y46 C17 H16 N4 O4 S c1ccc(cc1)....
8 4B2W - BZ0 C18 H16 N4 O3 c1ccc(cc1)....
9 1G0R - THM C10 H14 N2 O5 CC1=CN(C(=....
10 4ARW Kd = 0.074 uM HNR C15 H20 N4 O4 S CCCCN1C(=C....
11 3ZLL Kd = 0.395 uM 4WF C11 H11 N3 O3 c1ccc(cc1)....
12 4B5B ic50 = 0.387 uM BBE C19 H20 N4 O4 S Cc1cccc(c1....
13 4ASY - N5Y C19 H18 N4 O3 CN(C1=C(N(....
14 1FXO - TMP C10 H15 N2 O8 P CC1=CN(C(=....
15 4B3U ic50 = 4.7 uM NWL C13 H16 N4 O2 CCNC1=C(N(....
16 4B2X - NIQ C13 H22 N4 O2 CCCCN1C(=C....
17 1IIM - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
18 1IIN - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
19 1MP3 - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
20 1MP4 - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
21 3PKQ - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
22 6B5E - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
23 6B5K - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
24 1LVW - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
50% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4ASJ Kd = 0.028 uM N6A C18 H18 N4 O4 S CN(C1=C(N(....
2 1G1L - DAU C16 H26 N2 O16 P2 CC1=CN(C(=....
3 4B42 - 942 C16 H20 N4 O3 CCCCN1C(=C....
4 4B4G ic50 = 0.175 uM KKT C16 H22 N4 O4 S CCCCS(=O)(....
5 4B4B - GJB C12 H12 N2 O3 c1ccc(cc1)....
6 4B4M ic50 = 0.205 uM JWT C18 H17 F N4 O4 S CN(C1=C(N(....
7 3ZLK ic50 = 1.32 uM Y46 C17 H16 N4 O4 S c1ccc(cc1)....
8 4B2W - BZ0 C18 H16 N4 O3 c1ccc(cc1)....
9 1G0R - THM C10 H14 N2 O5 CC1=CN(C(=....
10 4ARW Kd = 0.074 uM HNR C15 H20 N4 O4 S CCCCN1C(=C....
11 3ZLL Kd = 0.395 uM 4WF C11 H11 N3 O3 c1ccc(cc1)....
12 4B5B ic50 = 0.387 uM BBE C19 H20 N4 O4 S Cc1cccc(c1....
13 4ASY - N5Y C19 H18 N4 O3 CN(C1=C(N(....
14 1FXO - TMP C10 H15 N2 O8 P CC1=CN(C(=....
15 4B3U ic50 = 4.7 uM NWL C13 H16 N4 O2 CCNC1=C(N(....
16 4B2X - NIQ C13 H22 N4 O2 CCCCN1C(=C....
17 1IIM - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
18 1IIN - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
19 1MP3 - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
20 1MP4 - UPG C15 H24 N2 O17 P2 C1=CN(C(=O....
21 3PKQ - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
22 6B5E - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
23 6B5K - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
24 1LVW - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: UPG; Similar ligands found: 101
No: Ligand ECFP6 Tc MDL keys Tc
1 GDU 1 1
2 UPG 1 1
3 UFM 1 1
4 USQ 0.8 0.846154
5 UFG 0.797619 0.943662
6 U2F 0.797619 0.943662
7 UPF 0.797619 0.943662
8 AWU 0.77381 0.970588
9 UD2 0.73913 0.985294
10 UD1 0.73913 0.985294
11 UGA 0.738636 0.985075
12 UGB 0.738636 0.985075
13 UDP 0.717949 0.941176
14 UDX 0.715909 0.970588
15 UDP GAL 0.715909 0.970588
16 UAD 0.715909 0.970588
17 UTP 0.7125 0.941176
18 U5F 0.703704 0.941176
19 IUG 0.693878 0.835443
20 UGF 0.692308 0.929577
21 G3N 0.692308 0.942857
22 C5G 0.688889 0.943662
23 URM 0.681818 0.956522
24 660 0.681818 0.956522
25 UPU 0.670588 0.970149
26 EPZ 0.650485 0.971014
27 3UC 0.648936 0.943662
28 UNP 0.647059 0.914286
29 EEB 0.644231 0.957143
30 EPU 0.644231 0.957143
31 U5P 0.641026 0.926471
32 U 0.641026 0.926471
33 HP7 0.636364 0.970588
34 UD7 0.636364 0.956522
35 2GW 0.632653 0.957143
36 MJZ 0.63 0.942857
37 F5P 0.623762 0.942857
38 F5G 0.623762 0.956522
39 UD4 0.623762 0.942857
40 UPP 0.615385 0.942029
41 UDZ 0.615385 0.88
42 UDH 0.615385 0.866667
43 UMA 0.598214 0.971014
44 44P 0.597561 0.901408
45 UDM 0.59596 0.942857
46 12V 0.592233 0.929577
47 HWU 0.592233 0.929577
48 1GW 0.590476 0.917808
49 2KH 0.586207 0.914286
50 Y6W 0.585106 0.916667
51 UDP UDP 0.576471 0.911765
52 U22 0.567797 0.8375
53 U21 0.567797 0.858974
54 U20 0.567797 0.858974
55 URI 0.552632 0.865672
56 CJB 0.551282 0.850746
57 UP5 0.527273 0.855263
58 UAG 0.523438 0.917808
59 2QR 0.520325 0.848101
60 DAU 0.519608 0.891892
61 UA3 0.511905 0.911765
62 U3P 0.511905 0.911765
63 CSV 0.504762 0.878378
64 CSQ 0.504762 0.878378
65 4TC 0.504425 0.833333
66 4RA 0.492308 0.857143
67 UD0 0.484848 0.846154
68 PUP 0.480392 0.887324
69 UML 0.478571 0.858974
70 U2P 0.476744 0.926471
71 CXY 0.471154 0.916667
72 GKE 0.463636 0.8
73 GDD 0.463636 0.8
74 GDC 0.463636 0.8
75 FZK 0.454545 0.780488
76 CTP 0.447917 0.888889
77 HF4 0.447917 0.888889
78 CDP 0.446809 0.888889
79 ADQ 0.443396 0.828947
80 BUP 0.443299 0.876712
81 DKX 0.44186 0.774648
82 U2S 0.43956 0.77027
83 UMF 0.438202 0.833333
84 LSU 0.436893 0.72093
85 U4S 0.433333 0.733333
86 DUT 0.43299 0.861111
87 U3S 0.423913 0.756757
88 YSU 0.422018 0.75
89 5GW 0.421569 0.915493
90 DUD 0.421053 0.861111
91 5FU 0.417582 0.863014
92 C2G 0.417476 0.902778
93 UPA 0.416667 0.868421
94 0RC 0.415842 0.866667
95 U1S 0.415842 0.776316
96 7XL 0.415842 0.890411
97 2TU 0.411765 0.777778
98 UTP U U U 0.409524 0.897059
99 139 0.406504 0.835443
100 APU 0.401639 0.831169
101 PMP UD1 0.40146 0.835443
Similar Ligands (3D)
Ligand no: 1; Ligand: UPG; Similar ligands found: 4
No: Ligand Similarity coefficient
1 TDX 0.9223
2 GDR 0.8995
3 GDX 0.8793
4 3R2 0.8519
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1IIM; Ligand: TTP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1iim.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1IIM; Ligand: TTP; 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: 1iim.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1IIM; Ligand: TTP; Similar sites found with APoc: 4
This union binding pocket(no: 3) in the query (biounit: 1iim.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
1 3JUK UPG 44.8399
2 3JUK UPG 44.8399
3 3JUK UPG 44.8399
4 3JUK UPG 44.8399
Pocket No.: 4; Query (leader) PDB : 1IIM; Ligand: TTP; 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: 1iim.bio1) has 38 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1IIM; Ligand: TTP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 1iim.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1IIM; Ligand: TTP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 1iim.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 1IIM; Ligand: TTP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 1iim.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 1IIM; Ligand: TTP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 1iim.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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