Receptor
PDB id Resolution Class Description Source Keywords
4Y7U 1.7 Å EC: 2.-.-.- STRUCTURAL ANALYSIS OF MURU PSEUDOMONAS PUTIDA (STRAIN BIRD-1) NUCLEOTIDYLTRANSFERASE FAMILY PROTEIN URIDYLTRANSFERASE ROFOLD MURNAC-1P TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF THE N-ACETYLMURAMIC ACID ALPHA-1-PHOSPHATE (MURNAC-ALPHA 1-P) URIDYLYLTRANSF MURU, A MINIMAL SUGAR NUCLEOTIDYLTRANSFERASE AND PO DRUG TARGET ENZYME IN GRAM-NEGATIVE PATHOGENS. J.BIOL.CHEM. V. 290 10804 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2KH A:306;
Valid;
none;
submit data
483.156 C9 H16 N3 O14 P3 C1=CN...
SO4 A:303;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
MG A:304;
A:305;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
GOL A:301;
A:302;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
491 A:307;
Valid;
none;
submit data
373.25 C11 H20 N O11 P C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4Y7U 1.7 Å EC: 2.-.-.- STRUCTURAL ANALYSIS OF MURU PSEUDOMONAS PUTIDA (STRAIN BIRD-1) NUCLEOTIDYLTRANSFERASE FAMILY PROTEIN URIDYLTRANSFERASE ROFOLD MURNAC-1P TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF THE N-ACETYLMURAMIC ACID ALPHA-1-PHOSPHATE (MURNAC-ALPHA 1-P) URIDYLYLTRANSF MURU, A MINIMAL SUGAR NUCLEOTIDYLTRANSFERASE AND PO DRUG TARGET ENZYME IN GRAM-NEGATIVE PATHOGENS. J.BIOL.CHEM. V. 290 10804 2015
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 4Y7V - 491 C11 H20 N O11 P C[C@H](C(=....
2 4Y7U - 491 C11 H20 N O11 P C[C@H](C(=....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 211 families.
1 4Y7V - 491 C11 H20 N O11 P C[C@H](C(=....
2 4Y7U - 491 C11 H20 N O11 P C[C@H](C(=....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 166 families.
1 4Y7V - 491 C11 H20 N O11 P C[C@H](C(=....
2 4Y7U - 491 C11 H20 N O11 P C[C@H](C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2KH; Similar ligands found: 90
No: Ligand ECFP6 Tc MDL keys Tc
1 2KH 1 1
2 U5P 0.735294 0.955224
3 UDP 0.722222 0.970149
4 UNP 0.710526 1
5 UTP 0.693333 0.970149
6 44P 0.680556 0.928571
7 UDP UDP 0.653333 0.911765
8 UPU 0.609756 0.913043
9 URM 0.604651 0.901408
10 660 0.604651 0.901408
11 GDU 0.586207 0.914286
12 UFM 0.586207 0.914286
13 UPG 0.586207 0.914286
14 GUD 0.586207 0.914286
15 DUP 0.585366 0.915493
16 UPP 0.574713 0.914286
17 UDH 0.574713 0.842105
18 UPF 0.566667 0.864865
19 UFG 0.566667 0.864865
20 U2F 0.566667 0.864865
21 U 0.565217 0.838235
22 URI 0.565217 0.838235
23 Y6W 0.561798 0.864865
24 UDP GAL 0.549451 0.887324
25 UDX 0.549451 0.914286
26 UAD 0.549451 0.914286
27 3UC 0.542553 0.864865
28 UDM 0.541667 0.888889
29 UGA 0.537634 0.927536
30 UGB 0.537634 0.927536
31 USQ 0.537634 0.8
32 G3N 0.531915 0.888889
33 UD2 0.530612 0.901408
34 UD1 0.530612 0.901408
35 U U 0.521739 0.927536
36 CJB 0.520548 0.797101
37 HP7 0.504951 0.914286
38 UD7 0.504951 0.901408
39 U3P 0.5 0.911765
40 CH 0.5 0.887324
41 UA3 0.5 0.911765
42 MJZ 0.5 0.888889
43 12V 0.495146 0.876712
44 HWU 0.495146 0.876712
45 UD4 0.495146 0.888889
46 CSV 0.494949 0.828947
47 CSQ 0.494949 0.828947
48 U4S 0.4875 0.733333
49 EPZ 0.481481 0.888889
50 EEB 0.477064 0.876712
51 EPU 0.477064 0.876712
52 UP5 0.476636 0.831169
53 UDZ 0.476636 0.88
54 U3S 0.47561 0.733333
55 U2S 0.47561 0.746667
56 IUG 0.471698 0.835443
57 U2P 0.4625 0.926471
58 U1S 0.461538 0.730769
59 DUN 0.45977 0.915493
60 4TC 0.454545 0.810127
61 UMA 0.444444 0.888889
62 DKX 0.443038 0.726027
63 5BU 0.440476 0.888889
64 PUP 0.438776 0.887324
65 A U 0.4375 0.78481
66 5FU 0.433735 0.888889
67 CDP 0.431818 0.915493
68 CAR 0.428571 0.901408
69 C 0.428571 0.901408
70 C5P 0.428571 0.901408
71 U U U U 0.427083 0.913043
72 U20 0.422764 0.790123
73 U21 0.422764 0.790123
74 U22 0.422764 0.771084
75 UTP U U U 0.42268 0.869565
76 UMF 0.421687 0.833333
77 DUD 0.420455 0.887324
78 16B 0.418605 0.890411
79 CTP 0.417582 0.915493
80 DUT 0.417582 0.887324
81 2QR 0.416 0.802469
82 UUA 0.415584 0.75
83 DU 0.411765 0.873239
84 UMP 0.411765 0.873239
85 CNU 0.409091 0.901408
86 5GW 0.40625 0.915493
87 4RA 0.40458 0.833333
88 N3E 0.404494 0.714286
89 UC5 0.404494 0.875
90 S5P 0.4 0.890411
Ligand no: 2; Ligand: 491; Similar ligands found: 10
No: Ligand ECFP6 Tc MDL keys Tc
1 491 1 1
2 AMU 0.603175 0.759259
3 GN1 0.555556 0.944444
4 NG1 0.555556 0.944444
5 EPZ 0.5 0.728571
6 AH0 0.438356 0.672414
7 UMA 0.419643 0.728571
8 EEB 0.411215 0.71831
9 MUR 0.405797 0.654545
10 GAL MGC 0.405405 0.706897
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4Y7U; Ligand: 2KH; Similar sites found: 28
This union binding pocket(no: 1) in the query (biounit: 4y7u.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5T96 79J 0.01261 0.43513 3.0303
2 5BXV MGP 0.02688 0.40911 3.125
3 1JV1 UD1 0.00009681 0.45105 3.4632
4 1LPD ADE 0.01137 0.42173 3.8961
5 1JJ7 ADP 0.02733 0.41566 3.8961
6 1QHH ATP 0.02491 0.40089 4.34783
7 5T46 MGP 0.04212 0.40008 5
8 2YQS UD1 0.0000267 0.47795 5.62771
9 2OEG UPG 0.00005376 0.45553 6.49351
10 1YP4 ADQ 0.0001199 0.45104 6.65188
11 1U1J MET 0.03037 0.40676 6.92641
12 4UP4 GAL NAG 0.01714 0.41377 8.22511
13 2Y6P CTP 0.00003438 0.53431 9.09091
14 2ICY UPG 0.00009218 0.47869 9.09091
15 3OH3 UAD 0.0003406 0.4338 9.09091
16 5FJJ MAN 0.03884 0.42244 9.09091
17 1H7F C5P 0.0004632 0.40098 9.09091
18 3K8D CTP 0.00006929 0.41866 9.95671
19 5U7W ADE 0.03026 0.41 14.2857
20 4KU7 PCG 0.01469 0.41222 16.9935
21 2PA4 UPG 0.0001111 0.46304 17.7489
22 5JAX 6J7 0.01774 0.40119 19.2593
23 5HS2 CTP 0.000001352 0.4718 19.8276
24 2XWL CTP 0.000004977 0.56053 28.2511
25 4G87 UD1 0.008181 0.43394 29.4372
26 1WVC CTP 0.001528 0.48968 44.1558
27 3JUK UPG 0.0004459 0.43306 45.8874
28 1H5T DAU 0.00006256 0.46929 47.1861
Pocket No.: 2; Query (leader) PDB : 4Y7U; Ligand: 491; Similar sites found: 6
This union binding pocket(no: 2) in the query (biounit: 4y7u.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3PE6 ZYH 0.008867 0.43333 3.0303
2 2VBF TPP 0.01742 0.42268 3.4632
3 2OEG UPG 0.01317 0.42244 6.49351
4 1YP4 ADQ 0.009615 0.43235 6.65188
5 2VZZ SCA 0.03828 0.40458 7.79817
6 1H5R G1P 0.005814 0.42603 47.1861
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