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 313 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 277 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 212 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 (2D)
Ligand no: 1; Ligand: 2KH; Similar ligands found: 97
No: Ligand ECFP6 Tc MDL keys Tc
1 2KH 1 1
2 U5P 0.735294 0.955224
3 U 0.735294 0.955224
4 UDP 0.722222 0.970149
5 UNP 0.710526 1
6 UTP 0.693333 0.970149
7 U5F 0.684211 0.970149
8 44P 0.680556 0.928571
9 UDP UDP 0.653333 0.911765
10 UPU 0.609756 0.913043
11 URM 0.604651 0.901408
12 660 0.604651 0.901408
13 GDU 0.586207 0.914286
14 UFM 0.586207 0.914286
15 UPG 0.586207 0.914286
16 DUP 0.585366 0.915493
17 UPP 0.574713 0.914286
18 UDH 0.574713 0.842105
19 UFG 0.566667 0.864865
20 UPF 0.566667 0.864865
21 U2F 0.566667 0.864865
22 URI 0.565217 0.838235
23 AWU 0.561798 0.914286
24 Y6W 0.561798 0.864865
25 UAD 0.549451 0.914286
26 UDX 0.549451 0.914286
27 UDP GAL 0.549451 0.887324
28 3UC 0.542553 0.864865
29 UDM 0.541667 0.888889
30 USQ 0.537634 0.8
31 UGA 0.537634 0.927536
32 UGB 0.537634 0.927536
33 UGF 0.531915 0.876712
34 G3N 0.531915 0.888889
35 UD1 0.530612 0.901408
36 UD2 0.530612 0.901408
37 CJB 0.520548 0.797101
38 FZK 0.505618 0.780488
39 UD7 0.504951 0.901408
40 HP7 0.504951 0.914286
41 U3P 0.5 0.911765
42 UA3 0.5 0.911765
43 MJZ 0.5 0.888889
44 UD4 0.495146 0.888889
45 HWU 0.495146 0.876712
46 12V 0.495146 0.876712
47 F5G 0.495146 0.901408
48 F5P 0.495146 0.888889
49 CSV 0.494949 0.828947
50 CSQ 0.494949 0.828947
51 U4S 0.4875 0.733333
52 LSU 0.483871 0.741176
53 EPZ 0.481481 0.888889
54 EEB 0.477064 0.876712
55 EPU 0.477064 0.876712
56 UDZ 0.476636 0.88
57 UP5 0.476636 0.831169
58 U3S 0.47561 0.733333
59 U2S 0.47561 0.746667
60 IUG 0.471698 0.835443
61 YSU 0.464646 0.75
62 U2P 0.4625 0.926471
63 U1S 0.461538 0.730769
64 DUN 0.45977 0.915493
65 4TC 0.454545 0.810127
66 UMA 0.444444 0.888889
67 DKX 0.443038 0.726027
68 5BU 0.440476 0.888889
69 PUP 0.438776 0.887324
70 5FU 0.433735 0.888889
71 CDP 0.431818 0.915493
72 CAR 0.428571 0.901408
73 BUP 0.428571 0.902778
74 C 0.428571 0.901408
75 C5P 0.428571 0.901408
76 2TM 0.423913 0.878378
77 U21 0.422764 0.790123
78 U20 0.422764 0.790123
79 U22 0.422764 0.771084
80 UTP U U U 0.42268 0.869565
81 UMF 0.421687 0.833333
82 DUD 0.420455 0.887324
83 16B 0.418605 0.890411
84 DUT 0.417582 0.887324
85 HF4 0.417582 0.915493
86 CTP 0.417582 0.915493
87 2QR 0.416 0.802469
88 UUA 0.415584 0.75
89 UMP 0.411765 0.873239
90 DU 0.411765 0.873239
91 CNU 0.409091 0.901408
92 5GW 0.40625 0.915493
93 4RA 0.40458 0.833333
94 N3E 0.404494 0.714286
95 UC5 0.404494 0.875
96 0KX 0.404255 0.853333
97 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 MGC GAL 0.405405 0.706897
Similar Ligands (3D)
Ligand no: 1; Ligand: 2KH; Similar ligands found: 20
No: Ligand Similarity coefficient
1 D3T 0.9355
2 DCP 0.9268
3 APC 0.9199
4 AGS 0.9090
5 ATP 0.8972
6 3AT 0.8966
7 DCT 0.8956
8 GTP 0.8870
9 ANP 0.8853
10 TTP 0.8825
11 DGT 0.8809
12 ADP ALF 0.8770
13 ADP BEF 0.8765
14 ACP 0.8740
15 GH3 0.8726
16 DTP 0.8700
17 HEJ 0.8596
18 TYD 0.8564
19 YYY 0.8540
20 AHX 0.8514
Ligand no: 2; Ligand: 491; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4Y7U; Ligand: 2KH; 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: 4y7u.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4Y7U; Ligand: 491; 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: 4y7u.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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