Receptor
PDB id Resolution Class Description Source Keywords
4x7r 2.15 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF S. AUREUS TARM G117R MUTANT IN COMPLEX FONDAPARINUX, ALPHA-GLCNAC-GLYCEROL AND UDP STAPHYLOCOCCUS AUREUS SUBSP. AUREUS 21ORGANISM_TAXID: 904724 GLYCOSYLTRANSFERASE GT-B RETAINING WALL TEICHOIC ACID TRANS
Ref.: STRUCTURE AND MECHANISM OF STAPHYLOCOCCUS AUREUS TA WALL TEICHOIC ACID ALPHA-GLYCOSYLTRANSFERASE. PROC.NATL.ACAD.SCI.USA V. 112 E576 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UDP A:501;
B:501;
 Valid;
Valid;
 none;
none;
 submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
3YW B:503;
A:503;
 Valid;
Valid;
 none;
none;
 submit data
295.286 C11 H21 N O8 CC(=O...
ZDO IDS SUS BDP SGN D:1;
C:1;
 Valid;
Valid;
 none;
none;
 submit data
1498.18 n/a S(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4X7R 2.15 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF S. AUREUS TARM G117R MUTANT IN COMPLEX FONDAPARINUX, ALPHA-GLCNAC-GLYCEROL AND UDP STAPHYLOCOCCUS AUREUS SUBSP. AUREUS 21ORGANISM_TAXID: 904724 GLYCOSYLTRANSFERASE GT-B RETAINING WALL TEICHOIC ACID TRANS
Ref.: STRUCTURE AND MECHANISM OF STAPHYLOCOCCUS AUREUS TA WALL TEICHOIC ACID ALPHA-GLYCOSYLTRANSFERASE. PROC.NATL.ACAD.SCI.USA V. 112 E576 2015
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 4X7R - 3YW C11 H21 N O8 CC(=O)N[C@....
2 4X7M - UD1 C17 H27 N3 O17 P2 CC(=O)N[C@....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 4X7R - 3YW C11 H21 N O8 CC(=O)N[C@....
2 4X7M - UD1 C17 H27 N3 O17 P2 CC(=O)N[C@....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 4X7R - 3YW C11 H21 N O8 CC(=O)N[C@....
2 4X7M - UD1 C17 H27 N3 O17 P2 CC(=O)N[C@....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: UDP; Similar ligands found: 123
No: Ligand ECFP6 Tc MDL keys Tc
1 UDP 1 1
2 UTP 0.892308 1
3 U5F 0.878788 1
4 UNP 0.8 0.970149
5 U5P 0.78125 0.984615
6 U 0.78125 0.984615
7 UPU 0.72973 0.940298
8 2KH 0.722222 0.970149
9 44P 0.720588 0.955882
10 UFM 0.717949 0.941176
11 URM 0.717949 0.927536
12 660 0.717949 0.927536
13 UPG 0.717949 0.941176
14 GDU 0.717949 0.941176
15 UDP UDP 0.714286 0.939394
16 UDH 0.705128 0.864865
17 UPP 0.705128 0.941176
18 UFG 0.691358 0.888889
19 U2F 0.691358 0.888889
20 UPF 0.691358 0.888889
21 AWU 0.6875 0.941176
22 UAD 0.670732 0.941176
23 UDX 0.670732 0.941176
24 3UC 0.658824 0.888889
25 UGA 0.654762 0.955224
26 UGB 0.654762 0.955224
27 USQ 0.654762 0.820513
28 G3N 0.647059 0.914286
29 UGF 0.647059 0.901408
30 UDM 0.636364 0.914286
31 URI 0.625 0.863636
32 UD1 0.622222 0.927536
33 UD2 0.622222 0.927536
34 UDP GAL 0.611765 0.913043
35 Y6W 0.607143 0.888889
36 CDP 0.605263 0.942029
37 HP7 0.591398 0.941176
38 UD7 0.591398 0.927536
39 MJZ 0.585106 0.914286
40 IUG 0.583333 0.810127
41 HWU 0.578947 0.901408
42 UD4 0.578947 0.914286
43 12V 0.578947 0.901408
44 F5G 0.578947 0.927536
45 F5P 0.578947 0.914286
46 CJB 0.573529 0.820895
47 UDZ 0.571429 0.853333
48 DUD 0.571429 0.913043
49 UP5 0.571429 0.853333
50 EPZ 0.56 0.914286
51 5GW 0.559524 0.942029
52 EEB 0.554455 0.901408
53 EPU 0.554455 0.901408
54 UA3 0.547945 0.939394
55 U3P 0.547945 0.939394
56 4TC 0.544554 0.831169
57 HF4 0.54321 0.942029
58 CTP 0.54321 0.942029
59 BUP 0.536585 0.928571
60 CSV 0.531915 0.851351
61 CSQ 0.531915 0.851351
62 DUT 0.52439 0.913043
63 4GW 0.516484 0.915493
64 UMA 0.513761 0.914286
65 U4S 0.513158 0.753425
66 U2P 0.506667 0.954545
67 U3S 0.5 0.753425
68 U2S 0.5 0.767123
69 FZK 0.494253 0.777778
70 PUP 0.48913 0.913043
71 U21 0.486957 0.810127
72 U20 0.486957 0.810127
73 U22 0.486957 0.790123
74 DKX 0.486486 0.746479
75 U1S 0.482759 0.75
76 0RC 0.482759 0.864865
77 2QR 0.478632 0.822785
78 5FU 0.474359 0.914286
79 LSU 0.472527 0.738095
80 8OD 0.47191 0.851351
81 C5G 0.468085 0.888889
82 7XL 0.465909 0.888889
83 UMF 0.461538 0.857143
84 G8D 0.460674 0.855263
85 2TM 0.45977 0.902778
86 UTP U U U 0.456522 0.895522
87 YSU 0.453608 0.746988
88 2TU 0.452055 0.774648
89 4RA 0.451613 0.855263
90 C2G 0.450549 0.901408
91 DU 0.45 0.898551
92 CAR 0.45 0.927536
93 UMP 0.45 0.898551
94 C5P 0.45 0.927536
95 C 0.45 0.927536
96 UAG 0.448 0.864865
97 CDC 0.446809 0.777778
98 5BU 0.444444 0.914286
99 UD0 0.444444 0.844156
100 N3E 0.440476 0.733333
101 UC5 0.440476 0.9
102 UUA 0.438356 0.772727
103 DUP 0.431818 0.887324
104 2GW 0.431373 0.901408
105 M7G 0.430108 0.780488
106 CNU 0.428571 0.927536
107 CDM 0.427083 0.842105
108 H6Y 0.425532 0.851351
109 16B 0.421687 0.888889
110 S5P 0.419753 0.915493
111 8GT 0.419355 0.855263
112 CDP MG 0.418605 0.885714
113 CXY 0.418367 0.888889
114 UPA 0.418182 0.842105
115 U2G 0.410714 0.822785
116 UML 0.408759 0.810127
117 UP6 0.407407 0.871429
118 M7M 0.40625 0.771084
119 1GW 0.40367 0.864865
120 BMP 0.402439 0.970149
121 APU 0.401786 0.828947
122 PMP UD1 0.401575 0.7875
123 DUT MG 0.4 0.857143
Ligand no: 2; Ligand: 3YW; Similar ligands found: 62
No: Ligand ECFP6 Tc MDL keys Tc
1 3YW 1 1
2 SER A2G 0.683333 0.877551
3 TNR 0.683333 0.895833
4 2F8 0.589286 0.933333
5 MAG 0.589286 0.933333
6 NG1 0.576271 0.745455
7 GN1 0.576271 0.745455
8 GAL NAG 0.560606 0.913043
9 MBG A2G 0.514706 0.875
10 RGG 0.508772 0.72093
11 NDG NAG 0.507246 0.84
12 HD4 0.506849 0.767857
13 57S 0.5 0.767857
14 ACE SER SER VAL GLY A2G 0.494118 0.811321
15 MAN NAG 0.492537 0.913043
16 GAL NGA 0.485714 0.934783
17 GYU 0.485294 0.796296
18 MBG NAG 0.478261 0.875
19 A2G NAG 0.478261 0.857143
20 GDL NAG 0.478261 0.857143
21 A2G GAL NAG 0.474359 0.857143
22 GAL NGA A2G 0.459459 0.857143
23 Z3Q NGA 0.455696 0.7
24 NAG NGO 0.454545 0.777778
25 BGC GAL NGA 0.453333 0.913043
26 NAG NAG NAG NAG NAG NAG NAG NAG 0.452055 0.84
27 NAG NAG NAG NAG NAG 0.452055 0.84
28 NAG NAG NAG NAG NAG NAG 0.452055 0.84
29 NDG NAG NAG NAG NAG 0.452055 0.84
30 NGA 0.448276 0.930233
31 BM3 0.448276 0.930233
32 NDG 0.448276 0.930233
33 A2G 0.448276 0.930233
34 HSQ 0.448276 0.930233
35 NAG 0.448276 0.930233
36 LEC 0.445946 0.650794
37 6ZC 0.445946 0.650794
38 A2G SER GAL 0.435897 0.843137
39 BMA MAN NAG 0.435897 0.913043
40 3QL 0.434211 0.792453
41 GYT 0.434211 0.728814
42 MAN MAN NAG 0.43038 0.914894
43 NM9 NAG 0.43038 0.807692
44 GYP GZL NAG 0.425287 0.86
45 MA8 0.424658 0.84
46 ACA SER SER VAL GLY A2G 0.424242 0.741379
47 MMA MAN NAG 0.423077 0.875
48 A2G THR GAL NAG 0.422222 0.807692
49 AMU NAG 0.419753 0.823529
50 AH0 NAG 0.419753 0.763636
51 GAL FUC A2G 0.417722 0.893617
52 NGA THR GAL NAG 0.417582 0.807692
53 SNG 0.412698 0.851064
54 NAG NAG NAG NAG 0.4125 0.811321
55 NAG NAG NAG NAG NAG NAG NAG 0.4125 0.811321
56 BGC GAL NAG 0.4125 0.913043
57 BMX BMX BMX BM3 0.4125 0.724138
58 NAG GAL NAG 0.4125 0.857143
59 NAG NAG NAG 0.4125 0.811321
60 NGT NAG 0.407407 0.711864
61 MAN MAN MAN NAG NAG 0.406977 0.857143
62 BGC GAL GLA NGA 0.404762 0.913043
Ligand no: 3; Ligand: ZDO IDS SUS BDP SGN; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 ZDO IDS SUS BDP SGN 1 1
2 IDS SGN IDS SGN IDS SUS IDS SGN 0.761062 0.969231
3 IDY SGN 0.641509 0.984615
4 SGN IDS SGN IDS 0.584746 0.953846
5 IDY SUS 0.558559 0.953846
6 SGN IDS SGN IDS SGN 0.543307 0.954545
7 IDS SGN IDS SGN IDS SGN 0.539062 0.954545
8 SGN IDS SGN IDS SGN UAP 0.534884 0.925373
9 SGN IDS SGN UAP 0.534884 0.925373
10 IDS SGN IDS SGN IDS 0.51938 0.939394
11 BDP NPO GNS IDS GNS BDP GNS 0.514706 0.828947
12 IDS SGN IDS SGN UAP 0.5 0.925373
13 IDY GNX 0.46087 0.939394
14 BDP NPO GNS BDP GNS BDP GNS 0.411765 0.828947
15 GNS IDR GNS IDR GNS IDR GNS IDR 0.409449 0.939394
16 BDP GNS BDP GNS BDP GNS BDP 0.401575 0.939394
Similar Ligands (3D)
Ligand no: 1; Ligand: UDP; Similar ligands found: 55
No: Ligand Similarity coefficient
1 YYY 0.9739
2 TYD 0.9699
3 TBD 0.9623
4 GCQ 0.9509
5 ADP 0.9410
6 DUN 0.9317
7 D4D 0.9237
8 ADX 0.9224
9 AU1 0.9218
10 AP2 0.9215
11 SON 0.9211
12 GDP 0.9193
13 DAT 0.9189
14 IDP 0.9155
15 PRX 0.9148
16 ADP MG 0.9122
17 BEF ADP 0.9122
18 AN2 0.9115
19 A12 0.9102
20 M33 0.9098
21 CA0 0.9083
22 G5A 0.9077
23 CUU 0.9055
24 GAP 0.8984
25 DGI 0.8977
26 GNH 0.8961
27 FZQ 0.8919
28 7D3 0.8915
29 DAL AMP 0.8905
30 H2U 0.8888
31 CH 0.8874
32 AZD 0.8849
33 PSU 0.8815
34 CK7 0.8802
35 AMP 0.8793
36 FN5 0.8781
37 6AD 0.8757
38 A5A 0.8754
39 HQ5 0.8747
40 DCM 0.8724
41 8LH 0.8718
42 8GD 0.8708
43 ATY 0.8691
44 BMQ 0.8679
45 U6M 0.8672
46 NUP 0.8671
47 DC 0.8658
48 DCP 0.8657
49 TMP 0.8642
50 C8M 0.8633
51 TTP 0.8581
52 ATP 0.8570
53 DDN 0.8568
54 C2R 0.8549
55 D4T 0.8531
Ligand no: 2; Ligand: 3YW; Similar ligands found: 6
No: Ligand Similarity coefficient
1 9GW 0.8957
2 9GZ 0.8879
3 9GT 0.8804
4 9GN 0.8681
5 DAN 0.8654
6 DF4 0.8572
Ligand no: 3; Ligand: ZDO IDS SUS BDP SGN; 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 : 4X7R; Ligand: UDP; Similar sites found with APoc: 4
This union binding pocket(no: 1) in the query (biounit: 4x7r.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4PQG UDP 30.0203
2 4PQG UDP 30.0203
3 4PQG UDP 30.0203
4 4PQG UDP 30.0203
Pocket No.: 2; Query (leader) PDB : 4X7R; Ligand: 3YW; 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: 4x7r.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4X7R; Ligand: 3YW; Similar sites found with APoc: 2
This union binding pocket(no: 3) in the query (biounit: 4x7r.bio2) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 4PQG NAG 30.0203
2 4PQG UDP 30.0203
Pocket No.: 4; Query (leader) PDB : 4X7R; Ligand: UDP; Similar sites found with APoc: 2
This union binding pocket(no: 4) in the query (biounit: 4x7r.bio2) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 4PQG NAG 30.0203
2 4PQG UDP 30.0203
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