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...
NTO B:502;
A:502;
Valid;
Valid;
none;
none;
submit data
1508.26 C31 H53 N3 O49 S8 CO[C@...
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 1256 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 1068 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 922 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
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
Ligand no: 2; Ligand: 3YW; Similar ligands found: 80
No: Ligand ECFP6 Tc MDL keys Tc
1 3YW 1 1
2 TNR 0.683333 0.895833
3 MAG 0.589286 0.933333
4 2F8 0.589286 0.933333
5 GN1 0.576271 0.745455
6 NG1 0.576271 0.745455
7 MBG A2G 0.514706 0.875
8 A2G MBG 0.514706 0.875
9 RGG 0.508772 0.72093
10 NAG GAL 0.507463 0.913043
11 NGA GAL 0.507463 0.913043
12 GAL NAG 0.507463 0.913043
13 NDG NAG 0.507246 0.84
14 57S 0.5 0.767857
15 ACE SER SER VAL GLY A2G 0.494118 0.811321
16 MAN NAG 0.492537 0.913043
17 GYU 0.485294 0.796296
18 NAG GDL 0.478261 0.857143
19 CBS CBS 0.478261 0.857143
20 NAG A2G 0.478261 0.857143
21 NAG NDG 0.478261 0.857143
22 NAG MBG 0.478261 0.875
23 CBS 0.478261 0.857143
24 NAG NGA 0.478261 0.857143
25 NGA GAL BGC 0.453333 0.913043
26 NDG NAG NAG NAG 0.452055 0.84
27 NDG NAG NAG 0.452055 0.84
28 NAG NAG NAG NDG 0.452055 0.84
29 CTO 0.452055 0.84
30 NDG NAG NAG NDG NAG 0.452055 0.84
31 NAG NAG NAG NAG NAG NAG NAG NAG 0.452055 0.84
32 NAG NAG NAG NAG 0.452055 0.84
33 NAG NAG NAG NAG NAG 0.452055 0.84
34 NAG NAG 0.452055 0.843137
35 NDG NAG NAG NDG 0.452055 0.84
36 NAG NAG NAG NAG NAG NAG 0.452055 0.84
37 NAG NAG NAG NAG NDG NAG 0.452055 0.84
38 NAG NAG NAG NAG NDG 0.452055 0.84
39 NAG NAG NAG 0.452055 0.84
40 NAG NAG NDG 0.452055 0.84
41 DLD 0.45 0.711864
42 A2G 0.448276 0.930233
43 BM3 0.448276 0.930233
44 HSQ 0.448276 0.930233
45 NAG 0.448276 0.930233
46 NGA 0.448276 0.930233
47 NDG 0.448276 0.930233
48 GAL SER A2G 0.447368 0.84
49 NGA SER GAL 0.447368 0.84
50 A2G SER GAL 0.447368 0.84
51 GAL TNR 0.447368 0.84
52 LEC 0.445946 0.650794
53 6ZC 0.445946 0.650794
54 3QL 0.434211 0.792453
55 GYT 0.434211 0.728814
56 MAN MAN NAG 0.43038 0.914894
57 NAG NM9 0.43038 0.807692
58 NAG NGO 0.428571 0.792453
59 ACA SER SER VAL GLY A2G 0.428571 0.754386
60 3PV 0.425287 0.86
61 NAG MAN BMA 0.425 0.913043
62 NAG MAN MAN 0.425 0.913043
63 MA8 0.424658 0.84
64 NAG MAN MMA 0.423077 0.875
65 NAG MUB 0.419753 0.823529
66 NAG AMU 0.419753 0.823529
67 AH0 NAG 0.419753 0.763636
68 FUC GLA A2G 0.417722 0.893617
69 A2G GAL FUC 0.417722 0.893617
70 A2G GLA FUC 0.417722 0.893617
71 FUC GAL A2G 0.417722 0.893617
72 NGA GAL FUC 0.417722 0.893617
73 FUC GL0 A2G 0.417722 0.893617
74 SNG 0.412698 0.851064
75 NAG GAL BGC 0.4125 0.913043
76 NAG GAL NAG 0.4125 0.857143
77 ACE SER THR VAL GLY A2G 0.411765 0.811321
78 NGT NAG 0.407407 0.711864
79 NAG MAN MAN MAN NAG 0.406977 0.857143
80 NGA GLA GAL BGC 0.404762 0.913043
Ligand no: 3; Ligand: NTO; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 NTO 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4X7R; Ligand: UDP; Similar sites found: 41
This union binding pocket(no: 1) in the query (biounit: 4x7r.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4F97 GDP 0.0006733 0.42243 1.21704
2 4F97 VDO 0.004195 0.42163 1.21704
3 3H4T UDP 0.001596 0.43174 1.23762
4 1XV5 UDP 0.0005533 0.43821 1.24688
5 4RIF 3R2 0.00008142 0.49797 1.31926
6 1H82 GZZ 0.04941 0.40023 1.69492
7 3R75 BEZ 0.01458 0.41254 1.82556
8 5V2J 7WV 0.0001736 0.4899 2.22717
9 5V2J UDP 0.0001736 0.4899 2.22717
10 3NKS FAD 0.01838 0.40439 2.30608
11 2C1X UDP 0.0202 0.40148 2.41228
12 1EM6 NBG 0.00001658 0.55246 2.43408
13 2VCH UDP 0.0002113 0.48123 2.5
14 5BNW 12V 0.006563 0.42075 2.83976
15 4GYW UDP 0.007741 0.41628 2.83976
16 5LWV UDP 0.009154 0.40786 2.83976
17 4N39 UDP 0.003855 0.40381 2.83976
18 2IYA UDP 0.0005957 0.44153 3.06604
19 3S2U UD1 0.00008838 0.48634 3.28767
20 2WTX UDP 0.000006091 0.56104 4.00844
21 2WTX VDO 0.0003139 0.47971 4.00844
22 3HBF MYC 0.008021 0.41791 4.18502
23 3HBF UDP 0.003104 0.4173 4.18502
24 2IV3 UDP 0.0000002132 0.5971 4.38596
25 1J39 UPG 0.001058 0.4499 4.5584
26 3CV3 UDP 0.00005893 0.48298 4.6798
27 2IYF UDP 0.001945 0.4142 4.81928
28 1NLM UD1 0.0005544 0.44201 4.94506
29 1QM5 PLP 0.000003466 0.58712 6.08519
30 1QM5 GLC GLC GLC PO4 SGC GLC 0.004615 0.42895 6.08519
31 2ACV UDP 0.001237 0.41921 7.34341
32 4OOP DUP 0.008828 0.40109 7.83133
33 3HBN UDP 0.0009789 0.43249 8.51064
34 4X1T UDP 0.0000266 0.48996 8.57843
35 1RZU ADP 0.0000108 0.48621 8.86598
36 2GEK GDP 0.00003703 0.47529 8.86699
37 3OKP GDD 0.00000002126 0.66434 20.0508
38 3OKA GDD 0.0000002942 0.53648 20.7349
39 2XA2 UPG 0.00005502 0.49528 24.5192
40 4PQG UDP 0.0000000001488 0.71199 30.0203
41 4PQG NAG 0.002223 0.44859 30.0203
Pocket No.: 2; Query (leader) PDB : 4X7R; Ligand: NTO; Similar sites found: 14
This union binding pocket(no: 2) in the query (biounit: 4x7r.bio1) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3R75 BEZ 0.0402 0.40709 1.82556
2 1EM6 NBG 0.00119 0.42391 2.43408
3 2WTX VDO 0.0001107 0.45525 4.00844
4 2WTX UDP 0.0003223 0.43548 4.00844
5 2IV3 UDP 0.000001681 0.45601 4.38596
6 1QM5 PLP 0.0000848 0.46953 6.08519
7 1RZU ADP 0.000009067 0.41147 8.86598
8 2QZS ADP 0.0000235 0.41725 11.7526
9 2QZS GLC 0.0000235 0.41725 11.7526
10 2QZS 250 0.0000235 0.41725 11.7526
11 3OKP GDD 0.0000001094 0.66434 20.0508
12 3OKA GDD 0.000001155 0.41571 20.7349
13 4PQG UDP 0.000000006998 0.68499 30.0203
14 4PQG NAG 0.00561 0.44828 30.0203
Pocket No.: 3; Query (leader) PDB : 4X7R; Ligand: 3YW; Similar sites found: 31
This union binding pocket(no: 3) in the query (biounit: 4x7r.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4F97 VDO 0.00005301 0.47821 1.21704
2 4RIF 3R2 0.001309 0.4229 1.31926
3 5V2J UDP 0.00124 0.42976 2.22717
4 5V2J 7WV 0.00124 0.42976 2.22717
5 1EM6 NBG 0.000004347 0.54646 2.43408
6 2VCH UDP 0.001281 0.42483 2.5
7 5BNW 12V 0.007326 0.40091 2.83976
8 3CV2 COA 0.03803 0.40215 3.24544
9 3S2U UD1 0.001366 0.40571 3.28767
10 2WTX UDP 0.000001078 0.55922 4.00844
11 2WTX VDO 0.000002754 0.53902 4.00844
12 1XXR MAN 0.02909 0.40338 4.34783
13 2IV3 UDP 0.0000009767 0.51206 4.38596
14 1J39 UPG 0.0004769 0.44196 4.5584
15 3CV3 UDP 0.000106 0.42986 4.6798
16 4RL4 PPV 0.01405 0.42594 5.66038
17 1QM5 PLP 0.00000223 0.56142 6.08519
18 1QM5 GLC GLC GLC PO4 SGC GLC 0.0001652 0.46965 6.08519
19 1Q8S MAN MMA 0.01621 0.42222 6.34921
20 4X1T UDP 0.00005414 0.43223 8.57843
21 1RZU ADP 0.00002082 0.4312 8.86598
22 2GEK GDP 0.0002683 0.40361 8.86699
23 1WZ1 DNS 0.03148 0.40449 8.94309
24 2QZS GLC 0.00000009575 0.45207 11.7526
25 2QZS ADP 0.00000009575 0.45207 11.7526
26 2QZS 250 0.00000009575 0.45207 11.7526
27 3OKP GDD 0.00000001619 0.68801 20.0508
28 3OKA GDD 0.0000001312 0.48746 20.7349
29 2XA2 UPG 0.000007019 0.48937 24.5192
30 4PQG NAG 0.000000002017 0.76678 30.0203
31 4PQG UDP 0.00000001694 0.6511 30.0203
Pocket No.: 4; Query (leader) PDB : 4X7R; Ligand: 3YW; Similar sites found: 6
This union binding pocket(no: 4) in the query (biounit: 4x7r.bio2) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3R75 BEZ 0.03064 0.41131 1.82556
2 3P13 RIP 0.01731 0.40096 2.77778
3 4RF7 ARG 0.03373 0.4022 2.83976
4 1YQC GLV 0.004824 0.44308 2.94118
5 1LNX URI 0.03947 0.40692 7.40741
6 2O2C G6Q 0.01856 0.40398 10.142
Pocket No.: 5; Query (leader) PDB : 4X7R; Ligand: UDP; Similar sites found: 9
This union binding pocket(no: 5) in the query (biounit: 4x7r.bio2) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3P13 RIP 0.01731 0.40096 2.77778
2 4RF7 ARG 0.03373 0.4022 2.83976
3 1YQC GLV 0.004824 0.44308 2.94118
4 4RL4 PPV 0.01842 0.42507 5.66038
5 1LNX URI 0.03947 0.40692 7.40741
6 2O2C G6Q 0.01856 0.40398 10.142
7 2QZS 250 0.0000001041 0.47662 11.7526
8 2QZS GLC 0.0000001041 0.47662 11.7526
9 2QZS ADP 0.0000001041 0.47662 11.7526
Pocket No.: 6; Query (leader) PDB : 4X7R; Ligand: NTO; Similar sites found: 5
This union binding pocket(no: 6) in the query (biounit: 4x7r.bio2) has 46 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1YQC GLV 0.00809 0.44308 2.94118
2 4RL4 PPV 0.02544 0.4287 5.66038
3 1QM5 GLC GLC GLC PO4 SGC GLC 0.00004182 0.41988 6.08519
4 1G3Q ADP 0.0316 0.41252 7.59494
5 2IOR ADP 0.02236 0.43217 12.766
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