Receptor
PDB id Resolution Class Description Source Keywords
6bsw 2.16 Å EC: 2.4.2.39 CRYSTAL STRUCTURE OF XYLOGLUCAN XYLOSYLTRANSFERASE 1 TERNARY ARABIDOPSIS THALIANA XYLOGLUCAN XYLOSYLTRANSFERASE TRANSFERASE
Ref.: STRUCTURE OF XYLOGLUCAN XYLOSYLTRANSFERASE 1 REVEAL STERIC RULES THAT DEFINE BIOLOGICAL PATTERNS OF XYL POLYMERS. PROC. NATL. ACAD. SCI. V. 115 6064 2018 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MN A:501;
B:501;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
54.938 Mn [Mn+2...
NO3 B:503;
 Invalid;
 none;
 submit data
62.005 N O3 [N+](...
UDP B:502;
A:502;
 Valid;
Valid;
 none;
none;
 submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
TRS B:504;
A:505;
 Invalid;
Invalid;
 none;
none;
 submit data
122.143 C4 H12 N O3 C(C(C...
GOL A:504;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
BGC BGC BGC BGC BGC BGC C:1;
 Valid;
 none;
 submit data
990.861 n/a O(C1C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6BSW 2.16 Å EC: 2.4.2.39 CRYSTAL STRUCTURE OF XYLOGLUCAN XYLOSYLTRANSFERASE 1 TERNARY ARABIDOPSIS THALIANA XYLOGLUCAN XYLOSYLTRANSFERASE TRANSFERASE
Ref.: STRUCTURE OF XYLOGLUCAN XYLOSYLTRANSFERASE 1 REVEAL STERIC RULES THAT DEFINE BIOLOGICAL PATTERNS OF XYL POLYMERS. PROC. NATL. ACAD. SCI. V. 115 6064 2018 U.S.A.
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6BSW - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 6BSV - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6BSW - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 6BSV - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6BSW - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
2 6BSV - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
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: BGC BGC BGC BGC BGC BGC; Similar ligands found: 134
No: Ligand ECFP6 Tc MDL keys Tc
1 GLC BGC BGC BGC 1 1
2 BGC BGC BGC BGC BGC BGC 1 1
3 BGC BGC BGC BGC BGC BGC BGC 1 1
4 BGC BGC BGC BGC BGC 1 1
5 BGC BGC BGC 1 1
6 GAL GLA 0.888889 1
7 BGC BGC BGC BGC 0.762712 1
8 MAN MAN M6P 0.716667 0.785714
9 BGC GAL GLA 0.709091 1
10 BGC BGC BGC BGC BGC BGC BGC BGC 0.689655 1
11 GAL NAG GAL NAG GAL 0.647059 0.6875
12 MBG GAL 0.641509 0.942857
13 BMA MAN MAN 0.627119 1
14 MAN MAN MAN GLC 0.622951 1
15 GAL SO4 GAL 0.606557 0.66
16 BQZ 0.58 0.909091
17 NAG GAL GAL 0.575758 0.733333
18 GAL NAG GAL 0.573529 0.733333
19 GCU BGC 0.55 0.914286
20 MAN MAN MAN 0.536232 0.970588
21 MAN BMA BMA BMA BMA BMA BMA 0.534483 1
22 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.534483 1
23 GLC GLC GLC GLC BGC GLC GLC 0.534483 1
24 AHR FUB 0.529412 0.857143
25 BMA MAN NAG 0.521127 0.733333
26 BGC GAL NAG GAL 0.520548 0.733333
27 GAL NAG FUC GAL 0.513158 0.717391
28 BGC GAL GLA NGA GAL 0.513158 0.733333
29 FUC GAL 0.508475 0.941176
30 BGC GLA GAL 0.5 1
31 GAL AAL GAL AAL GAL AAL 0.493333 0.891892
32 NAG GAL NAG GAL NAG GAL 0.493333 0.673469
33 NAG GAL NAG GAL 0.493333 0.6875
34 GAL AAL GAL AAL 0.493333 0.891892
35 GAL NGA A2G 0.485714 0.6875
36 BGC FUC GAL 0.484848 0.970588
37 GLC BGC FUC GAL 0.484848 0.970588
38 MMA MAN MAN 0.484848 0.942857
39 MAN BMA BMA 0.484375 0.942857
40 A2G GAL 0.484375 0.733333
41 BGC GAL GLA NGA 0.480519 0.733333
42 MGL GAL 0.474576 0.942857
43 MBG GLA 0.473684 0.942857
44 BGC GAL NAG 0.472973 0.733333
45 BGC FUC GAL NAG GAL 0.470588 0.717391
46 GAL FUC GAL 0.469697 0.970588
47 47N 0.46875 0.891892
48 GAL AAL 0.46875 0.891892
49 MAN MAN MAN MAN MAN MAN MAN 0.467532 1
50 RR7 GLC 0.466667 0.942857
51 NAG NAG BMA MAN 0.463415 0.634615
52 G2F SHG BGC BGC 0.461538 0.891892
53 NOY BGC 0.460317 0.702128
54 MAN MAN 0.457627 0.941176
55 GLA NAG GAL FUC 0.455696 0.717391
56 RAM MAN GLA ABE RAM MAN GLA ABE 0.454545 0.868421
57 MAN MAN MAN MAN MAN MAN MAN MAN 0.452381 0.846154
58 OPM MAN MAN 0.452055 0.804878
59 5QP 0.451613 0.885714
60 BGC FUC GAL NAG 0.451219 0.717391
61 RZM 0.45 0.688889
62 BGC OXZ 0.444444 0.666667
63 IFM BGC 0.444444 0.711111
64 MAN GLA ABE 0.444444 0.916667
65 9MR 0.444444 0.744186
66 GLC EDO GLC 0.444444 0.942857
67 7D1 MAN 0.442623 0.888889
68 G2F BGC BGC BGC BGC BGC 0.441176 0.868421
69 MAN MAN BMA 0.441176 0.942857
70 MGC GAL 0.439394 0.702128
71 NAG GAL 0.439394 0.733333
72 NOJ GLC 0.4375 0.695652
73 GLC DMJ 0.4375 0.695652
74 MAN MNM 0.4375 0.702128
75 NAG GAL NAG 0.434211 0.6875
76 BGC GAL NGA GAL 0.434211 0.733333
77 BGC XGP 0.430769 0.785714
78 CJX 0.430769 0.717391
79 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.430556 1
80 BMA BMA BMA BMA GLA 0.430556 1
81 FRU BMA 0.428571 0.842105
82 MAN IPD MAN 0.428571 0.785714
83 RAM MAN GLA ABE RAM MAN GLA 0.425532 0.868421
84 BGC ZZ1 BGC 0.425 0.767442
85 GDQ GLC 0.424242 0.666667
86 MAN G63 0.424242 0.653061
87 IPD MAN 0.421875 0.738095
88 BGC GAL FUC GLA 0.421053 0.970588
89 NAG BMA 0.42029 0.653061
90 BGC GLC GLC 0.42029 1
91 1GN ACY GAL 1GN BGC ACY GAL BGC 0.418605 0.6875
92 NAG BMA MAN MAN MAN MAN 0.418605 0.733333
93 BGC 5VQ GAL GLA 0.41791 0.891892
94 GLC GAL NAG GAL FUC GLA 0.417582 0.717391
95 GAL NAG GAL FUC FUC 0.416667 0.702128
96 BGC GLC GLC GLC 0.416667 1
97 GLC GLC GLC GLC GLC 0.416667 1
98 NAG BMA MAN MAN MAN MAN MAN 0.4125 0.868421
99 GLC BGC BGC 0.410959 0.942857
100 BMA MAN MAN MAN MAN 0.410256 0.942857
101 ABL 0.409091 0.702128
102 BGC GAL NAG GAL FUC 0.409091 0.717391
103 G3I 0.408451 0.767442
104 G2I 0.408451 0.767442
105 BGC OXZ BGC 0.408451 0.6875
106 GLC 0.408163 0.848485
107 GLA 0.408163 0.848485
108 BGC 0.408163 0.848485
109 MAN 0.408163 0.848485
110 BMA 0.408163 0.848485
111 GAL 0.408163 0.848485
112 ALL 0.408163 0.848485
113 GXL 0.408163 0.848485
114 GLC GLC 0.408163 0.848485
115 BGC GAL 0.408163 0.848485
116 GIV 0.408163 0.848485
117 GAL GAL 0.408163 0.848485
118 WOO 0.408163 0.848485
119 BGC BGC XYS GAL 0.407895 0.942857
120 GLC U8V 0.40625 0.916667
121 DGO MAN 0.40625 0.914286
122 MMA GLA ABE 0.405405 0.868421
123 BGC BGC BGC XYS BGC XYS 0.405063 0.942857
124 MAN BMA MAN MAN MAN MAN MAN 0.404762 0.942857
125 BGC GAL NAG NAG GAL GAL 0.404494 0.6875
126 NAG NAG MAN MAN MAN 0.404494 0.6875
127 3MG 0.403846 0.857143
128 ZB1 0.403846 0.857143
129 GPM GLC 0.402985 0.767442
130 GLC GLC GLC 0.402778 0.942857
131 SOR GLC GLC 0.402778 0.970588
132 GLC NBU GAL GLA 0.4 0.846154
133 2M8 0.4 0.911765
134 ISX 0.4 0.761905
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: BGC BGC BGC BGC BGC BGC; Similar ligands found: 2
No: Ligand Similarity coefficient
1 GLC GLC GLC GLC GLC GLC 0.9686
2 GLC GLC G6D ADH GLC GLC 0.8593
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6BSW; Ligand: BGC BGC BGC BGC BGC BGC; 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: 6bsw.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6BSW; Ligand: UDP; 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: 6bsw.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6BSW; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 6bsw.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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