Receptor
PDB id Resolution Class Description Source Keywords
2GN4 1.9 Å EC: 4.2.1.- CRYSTAL STRUCTURE OF UDP-GLCNAC INVERTING 4,6-DEHYDRATASE IN WITH NADPH AND UDP-GLCNAC HELICOBACTER PYLORI ROSSMANN FOLD TYK TRIAD SDR ENZYME DEHYDRATASE UDP-GLCNNADPH LYASE
Ref.: STRUCTURAL STUDIES OF FLAA1 FROM HELICOBACTER PYLOR THE MECHANISM FOR INVERTING 4,6-DEHYDRATASE ACTIVIT J.BIOL.CHEM. V. 281 24489 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MES B:336;
B:337;
Invalid;
Invalid;
none;
none;
submit data
195.237 C6 H13 N O4 S C1COC...
NDP A:334;
B:334;
Valid;
Valid;
none;
none;
submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
UD1 A:335;
B:335;
Valid;
Valid;
none;
none;
submit data
607.354 C17 H27 N3 O17 P2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2GN4 1.9 Å EC: 4.2.1.- CRYSTAL STRUCTURE OF UDP-GLCNAC INVERTING 4,6-DEHYDRATASE IN WITH NADPH AND UDP-GLCNAC HELICOBACTER PYLORI ROSSMANN FOLD TYK TRIAD SDR ENZYME DEHYDRATASE UDP-GLCNNADPH LYASE
Ref.: STRUCTURAL STUDIES OF FLAA1 FROM HELICOBACTER PYLOR THE MECHANISM FOR INVERTING 4,6-DEHYDRATASE ACTIVIT J.BIOL.CHEM. V. 281 24489 2006
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2GN4 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 2GN8 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2GN4 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 2GN8 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2GN4 - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 2GN8 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
3 3W1V - UDZ C17 H27 N6 O16 P2 CC(=O)N[C@....
4 3VVC - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
5 4G5H - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NDP; Similar ligands found: 172
No: Ligand ECFP6 Tc MDL keys Tc
1 NDP 1 1
2 0WD 0.827273 1
3 NAI 0.803738 0.986842
4 NMN AMP PO4 0.794643 0.948052
5 NPW 0.692308 0.962025
6 NZQ 0.686441 0.987013
7 1DG 0.68 1
8 DG1 0.68 1
9 A2R 0.650943 0.909091
10 A22 0.64486 0.934211
11 TXP 0.644628 0.924051
12 ATR 0.640777 0.894737
13 NA7 0.636364 0.886076
14 XNP 0.620968 0.949367
15 AP0 0.598361 0.948718
16 A2P 0.598039 0.881579
17 NJP 0.574803 0.923077
18 25L 0.550847 0.934211
19 ODP 0.550388 0.936709
20 NAX 0.544 0.949367
21 25A 0.53913 0.921053
22 80F 0.537879 0.914634
23 2AM 0.529412 0.87013
24 6V0 0.519685 0.974026
25 NAP 0.514493 0.922078
26 7L1 0.507143 0.763441
27 EAD 0.507143 0.949367
28 A2D 0.504673 0.921053
29 TXE 0.503876 0.935897
30 NA0 0.496454 0.910256
31 TXD 0.496124 0.911392
32 SAP 0.495575 0.875
33 AGS 0.495575 0.875
34 P1H 0.493056 0.925926
35 CO7 0.489796 0.791209
36 TAP 0.489362 0.864198
37 PAP 0.482456 0.907895
38 BA3 0.481818 0.921053
39 NAJ PZO 0.478261 0.924051
40 ATP 0.477876 0.921053
41 HEJ 0.477876 0.921053
42 B4P 0.477477 0.921053
43 AP5 0.477477 0.921053
44 ADP 0.477477 0.921053
45 OAD 0.47541 0.897436
46 AR6 0.473684 0.896104
47 AQP 0.473684 0.921053
48 5FA 0.473684 0.921053
49 APR 0.473684 0.896104
50 AN2 0.473214 0.909091
51 3OD 0.467742 0.897436
52 50T 0.464912 0.884615
53 NAJ PYZ 0.464789 0.879518
54 9X8 0.463415 0.851852
55 PO4 PO4 A A A A PO4 0.463415 0.857143
56 V3L 0.461538 0.896104
57 2A5 0.46087 0.85
58 AT4 0.460177 0.886076
59 A1R 0.459016 0.841463
60 4AD 0.459016 0.875
61 ADQ 0.459016 0.897436
62 OVE 0.458716 0.8375
63 OMR 0.458647 0.813953
64 PPS 0.457627 0.811765
65 AD9 0.456897 0.897436
66 CA0 0.45614 0.897436
67 M33 0.45614 0.884615
68 ADJ 0.455882 0.879518
69 A3P 0.455357 0.894737
70 ACP 0.452174 0.897436
71 ENP 0.451613 0.85
72 UP5 0.451128 0.948052
73 SRP 0.45 0.8625
74 ANP 0.449153 0.897436
75 ACQ 0.449153 0.897436
76 PRX 0.448276 0.82716
77 A3R 0.447154 0.841463
78 5AL 0.445378 0.884615
79 7D4 0.443478 0.8375
80 ADX 0.443478 0.811765
81 6YZ 0.438017 0.897436
82 A 0.436364 0.894737
83 AMP 0.436364 0.894737
84 4TC 0.433824 0.924051
85 7D3 0.433628 0.8375
86 DCA 0.433566 0.788889
87 ETB 0.433566 0.797753
88 BIS 0.433071 0.864198
89 1ZZ 0.433071 0.802326
90 00A 0.432 0.864198
91 ATF 0.429752 0.886076
92 DQV 0.428571 0.934211
93 0T1 0.427586 0.788889
94 5SV 0.427419 0.788235
95 8QN 0.427419 0.884615
96 3AM 0.427273 0.857143
97 N01 0.426573 0.884615
98 PR8 0.425197 0.811765
99 LAD 0.425197 0.821429
100 WAQ 0.425197 0.841463
101 DTP 0.425 0.8375
102 AMO 0.424 0.886076
103 PAJ 0.424 0.843373
104 APC 0.423729 0.886076
105 UPA 0.423358 0.935897
106 48N 0.422222 0.853659
107 FYA 0.421875 0.860759
108 PTJ 0.421875 0.853659
109 CNA 0.421429 0.910256
110 PUA 0.42069 0.9125
111 DND 0.419118 0.910256
112 NXX 0.419118 0.910256
113 AV2 0.418033 0.848101
114 COA 0.417808 0.788889
115 3UK 0.417323 0.897436
116 OOB 0.416 0.909091
117 IVC 0.415584 0.78022
118 DAT 0.415254 0.8375
119 NDO 0.414966 0.897436
120 139 0.414286 0.901235
121 B5V 0.414062 0.886076
122 T99 0.413223 0.886076
123 TAT 0.413223 0.886076
124 3AT 0.413223 0.896104
125 YLB 0.413043 0.784091
126 62F 0.4125 0.823529
127 ABM 0.412281 0.848101
128 B5M 0.412214 0.875
129 YAP 0.412214 0.875
130 YLP 0.411765 0.784091
131 NB8 0.410853 0.853659
132 ME8 0.410853 0.802326
133 SON 0.410256 0.886076
134 DLL 0.409449 0.909091
135 AHX 0.409449 0.853659
136 CAO 0.409396 0.763441
137 30N 0.409396 0.72449
138 AMX 0.409396 0.797753
139 COS 0.409396 0.771739
140 7D5 0.409091 0.8125
141 4UW 0.408759 0.9125
142 F2R 0.408451 0.825581
143 APX 0.407692 0.841463
144 SRA 0.40708 0.85
145 CMX 0.406667 0.788889
146 SCO 0.406667 0.788889
147 TYM 0.405797 0.886076
148 COD 0.405594 0.777778
149 CA6 0.405229 0.70297
150 OXK 0.405229 0.771739
151 AP2 0.405172 0.886076
152 A12 0.405172 0.886076
153 9SN 0.40458 0.853659
154 LAQ 0.404412 0.802326
155 T5A 0.404255 0.914634
156 FAM 0.403974 0.771739
157 ACO 0.403974 0.763441
158 FCX 0.403974 0.763441
159 VO4 ADP 0.403226 0.860759
160 ADP VO4 0.403226 0.860759
161 YLC 0.402878 0.823529
162 1VU 0.402597 0.763441
163 B5Y 0.401515 0.875
164 FA5 0.401515 0.886076
165 HAX 0.401316 0.771739
166 AR6 AR6 0.4 0.871795
167 CAJ 0.4 0.771739
168 AFH 0.4 0.843373
169 APU 0.4 0.923077
170 A U 0.4 0.898734
171 TXA 0.4 0.886076
172 4UU 0.4 0.948052
Ligand no: 2; Ligand: UD1; Similar ligands found: 79
No: Ligand ECFP6 Tc MDL keys Tc
1 UD2 1 1
2 UD1 1 1
3 UDZ 0.8 0.893333
4 HP7 0.793814 0.985294
5 EPZ 0.75 0.985507
6 EPU 0.742857 0.971429
7 EEB 0.742857 0.971429
8 F5P 0.742574 0.957143
9 UD4 0.742574 0.957143
10 F5G 0.742574 0.971014
11 UFM 0.73913 0.985294
12 GUD 0.73913 0.985294
13 UPG 0.73913 0.985294
14 GDU 0.73913 0.985294
15 UD7 0.722772 0.971014
16 MJZ 0.715686 0.957143
17 U2F 0.697917 0.930556
18 UPF 0.697917 0.930556
19 UMA 0.690265 0.985507
20 UDM 0.683168 0.957143
21 UFG 0.663265 0.930556
22 12V 0.660377 0.943662
23 HWU 0.660377 0.943662
24 U22 0.655462 0.85
25 U20 0.655462 0.871795
26 U21 0.655462 0.871795
27 UGB 0.65 0.970588
28 UGA 0.65 0.970588
29 USQ 0.633663 0.835443
30 UDX 0.63 0.956522
31 UAD 0.63 0.956522
32 UDP 0.622222 0.927536
33 UTP 0.619565 0.927536
34 UAG 0.617188 0.931507
35 660 0.6 0.942857
36 URM 0.6 0.942857
37 G3N 0.596154 0.929577
38 UPU 0.587629 0.955882
39 4RA 0.584615 0.87013
40 UNP 0.583333 0.901408
41 3UC 0.575472 0.930556
42 UML 0.564286 0.871795
43 IUG 0.561404 0.825
44 U5P 0.555556 0.913043
45 U 0.555556 0.913043
46 UD0 0.552239 0.858974
47 UPP 0.543689 0.928571
48 UDH 0.543689 0.855263
49 2KH 0.530612 0.901408
50 44P 0.521277 0.888889
51 C5G 0.518519 0.930556
52 UDP UDP 0.505155 0.898551
53 Y6W 0.504673 0.90411
54 2QR 0.485075 0.860759
55 2GW 0.482759 0.943662
56 URI 0.477273 0.852941
57 UP5 0.47541 0.844156
58 PMP UD1 0.467626 0.848101
59 1GW 0.467213 0.905405
60 CJB 0.461538 0.838235
61 UAG API 0.457516 0.87013
62 4TC 0.456 0.822785
63 CSV 0.452991 0.866667
64 CSQ 0.452991 0.866667
65 U3P 0.447917 0.898551
66 UA3 0.447917 0.898551
67 U U 0.446429 0.914286
68 NG1 0.444444 0.753623
69 GN1 0.444444 0.753623
70 C30 0.433628 0.696203
71 PUP 0.429825 0.875
72 CXY 0.422414 0.90411
73 A U 0.418605 0.820513
74 U2P 0.418367 0.913043
75 UMA FGA LYS DAL DAL 0.414634 0.8375
76 U1S 0.409091 0.789474
77 FN5 0.40458 0.883117
78 DAU 0.403361 0.905405
79 G U 0.401515 0.780488
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2GN4; Ligand: NDP; Similar sites found with APoc: 16
This union binding pocket(no: 1) in the query (biounit: 2gn4.bio1) has 92 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZEM NAD 3.81679
2 1E6W NAD 3.84615
3 1Q7B NAP 6.96721
4 1W73 NAP 8.9404
5 1W8D NAP 8.9404
6 1W6U NAP 8.9404
7 4J1Q NDP 11.0465
8 1YXM ADE 12.5413
9 2PK3 A2R 14.0187
10 1BXK NAD 17.4419
11 1RKX NAD 17.7326
12 1SB8 NAD 24.1477
13 3LU1 NAD 24.4186
14 6BWL NAD 39.939
15 5BJX NAD 44.186
16 5BJX UDP 44.186
Pocket No.: 2; Query (leader) PDB : 2GN4; Ligand: NDP; 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: 2gn4.bio1) has 92 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2GN4; Ligand: NDP; 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: 2gn4.bio1) has 92 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2GN4; Ligand: UD1; Similar sites found with APoc: 17
This union binding pocket(no: 4) in the query (biounit: 2gn4.bio1) has 95 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZEM NAD 3.81679
2 1E6W NAD 3.84615
3 1W73 NAP 8.9404
4 1W8D NAP 8.9404
5 1W6U NAP 8.9404
6 4J1Q NDP 11.0465
7 1YXM ADE 12.5413
8 2PK3 A2R 14.0187
9 1BXK NAD 17.4419
10 1RKX NAD 17.7326
11 1SB8 NAD 24.1477
12 1SB8 UD2 24.1477
13 1VL0 NAI 24.3151
14 3LU1 NAD 24.4186
15 6BWL NAD 39.939
16 5BJX NAD 44.186
17 5BJX UDP 44.186
Pocket No.: 5; Query (leader) PDB : 2GN4; Ligand: UD1; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 2gn4.bio1) has 95 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2GN4; Ligand: UD1; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2gn4.bio1) has 95 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2GN4; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 2gn4.bio1) has 92 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 2GN4; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 2gn4.bio1) has 92 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 2GN4; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 2gn4.bio1) has 92 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 2GN4; Ligand: UD1; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 2gn4.bio1) has 52 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 2GN4; Ligand: UD1; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 2gn4.bio1) has 52 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 2GN4; Ligand: UD1; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 2gn4.bio1) has 52 residues
No: Leader PDB Ligand Sequence Similarity
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