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Receptor
PDB id Resolution Class Description Source Keywords
5TPR 1.7 Å EC: 4.2.3.4 DESMETHYL-4-DEOXYGADUSOL SYNTHASE FROM ANABAENA VARIABILIS ( WITH NAD+ AND ZN2+ BOUND ANABAENA VARIABILIS (STRAIN ATCC 294137937) SUGAR PHOSPHATE CYCLASE SEDOHEPTULOSE 7-PHOSPHATE CYCLASE PRODUCTS ROSSMANN FOLD SECONDARY METABOLISM LYASE
Ref.: EVOLUTION AND DISTRIBUTION OF C7-CYCLITOL SYNTHASES PROKARYOTES AND EUKARYOTES. ACS CHEM. BIOL. V. 12 979 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:507;
B:503;
A:505;
B:504;
A:502;
A:504;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
ZN A:501;
B:501;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
NAD B:502;
A:503;
Valid;
Valid;
none;
none;
submit data
663.425 C21 H27 N7 O14 P2 c1cc(...
GOL B:506;
A:507;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PEG A:506;
B:505;
Invalid;
Invalid;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5TPR 1.7 Å EC: 4.2.3.4 DESMETHYL-4-DEOXYGADUSOL SYNTHASE FROM ANABAENA VARIABILIS ( WITH NAD+ AND ZN2+ BOUND ANABAENA VARIABILIS (STRAIN ATCC 294137937) SUGAR PHOSPHATE CYCLASE SEDOHEPTULOSE 7-PHOSPHATE CYCLASE PRODUCTS ROSSMANN FOLD SECONDARY METABOLISM LYASE
Ref.: EVOLUTION AND DISTRIBUTION OF C7-CYCLITOL SYNTHASES PROKARYOTES AND EUKARYOTES. ACS CHEM. BIOL. V. 12 979 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5TPR - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5TPR - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5TPR - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAD; Similar ligands found: 230
No: Ligand ECFP6 Tc MDL keys Tc
1 A3D 0.872727 0.986111
2 NHD 0.821429 0.972222
3 NAP 0.811966 0.986111
4 NFD 0.791304 0.946667
5 NXX 0.765766 0.972603
6 DND 0.765766 0.972603
7 AMP NAD 0.74359 0.972222
8 ZID 0.737705 0.986111
9 NAQ 0.729508 0.934211
10 NAE 0.721311 0.959459
11 NA0 0.712 0.972603
12 TAP 0.704 0.921053
13 NDE 0.689922 0.972603
14 NAJ 0.683333 0.972222
15 NDC 0.679389 0.934211
16 NDO 0.674603 0.958904
17 N01 0.656 0.972222
18 CNA 0.642276 0.972603
19 NBP 0.621212 0.922078
20 8ID 0.609756 0.922078
21 A2D 0.576923 0.958333
22 ADP 0.575472 0.931507
23 NGD 0.574803 0.922078
24 BA3 0.566038 0.958333
25 M33 0.564815 0.918919
26 ADP PO3 0.563636 0.957747
27 B4P 0.560748 0.958333
28 AP5 0.560748 0.958333
29 AN2 0.555556 0.918919
30 AT4 0.555556 0.894737
31 GAP 0.553571 0.932432
32 OOB 0.551724 0.972222
33 CA0 0.550459 0.932432
34 9JJ 0.546053 0.898734
35 HEJ 0.545455 0.931507
36 ACP 0.545455 0.906667
37 ATP 0.545455 0.931507
38 DQV 0.544 0.972222
39 ADP ALF 0.54386 0.883117
40 ALF ADP 0.54386 0.883117
41 DAL AMP 0.543103 0.945205
42 APR 0.540541 0.931507
43 AQP 0.540541 0.931507
44 AR6 0.540541 0.931507
45 5FA 0.540541 0.931507
46 ADP VO4 0.53913 0.945205
47 VO4 ADP 0.53913 0.945205
48 AD9 0.535714 0.906667
49 SAP 0.535714 0.883117
50 AGS 0.535714 0.883117
51 WAQ 0.533333 0.896104
52 ABM 0.53271 0.905405
53 DLL 0.529412 0.972222
54 00A 0.529412 0.921053
55 ACQ 0.526316 0.906667
56 NJP 0.526316 0.959459
57 ANP 0.526316 0.906667
58 OAD 0.525 0.932432
59 ADX 0.522523 0.839506
60 5AL 0.521739 0.945205
61 A1R 0.521008 0.871795
62 9SN 0.520325 0.909091
63 A 0.518868 0.930556
64 AMP 0.518868 0.930556
65 50T 0.517857 0.893333
66 ATF 0.517241 0.894737
67 1ZZ 0.516393 0.851852
68 3OD 0.516393 0.932432
69 SON 0.513514 0.92
70 PRX 0.513274 0.881579
71 6YZ 0.512821 0.906667
72 SRP 0.512821 0.92
73 9X8 0.512397 0.883117
74 ADP BMA 0.512397 0.932432
75 3UK 0.512397 0.958904
76 MYR AMP 0.512195 0.851852
77 NAJ PZO 0.510949 0.909091
78 NMN 0.509434 0.875
79 A3R 0.508333 0.871795
80 B5V 0.508197 0.945946
81 AMP DBH 0.507937 0.906667
82 A22 0.504202 0.945205
83 ATP A A A 0.504 0.971831
84 B5M 0.504 0.933333
85 FA5 0.504 0.945946
86 8QN 0.5 0.945205
87 NAX 0.496183 0.886076
88 TYR AMP 0.496063 0.933333
89 PR8 0.495935 0.8625
90 AMO 0.495868 0.92
91 ADQ 0.495868 0.932432
92 4AD 0.495868 0.933333
93 PAJ 0.495868 0.873418
94 A12 0.495495 0.894737
95 AP2 0.495495 0.894737
96 AHZ 0.492308 0.851852
97 YAP 0.492063 0.933333
98 FYA 0.491935 0.918919
99 AHX 0.491803 0.884615
100 4UU 0.488372 0.933333
101 5SV 0.487603 0.8375
102 TAT 0.487179 0.894737
103 T99 0.487179 0.894737
104 APC 0.486957 0.894737
105 SRA 0.486239 0.881579
106 6V0 0.484848 0.909091
107 NAI 0.484848 0.921053
108 GTA 0.484615 0.898734
109 A A 0.483871 0.958333
110 LAD 0.483871 0.873418
111 AU1 0.482456 0.906667
112 F2R 0.481752 0.831325
113 OMR 0.481203 0.841463
114 TXE 0.481203 0.921053
115 AF3 ADP 3PG 0.481203 0.873418
116 LAQ 0.480916 0.851852
117 G3A 0.48062 0.909091
118 B5Y 0.480315 0.933333
119 NB8 0.48 0.884615
120 TXA 0.48 0.92
121 BIS 0.48 0.871795
122 ME8 0.48 0.851852
123 PTJ 0.48 0.884615
124 139 0.477941 0.886076
125 LPA AMP 0.477273 0.851852
126 AFH 0.476923 0.873418
127 AR6 AR6 0.476923 0.958333
128 G5P 0.476923 0.909091
129 ARG AMP 0.476923 0.841463
130 25L 0.47619 0.945205
131 NAJ PYZ 0.475524 0.864198
132 25A 0.47541 0.958333
133 9ZA 0.47541 0.896104
134 9ZD 0.47541 0.896104
135 DZD 0.47482 0.897436
136 TXD 0.473684 0.921053
137 4UV 0.472868 0.933333
138 TYM 0.470149 0.945946
139 RBY 0.470085 0.894737
140 ADV 0.470085 0.894737
141 4TA 0.467626 0.864198
142 48N 0.466165 0.884615
143 XAH 0.465116 0.851852
144 4UW 0.462687 0.897436
145 M24 0.461538 0.886076
146 80F 0.460993 0.853659
147 IOT 0.459854 0.821429
148 T5A 0.456522 0.853659
149 EAD 0.455782 0.886076
150 MAP 0.455285 0.883117
151 GA7 0.454545 0.894737
152 BT5 0.453901 0.821429
153 A4P 0.452555 0.833333
154 UP5 0.451852 0.933333
155 PAP 0.445378 0.917808
156 4TC 0.445255 0.909091
157 AP0 0.445255 0.884615
158 YLP 0.444444 0.831325
159 P1H 0.443709 0.864198
160 AOC 0.442478 0.810811
161 Z5A 0.439189 0.833333
162 LMS 0.4375 0.817073
163 2A5 0.436975 0.857143
164 A G 0.43662 0.921053
165 G A A A 0.43662 0.909091
166 COD 0.43662 0.802326
167 ADJ 0.435714 0.841463
168 YLB 0.434783 0.831325
169 YLC 0.434783 0.851852
170 U A G G 0.433566 0.921053
171 ATR 0.433333 0.90411
172 7MD 0.432836 0.851852
173 8X1 0.432 0.764045
174 G5A 0.429752 0.790698
175 PO4 PO4 A A A A PO4 0.429688 0.943662
176 TAD 0.42963 0.873418
177 5AS 0.42735 0.770115
178 BTX 0.426573 0.831325
179 YLA 0.425532 0.831325
180 DSZ 0.425197 0.790698
181 NCN 0.424779 0.805556
182 UPA 0.42446 0.921053
183 8PZ 0.424242 0.811765
184 VMS 0.424 0.8
185 54H 0.424 0.8
186 9K8 0.423077 0.744444
187 N0B 0.422819 0.853659
188 6AD 0.422764 0.85
189 AYB 0.422535 0.821429
190 7D3 0.422414 0.844156
191 YLY 0.421769 0.821429
192 TSB 0.420635 0.809524
193 ODP 0.41958 0.922078
194 AV2 0.419355 0.855263
195 FB0 0.419355 0.775281
196 A5A 0.419355 0.819277
197 NNR 0.419048 0.739726
198 A A A 0.418605 0.918919
199 U A 0.417808 0.946667
200 649 0.417266 0.775281
201 NMN AMP PO4 0.416667 0.933333
202 SSA 0.416 0.790698
203 P5A 0.415385 0.755556
204 LSS 0.414062 0.772727
205 A2R 0.412698 0.918919
206 52H 0.412698 0.790698
207 JB6 0.412214 0.896104
208 5N5 0.411215 0.783784
209 YSA 0.410448 0.811765
210 53H 0.409449 0.790698
211 5CA 0.409449 0.790698
212 ITT 0.408333 0.878378
213 7D4 0.408333 0.844156
214 NA7 0.407692 0.894737
215 LEU LMS 0.407692 0.784091
216 5CD 0.407407 0.794521
217 0WD 0.406897 0.909091
218 A3P 0.40678 0.930556
219 HFD 0.406504 0.883117
220 AVV 0.40625 0.860759
221 RAB 0.40566 0.808219
222 XYA 0.40566 0.808219
223 ADN 0.40566 0.808219
224 FDA 0.405063 0.823529
225 GSU 0.40458 0.790698
226 7MC 0.404255 0.831325
227 NSS 0.403101 0.811765
228 6FA 0.402516 0.853659
229 PPS 0.4 0.817073
230 NVA LMS 0.4 0.784091
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5TPR; Ligand: NAD; Similar sites found with APoc: 71
This union binding pocket(no: 1) in the query (biounit: 5tpr.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 1OYJ GSH 1.8018
2 5YVR NDP 1.95599
3 4XFR CIT 2.02703
4 1O2D NAP 2.15633
5 1VHD NAP 2.15633
6 5LKC FUC GLA A2G 2.27273
7 5A1S FLC 2.47748
8 4UDK BMA 2.59366
9 4DDY DN6 2.6616
10 4UAA 3GK 2.6616
11 1D8C GLV 2.7027
12 1JQ5 NAD 2.7027
13 1P7T PYR 2.7027
14 5F7U GLC GLC 2.7027
15 3E70 GDP 2.7439
16 2WMC MGP 2.80899
17 3NOJ PYR 2.94118
18 2VWT PYR 2.99625
19 4GN8 ASO 3.01003
20 3THR C2F 3.07167
21 1VBH PEP 3.15315
22 2YVE MBT 3.24324
23 1RRM APR 3.36788
24 3ZUY TCH 3.40557
25 1NE7 16G 3.46021
26 1U26 IHS 3.56083
27 6FOG OXL 3.57143
28 2FSH ANP 3.6036
29 2DVZ GLU 3.82166
30 1H3F TYE 3.93519
31 1PCA CIT 4.27928
32 4WBD ADP 4.27928
33 4L80 OXL 4.31034
34 1HSL HIS 4.62185
35 5KZV HCD 4.72441
36 3N75 G4P 4.72973
37 5W3Y ACO 4.82955
38 4L9Z OXL 5.30973
39 3W9F I3P 5.38462
40 3HCH RSM 5.47945
41 3B8I OXL 5.57491
42 3IWK NAD 5.63063
43 1SZO CAX 5.83658
44 4RGQ NDP 6.25
45 4RGQ 1GP 6.25
46 4RGQ 13P 6.25
47 2Y7P SAL 6.42202
48 2F9W PAU 6.53153
49 2J5V PCA 6.53951
50 5U83 ZN8 7.07547
51 1RJW ETF 7.07965
52 4NAE 1GP 7.11111
53 5N53 8NB 7.17949
54 6CS8 F9Y 7.26073
55 5K8C NAD 7.26257
56 1NXJ TLA 7.65027
57 4WOE 3S5 7.65766
58 1TIP F6P 7.8534
59 1SJD NPG 8.15217
60 2NV2 GLN 8.82353
61 5J3R GSH 9.35961
62 2B99 RDL 9.61539
63 1LNX URI 11.1111
64 3QDV A2G 11.8881
65 3QDW A2G 11.8881
66 4WGF HX2 13.1707
67 1OJ7 NZQ 13.7255
68 6GMN F4E 14.4231
69 5FB3 NDP 16.2722
70 1VLJ NAP 24.8157
71 2GRU NAD 34.5109
Pocket No.: 2; Query (leader) PDB : 5TPR; Ligand: NAD; Similar sites found with APoc: 26
This union binding pocket(no: 2) in the query (biounit: 5tpr.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 4CSD MFU 1.83824
2 6BU3 3GK 2.67176
3 4Z87 GDP 2.7027
4 1KZL CRM 2.88462
5 3FU7 3DM 2.92793
6 5CKS GAL 3.1339
7 5CQG 55C 3.18792
8 3ZW0 FUC 3.44828
9 1OFZ FUC 4.16667
10 1OFZ FUL 4.16667
11 4YMJ 4EJ 4.27632
12 5HC0 NPO 4.38356
13 1TKU 5RP 4.41176
14 6F7X MFU 4.44444
15 2XZ9 PYR 4.62963
16 1LSH PLD 5.18018
17 4PQG NAG 5.18018
18 2W47 UNF 6.25
19 2IOR ADP 6.38298
20 4URN NOV 6.66667
21 2HW1 FRU 6.71141
22 1KC7 PPR 7.43243
23 3LN9 FLC 9.35252
24 5ZI9 FLC 10
25 3R9V DXC 15.3846
26 2OFD NGA 26.7606
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