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Receptor
PDB id Resolution Class Description Source Keywords
3EFV 1.9 Å EC: 1.2.1.- CRYSTAL STRUCTURE OF A PUTATIVE SUCCINATE-SEMIALDEHYDE DEHYD FROM SALMONELLA TYPHIMURIUM LT2 WITH BOUND NAD SALMONELLA TYPHIMURIUM PUTATIVE SUCCINATE-SEMIALDEHYDE DEHYDROGENASE CENTER FOR STGENOMICS OF INFECTIOUS DISEASES OXIDOREDUCTASE CSGID
Ref.: STRUCTURE AND ACTIVITY OF THE NAD(P)(+) -DEPENDENT SEMIALDEHYDE DEHYDROGENASE YNEI FROM SALMONELLA TYP PROTEINS V. 81 1031 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAD A:463;
B:463;
C:463;
D:463;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
663.425 C21 H27 N7 O14 P2 c1cc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3EFV 1.9 Å EC: 1.2.1.- CRYSTAL STRUCTURE OF A PUTATIVE SUCCINATE-SEMIALDEHYDE DEHYD FROM SALMONELLA TYPHIMURIUM LT2 WITH BOUND NAD SALMONELLA TYPHIMURIUM PUTATIVE SUCCINATE-SEMIALDEHYDE DEHYDROGENASE CENTER FOR STGENOMICS OF INFECTIOUS DISEASES OXIDOREDUCTASE CSGID
Ref.: STRUCTURE AND ACTIVITY OF THE NAD(P)(+) -DEPENDENT SEMIALDEHYDE DEHYDROGENASE YNEI FROM SALMONELLA TYP PROTEINS V. 81 1031 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3EFV - 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 3 families.
1 3EFV - 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 3 families.
1 3EFV - 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 : 3EFV; Ligand: NAD; Similar sites found with APoc: 90
This union binding pocket(no: 1) in the query (biounit: 3efv.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 6B79 ORA None
2 3KVY URA 0.970874
3 5WZE PRO 1.32743
4 5KJW 53C 1.40515
5 1KYA XYD 1.51515
6 4GKY MAN 1.91571
7 3O9Z NAD 1.92308
8 4CIB 7UZ 1.97802
9 2JE7 XMM 2.09205
10 1SES AMP 2.13777
11 1YFS ALA 2.1645
12 5IFK HPA 2.24359
13 1MVQ MMA 2.54237
14 5F7J ADE 2.8125
15 5G48 1FL 2.94118
16 1I7M CG 2.99625
17 3DZ6 M8E 2.99625
18 5W75 SUC 3.06122
19 3BRE C2E 3.07263
20 1C1X HFA 3.09859
21 1F9V ADP 3.17003
22 3G5N PB2 3.24675
23 1VBO MAN MAN MAN 3.3557
24 4FK7 P34 3.49345
25 4XFR CIT 3.51288
26 2IZ1 ATR 3.67965
27 2IBN I1N 4
28 2O1C PPV 4
29 4XFM THE 4.11255
30 1C3X 8IG 4.13534
31 1VMK GUN 4.33213
32 4O4Z N2O 4.54545
33 3QPB URA 4.60993
34 3ESS 18N 4.78261
35 5F1H 5U6 4.87805
36 3ERR AMP 4.97835
37 5ZI9 FLC 5.38462
38 3I7S PYR 5.47945
39 2YN4 39J 5.50847
40 4R84 CSF 5.62771
41 3GUZ PAF 5.68182
42 1JAY F42 6.60377
43 2XG5 EC5 6.93642
44 2XG5 EC2 6.93642
45 1ONI BEZ 7.24638
46 2WM1 13P 7.44048
47 1UPR 4IP 8.13008
48 3LGS ADE 8.98876
49 4TS1 TYR 9.71787
50 5LX9 OLB 9.77199
51 5TVF CGQ 10.5882
52 2IMG MLT 11.2583
53 5JFL NAD 15.1515
54 5DBV COA 20.8989
55 1L5Y BEF 25.1613
56 4NS3 NAD 30.9524
57 4OE4 NAD 35.7143
58 2Y5D NAP 36.3636
59 5KF6 NAD 36.7965
60 1EZ0 NAP 36.7965
61 3HAZ NAD 37.2294
62 4LH0 GLV 37.4459
63 5UCD NAP 39.8249
64 2BJK NAD 40.4762
65 4I3V NAD 40.7787
66 4ZUL UN1 41.342
67 5N5S NAP 42.4242
68 4I8P NAD 44.1558
69 1KY8 NAP 44.1558
70 4PXL NAD 44.5887
71 5L13 6ZE 45.0216
72 4PZ2 NAD 45.2381
73 1T90 NAD 45.2381
74 5L2M 6ZY 45.4545
75 5IUW NAD 45.8874
76 5IUW IAC 45.8874
77 1O9J NAD 45.8874
78 2QE0 NAP 45.8874
79 3RHJ NAP 46.3203
80 6B5G NAD 46.5368
81 6B5G CQY 46.5368
82 6FK3 PPI 46.7532
83 6MVU K4V 46.9697
84 3IWJ NAD 47.1861
85 3IWK NAD 48.0519
86 4A0M NAD 48.2684
87 2WOX NDP 49.1342
88 4I9B NAD 49.1342
89 2WME NAP 49.1342
90 5X5U NAD 49.5671
Pocket No.: 2; Query (leader) PDB : 3EFV; Ligand: NAD; Similar sites found with APoc: 12
This union binding pocket(no: 2) in the query (biounit: 3efv.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 1RQH PYR 2.38095
2 1O8B ABF 2.73973
3 1FDJ 13P 2.75482
4 4DE2 DN3 3.4632
5 1X8X TYR 3.72671
6 5AOG IAC 4.23453
7 2VFK AMP 4.39024
8 43CA NPO 4.42478
9 5X7Q GLC GLC 4.7619
10 4P8O 883 7.14286
11 4XZ3 ACP 16.087
12 4I9B 1KA 49.1342
Pocket No.: 3; Query (leader) PDB : 3EFV; Ligand: NAD; Similar sites found with APoc: 15
This union binding pocket(no: 3) in the query (biounit: 3efv.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 4WCX MET 1.51515
2 3BJE URA 2.1645
3 5NC1 NAG 2.53165
4 1NW4 IMH 2.89855
5 4HZ0 1AV 4.22535
6 2ZUX RAM 4.329
7 5E58 CPZ 4.329
8 1J78 OLA 4.58515
9 4JCA CIT 4.79042
10 3R7F CP 5.19481
11 3NZ1 3NY 5.36398
12 1GZF NIR 5.6872
13 5LNE A2G GAL 6.70732
14 3JQQ A2P 7.59494
15 3LGS SAH 8.98876
Pocket No.: 4; Query (leader) PDB : 3EFV; Ligand: NAD; Similar sites found with APoc: 2
This union binding pocket(no: 4) in the query (biounit: 3efv.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 2P4S DIH 3.21716
2 5YSI NCA 10.5263
Pocket No.: 5; Query (leader) PDB : 3EFV; Ligand: NAD; 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: 3efv.bio3) has 29 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3EFV; Ligand: NAD; 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: 3efv.bio3) has 30 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3EFV; Ligand: NAD; 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: 3efv.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 3EFV; Ligand: NAD; 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: 3efv.bio2) has 30 residues
No: Leader PDB Ligand Sequence Similarity
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