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Receptor
PDB id Resolution Class Description Source Keywords
1DHS 2.2 Å EC: 2.5.1.46 CRYSTAL STRUCTURE OF THE NAD COMPLEX OF HUMAN DEOXYHYPUSINE HOMO SAPIENS SPERMIDINE INITIATION FACTOR 5A NAD SUBUNIT INTERACTIONSOXIDOREDUCTASE
Ref.: CRYSTAL STRUCTURE OF THE NAD COMPLEX OF HUMAN DEOXY SYNTHASE: AN ENZYME WITH A BALL-AND-CHAIN MECHANISM BLOCKING THE ACTIVE SITE. STRUCTURE V. 6 23 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAD A:700;
Valid;
none;
submit data
663.425 C21 H27 N7 O14 P2 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1RLZ 2.15 Å EC: 2.5.1.46 DEOXYHYPUSINE SYNTHASE HOLOENZYME IN ITS HIGH IONIC STRENGTH CRYSTAL FORM HOMO SAPIENS ROSSMANN FOLD NAD COFACTOR DEOXYHYPUSINE HYPUSINE SPERMITRANSFERASE
Ref.: A NEW CRYSTAL STRUCTURE OF DEOXYHYPUSINE SYNTHASE R THE CONFIGURATION OF THE ACTIVE ENZYME AND OF AN ENZYME-NAD-INHIBITOR TERNARY COMPLEX J.BIOL.CHEM. V. 279 28697 2004
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1DHS - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 1ROZ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 1RLZ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1DHS - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 1ROZ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 1RLZ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1DHS - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 1ROZ - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 1RLZ - 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 : 1RLZ; 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: 1) in the query (biounit: 1rlz.bio1) has 63 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1RLZ; Ligand: NAD; Similar sites found with APoc: 206
This union binding pocket(no: 2) in the query (biounit: 1rlz.bio1) has 63 residues
No: Leader PDB Ligand Sequence Similarity
1 4J5R A1R None
2 1Q19 SSC 1.08401
3 6F5W KG1 1.35501
4 1U2Z SAH 1.35501
5 1XDS SAM 1.62602
6 3I53 SAH 1.62602
7 6GNF GLC 1.62602
8 1QZZ SAM 1.62602
9 6GNF ADP 1.62602
10 3LST SAH 1.72414
11 5OJ7 AR6 1.74825
12 2WA2 SAM 1.81159
13 3VSE SAH 1.89702
14 3PT9 SAH 1.89702
15 4N49 SAM 1.89702
16 1ZGA SAH 1.96078
17 3ZG6 APR 2.02703
18 3GRU AMP 2.0339
19 2AJH MET 2.04082
20 4DMG SAM 2.16802
21 4R84 CSF 2.16802
22 5TVI O8N 2.17391
23 1F3L SAH 2.18069
24 1R18 SAH 2.20264
25 6ECU SAH 2.21519
26 5E9W SAH 2.24359
27 5DWQ SFG 2.29226
28 5DXA SFG 2.29226
29 5DX8 SFG 2.29226
30 5IL1 SAM 2.35849
31 2R68 SUP 2.43902
32 3GXO SAH 2.43902
33 2ZWI C5P 2.43902
34 3GWZ SAH 2.43902
35 1ZQ9 SAM 2.43902
36 1IM8 SAI 2.45902
37 2XVM SAH 2.51256
38 4D79 ATP 2.53623
39 6EQS BV8 2.54545
40 3VC1 SAH 2.5641
41 3RIY NAD 2.5641
42 3A27 SAM 2.57353
43 5LOG SAH 2.57511
44 3FUU ADN 2.58303
45 1L3I SAH 2.60417
46 4IWN GEK 2.62009
47 6DUB SAH 2.7027
48 4KRI SAH 2.71003
49 5F8F SFG 2.71003
50 4LWP SAH 2.71739
51 5F7J ADE 2.8125
52 5HJM MTA 2.84091
53 1QAN SAH 2.86885
54 4OWK NGA 2.89855
55 2UYQ SAM 2.90323
56 3VYW SAM 2.92208
57 3L9W AMP 2.98103
58 5X62 SAH 2.98103
59 5C9P FUC 2.98103
60 3T7S SAM 2.98507
61 4MO2 FAD 2.98913
62 4MO2 FDA 2.98913
63 3O7W SAM 3.06122
64 4KIB SAH 3.08123
65 2NXE SAM 3.14961
66 3GCZ SAM 3.19149
67 3GEG NAD 3.23887
68 1PJS NAD 3.25203
69 2VDV SAM 3.25203
70 1XF1 CIT 3.25203
71 2P41 SAH 3.27869
72 6FDF SAH 3.29341
73 6MDE MEV 3.30033
74 5T52 A2G 3.30579
75 5T52 NGA 3.30579
76 1P77 ATR 3.30882
77 3A25 SAM 3.32226
78 1G55 SAH 3.49854
79 2EFJ SAH 3.52304
80 5WP4 SAH 3.52304
81 5XVS UDP 3.52304
82 1LSS NAD 3.57143
83 3FSY SCA 3.61446
84 3EVG SAH 3.63636
85 3DXY SAM 3.66972
86 3AJM 4IP 3.75587
87 3BXO SAM 3.76569
88 5KOK SAH 3.79404
89 1X87 NAD 3.79404
90 5JGL SAM 3.80623
91 3GU3 SAH 3.87324
92 3SIG AR6 3.97112
93 1ZX5 LFR 4
94 3G2O SAM 4.01338
95 5GM1 SAH 4.0404
96 5DNK SAH 4.06504
97 6C8R SAH 4.06504
98 2EG5 SAH 4.06504
99 6C8R EQV 4.06504
100 4NEC SAH 4.06504
101 5XNC MTA 4.06504
102 4WBD CIT 4.06504
103 1V59 NAD 4.1841
104 4A6D SAM 4.24929
105 1FP1 SAH 4.33604
106 3LKZ SFG 4.36137
107 3EGI ADP 4.36893
108 4OIT MAN 4.42478
109 6DWI HD4 4.52675
110 4Y9D NAI 4.59016
111 4JLS 3ZE 4.60526
112 1P31 EPU 4.60705
113 3IX1 NFM 4.63576
114 2BZG SAH 4.74138
115 5DUS APR 4.7619
116 4K7O EKZ 4.7619
117 4KXQ APR 4.87805
118 1KYZ SAH 4.93151
119 1UAY ADN 4.95868
120 3K7S R52 5.02793
121 1KYQ NAD 5.10949
122 1R6N 434 5.21327
123 1L1E SAH 5.22648
124 5WP5 SAH 5.29532
125 1RJW ETF 5.30973
126 1DJN ADP 5.42005
127 2PWY SAH 5.42636
128 4OBW SAM 5.44747
129 1I8T FAD 5.44959
130 1EFV FAD 5.4902
131 5V8E CIT 5.50162
132 3JWH SAH 5.52995
133 1JG3 ADN 5.53191
134 3KIF GDL 5.66038
135 1O97 FAD 5.68182
136 1O97 AMP 5.68182
137 1O94 ADP 5.68182
138 4LHD GLY 5.69106
139 5JAQ NAI 5.69106
140 4KRG SAH 5.69106
141 2QQF A1R 5.69106
142 2OD9 A1R NCA 5.69106
143 6GKV SAH 5.69801
144 3WDM ADN 5.74713
145 4IF4 BEF 5.76923
146 4YMH SAH 5.83333
147 3U31 NAD 5.86207
148 4RDH AMP 5.90278
149 4RDI ATP 5.90278
150 5MGZ SAH 5.9322
151 5ERG SAM 5.96206
152 1C3X 8IG 6.01504
153 3G89 SAM 6.0241
154 1EJ0 SAM 6.11111
155 1RZU ADP 6.18557
156 3ITJ CIT 6.21302
157 2Z4T C5P 6.23306
158 1FP2 SAH 6.25
159 5OVK NDP 6.25
160 2HNK SAH 6.27615
161 4YAC NAI 6.39731
162 2AOT SAH 6.50685
163 1WY7 SAH 6.76329
164 5NM7 GLY 6.76692
165 5KVA SAM 6.83453
166 1UWK URO 7.04607
167 1UWK NAD 7.04607
168 4NTO 1PW 7.24638
169 3RKR NAP 7.25191
170 4BUZ NAD 7.31707
171 2JK0 ASP 7.38462
172 3LCC SAH 7.65957
173 1I9G SAM 7.85714
174 3TKY SAH 7.88043
175 5W7K SAH 8.01282
176 5FA5 MTA 8.13008
177 4QTU SAM 8.14815
178 1YXM ADE 8.25082
179 5E5U MLI 8.33333
180 1KNM LAT 8.46154
181 4FGC PQ0 8.48485
182 3H8V ATP 8.56164
183 2YVJ NAI 9.17431
184 2YX1 SFG 9.22619
185 5FA8 SAM 9.31677
186 1K4M CIT 9.38967
187 1EJH M7G 9.47368
188 2JHP SAH 9.4851
189 4J51 N75 9.5092
190 4II2 ATP 9.7561
191 1S7G APR 9.88142
192 1S7G NAD 9.88142
193 2WPB ZZI 10.1974
194 2P0D I3P 10.8527
195 5L95 AMP 11.25
196 1C4Q GLA GAL BGC 11.5942
197 5BW4 SAM 11.6105
198 3WUR O4B 11.6959
199 2HMT NAI 11.8056
200 5BSZ SAH 12
201 5E8J SAH 13.6364
202 3K1X DBX 16.9231
203 5BXV MGP 18.1818
204 1GXU 2HP 18.6813
205 3MB5 SAM 21.1765
206 5URY PAM 23.2877
Pocket No.: 3; Query (leader) PDB : 1RLZ; 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: 3) in the query (biounit: 1rlz.bio1) has 63 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1RLZ; 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: 4) in the query (biounit: 1rlz.bio1) has 63 residues
No: Leader PDB Ligand Sequence Similarity
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