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(...
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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: 220
No: Ligand ECFP6 Tc MDL keys Tc
1 A3D 0.872727 0.986111
2 NAD IBO 0.845455 0.933333
3 NHD 0.821429 0.972222
4 NAP 0.811966 0.986111
5 NAJ PYZ 0.803419 0.910256
6 NFD 0.791304 0.946667
7 NXX 0.765766 0.972603
8 DND 0.765766 0.972603
9 ZID 0.737705 0.986111
10 NAQ 0.729508 0.934211
11 NAE 0.721311 0.959459
12 NA0 0.712 0.972603
13 TAP 0.704 0.921053
14 AMP NAD 0.696 0.945946
15 NDE 0.689922 0.972603
16 NAJ 0.683333 0.972222
17 NDC 0.679389 0.934211
18 NDO 0.674603 0.958904
19 N01 0.656 0.972222
20 CNA 0.642276 0.972603
21 NBP 0.621212 0.922078
22 NAD BBN 0.609929 0.876543
23 8ID 0.609756 0.922078
24 NAD CJ3 0.601399 0.845238
25 ADP MG 0.579439 0.918919
26 A2D 0.576923 0.958333
27 ADP 0.575472 0.931507
28 NGD 0.574803 0.922078
29 BEF ADP 0.574074 0.894737
30 ADP BEF 0.574074 0.894737
31 BA3 0.566038 0.958333
32 NAD NDT 0.565789 0.755319
33 M33 0.564815 0.918919
34 ADP PO3 0.563636 0.957747
35 B4P 0.560748 0.958333
36 AP5 0.560748 0.958333
37 ATP MG 0.558559 0.918919
38 AN2 0.555556 0.918919
39 GAP 0.553571 0.932432
40 OOB 0.551724 0.972222
41 CA0 0.550459 0.932432
42 ATP 0.545455 0.931507
43 ACP 0.545455 0.906667
44 NAD TDB 0.544872 0.70297
45 ADP ALF 0.54386 0.883117
46 ALF ADP 0.54386 0.883117
47 5FA 0.540541 0.931507
48 AQP 0.540541 0.931507
49 APR 0.540541 0.931507
50 AR6 0.540541 0.931507
51 ANP MG 0.53913 0.907895
52 VO4 ADP 0.53913 0.945205
53 ADP VO4 0.53913 0.945205
54 AGS 0.535714 0.883117
55 SAP 0.535714 0.883117
56 AD9 0.535714 0.906667
57 WAQ 0.533333 0.896104
58 ABM 0.53271 0.905405
59 00A 0.529412 0.921053
60 DLL 0.529412 0.972222
61 ANP 0.526316 0.906667
62 NJP 0.526316 0.959459
63 ACQ 0.526316 0.906667
64 OAD 0.525 0.932432
65 AMP MG 0.523364 0.905405
66 ADX 0.522523 0.839506
67 5AL 0.521739 0.945205
68 A1R 0.521008 0.871795
69 9SN 0.520325 0.909091
70 AMP 0.518868 0.930556
71 A 0.518868 0.930556
72 50T 0.517857 0.893333
73 ATF 0.517241 0.894737
74 DAL AMP 0.516949 0.945205
75 3OD 0.516393 0.932432
76 1ZZ 0.516393 0.851852
77 SON 0.513514 0.92
78 PRX 0.513274 0.881579
79 SRP 0.512821 0.92
80 ADP BMA 0.512397 0.932432
81 3UK 0.512397 0.958904
82 MYR AMP 0.512195 0.851852
83 NAJ PZO 0.510949 0.909091
84 NMN 0.509434 0.875
85 AMP DBH 0.507937 0.906667
86 A22 0.504202 0.945205
87 FA5 0.504 0.945946
88 ATP A A A 0.504 0.971831
89 TYR AMP 0.5 0.945946
90 8QN 0.5 0.945205
91 NAX 0.496183 0.886076
92 PR8 0.495935 0.8625
93 PAJ 0.495868 0.873418
94 4AD 0.495868 0.933333
95 AMO 0.495868 0.92
96 ADQ 0.495868 0.932432
97 A12 0.495495 0.894737
98 AP2 0.495495 0.894737
99 ALF ADP 3PG 0.492424 0.873418
100 LA8 ALF 3PG 0.492424 0.873418
101 AHZ 0.492308 0.851852
102 YAP 0.492063 0.933333
103 FYA 0.491935 0.918919
104 AHX 0.491803 0.884615
105 4UU 0.488372 0.933333
106 5SV 0.487603 0.8375
107 TAT 0.487179 0.894737
108 APC 0.486957 0.894737
109 SRA 0.486239 0.881579
110 NAI 0.484848 0.921053
111 6V0 0.484848 0.909091
112 GTA 0.484615 0.898734
113 A A 0.483871 0.958333
114 LAD 0.483871 0.873418
115 AU1 0.482456 0.906667
116 TXE 0.481203 0.921053
117 AF3 ADP 3PG 0.481203 0.873418
118 OMR 0.481203 0.841463
119 LAQ 0.480916 0.851852
120 G3A 0.48062 0.909091
121 TXA 0.48 0.92
122 NB8 0.48 0.884615
123 ME8 0.48 0.851852
124 BIS 0.48 0.871795
125 PTJ 0.48 0.884615
126 139 0.477941 0.886076
127 LPA AMP 0.477273 0.851852
128 AR6 AR6 0.476923 0.958333
129 G5P 0.476923 0.909091
130 AFH 0.476923 0.873418
131 25L 0.47619 0.945205
132 25A 0.47541 0.958333
133 DZD 0.47482 0.897436
134 TXD 0.473684 0.921053
135 4UV 0.472868 0.933333
136 TYM 0.470149 0.945946
137 ADV 0.470085 0.894737
138 RBY 0.470085 0.894737
139 ARG AMP 0.469697 0.841463
140 4TA 0.467626 0.864198
141 48N 0.466165 0.884615
142 XAH 0.465116 0.851852
143 4UW 0.462687 0.897436
144 M24 0.461538 0.886076
145 IOT 0.459854 0.821429
146 T5A 0.456522 0.853659
147 EAD 0.455782 0.886076
148 MAP 0.455285 0.883117
149 BT5 0.453901 0.821429
150 A4P 0.452555 0.833333
151 UP5 0.451852 0.933333
152 PAP 0.445378 0.917808
153 AP0 0.445255 0.884615
154 4TC 0.445255 0.909091
155 YLP 0.444444 0.831325
156 P1H 0.443709 0.864198
157 AOC 0.442478 0.810811
158 Z5A 0.439189 0.833333
159 2A5 0.436975 0.857143
160 G A A A 0.43662 0.909091
161 COD 0.43662 0.802326
162 ADJ 0.435714 0.841463
163 YLC 0.434783 0.851852
164 YLB 0.434783 0.831325
165 U A G G 0.433566 0.921053
166 ATR 0.433333 0.90411
167 7MD 0.432836 0.851852
168 G5A 0.429752 0.790698
169 PO4 PO4 A A A A PO4 0.429688 0.943662
170 TAD 0.42963 0.873418
171 5AS 0.42735 0.770115
172 BTX 0.426573 0.831325
173 YLA 0.425532 0.831325
174 DSZ 0.425197 0.790698
175 NCN 0.424779 0.805556
176 UPA 0.42446 0.921053
177 VMS 0.424 0.8
178 54H 0.424 0.8
179 N0B 0.422819 0.853659
180 6AD 0.422764 0.85
181 AYB 0.422535 0.821429
182 7D3 0.422414 0.844156
183 YLY 0.421769 0.821429
184 TSB 0.420635 0.809524
185 ODP 0.41958 0.922078
186 AV2 0.419355 0.855263
187 FB0 0.419355 0.775281
188 A5A 0.419355 0.819277
189 NNR 0.419048 0.739726
190 A A A 0.418605 0.918919
191 LEU LMS 0.418605 0.793103
192 649 0.417266 0.775281
193 NMN AMP PO4 0.416667 0.933333
194 SSA 0.416 0.790698
195 P5A 0.415385 0.755556
196 LSS 0.414062 0.772727
197 A2R 0.412698 0.918919
198 52H 0.412698 0.790698
199 JB6 0.412214 0.896104
200 5N5 0.411215 0.783784
201 YSA 0.410448 0.811765
202 5CA 0.409449 0.790698
203 53H 0.409449 0.790698
204 ITT 0.408333 0.878378
205 7D4 0.408333 0.844156
206 NA7 0.407692 0.894737
207 5CD 0.407407 0.794521
208 0WD 0.406897 0.909091
209 A3P 0.40678 0.930556
210 AVV 0.40625 0.860759
211 RAB 0.40566 0.808219
212 ADN 0.40566 0.808219
213 XYA 0.40566 0.808219
214 FDA 0.405063 0.823529
215 GSU 0.40458 0.790698
216 7MC 0.404255 0.831325
217 NSS 0.403101 0.811765
218 6FA 0.402516 0.853659
219 NVA LMS 0.4 0.793103
220 PPS 0.4 0.817073
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1RLZ; Ligand: NAD; Similar sites found: 61
This union binding pocket(no: 1) in the query (biounit: 1rlz.bio1) has 63 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1XDS SAM 0.005345 0.43361 1.62602
2 1VKO NAD 0.00000009778 0.43025 1.62602
3 4Q3S X7A 0.001448 0.42993 1.62602
4 3MAG SAH 0.02036 0.40216 1.62866
5 3LST SAH 0.02206 0.40369 1.72414
6 1EJE FMN 0.01431 0.4112 2.60417
7 1SS4 GSH 0.009817 0.49273 2.61438
8 4Q0P 0MK 0.00001058 0.41338 2.69231
9 1GR0 NAD 0.0000002162 0.43367 2.99728
10 1HKU NAD 0.001433 0.41582 3.07263
11 2NXE SAM 0.01288 0.40497 3.14961
12 2PP3 LGT 0.00003195 0.44837 3.25203
13 1I2B UPG 0.0000123 0.42482 3.25203
14 1I2B USQ 0.0000123 0.42482 3.25203
15 2VDV SAM 0.0121 0.41639 3.25203
16 3FPZ AHZ 0.00000004986 0.44957 3.37423
17 1G55 SAH 0.006048 0.41658 3.49854
18 1V5F TPP 0.000002462 0.44804 3.52304
19 1SAZ ACP 0.00001071 0.40327 3.52304
20 1LSS NAD 0.0004837 0.40122 3.57143
21 1TV5 N8E 0.0011 0.45578 3.61174
22 1TV5 ORO 0.002209 0.44964 3.61174
23 3F81 STT 0.04725 0.43059 3.82514
24 2E1A MSE 0.004051 0.45849 4
25 3G2O SAM 0.001005 0.45531 4.01338
26 4NEC SAH 0.01656 0.40977 4.06504
27 1DXY NAD 0.000008197 0.41427 4.5045
28 1SAY PYR 0.000005531 0.4306 4.60705
29 2Z9V PXM 0.02072 0.42965 4.87805
30 1ONX ASP 0.00298 0.4161 4.87805
31 1C1L GAL BGC 0.0484 0.42484 5.10949
32 1JQN DCO 0.002251 0.40472 5.14905
33 4TMK T5A 0.00003521 0.41042 5.16432
34 1G8S MET 0.0211 0.43872 5.21739
35 1I8T FAD 0.002214 0.4155 5.44959
36 1EFV FAD 0.009321 0.40467 5.4902
37 4IXW IXW 0.0473 0.40849 5.51181
38 1O97 AMP 0.005094 0.41458 5.68182
39 3WDM ADN 0.001865 0.40111 5.74713
40 1V6A TRE 0.003812 0.47055 6.0241
41 2Z4T C5P 0.02404 0.40895 6.23306
42 1T26 NAI 0.000009785 0.41406 6.77507
43 1T26 GBD 0.000009785 0.41406 6.77507
44 1UWK URO 0.002423 0.41997 7.04607
45 4COQ SAN 0.01626 0.44452 7.28745
46 4F4S EFO 0.04159 0.41498 7.89474
47 2ZO9 MLI 0.01816 0.42213 8.0292
48 1RSD PSB 0.000486 0.40283 8.26446
49 2DT5 NAD 0.002328 0.41165 8.53081
50 1MXI SAH 0.02212 0.40358 8.75
51 2Q37 3AL 0.01699 0.43849 9.39227
52 1EXB NDP 0.000001957 0.41386 9.70874
53 1S7G APR 0.002036 0.40989 9.88142
54 1CFV E3G 0.006722 0.40652 10.9244
55 3U7Y FLC 0.04203 0.45784 12.8571
56 3EGV SAH 0.01185 0.40986 14.2857
57 2A2X NA9 0.01485 0.41055 14.7059
58 2NCD ADP 0.001381 0.49226 15.7182
59 3S9K CIT 0.0009939 0.57177 17.7966
60 1GXU 2HP 0.006276 0.42082 18.6813
61 3KPE TM3 0.01313 0.44927 37.2549
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