Receptor
PDB id Resolution Class Description Source Keywords
3B82 2.35 Å EC: 2.4.2.36 STRUCTURE OF THE EEF2-EXOA(E546H)-NAD+ COMPLEX SACCHAROMYCES CEREVISIAE ELONGATION FACTOR TOXIN ADP-RIBOSYLATION TOXIN-SUBSTRATE COMPLEX CYTOPLASM GTP-BINDING NUCLEOTIDE-BINDING PHOSPHORYLATION PROTEIN BIOSYNTHESIS RNA-BINDING RRNA- BINDING GLYCOSYLTRANSFERASE NAD TRANSFERASE BIOSYNTHETIC PROTEIN/TRANSFERASE COMPLEX
Ref.: THE NATURE AND CHARACTER OF THE TRANSITION STATE FOR THE ADP-RIBOSYLTRANSFERASE REACTION. EMBO REP. V. 9 802 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAD B:700;
D:701;
F:702;
Valid;
Valid;
Valid;
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
3B82 2.35 Å EC: 2.4.2.36 STRUCTURE OF THE EEF2-EXOA(E546H)-NAD+ COMPLEX SACCHAROMYCES CEREVISIAE ELONGATION FACTOR TOXIN ADP-RIBOSYLATION TOXIN-SUBSTRATE COMPLEX CYTOPLASM GTP-BINDING NUCLEOTIDE-BINDING PHOSPHORYLATION PROTEIN BIOSYNTHESIS RNA-BINDING RRNA- BINDING GLYCOSYLTRANSFERASE NAD TRANSFERASE BIOSYNTHETIC PROTEIN/TRANSFERASE COMPLEX
Ref.: THE NATURE AND CHARACTER OF THE TRANSITION STATE FOR THE ADP-RIBOSYLTRANSFERASE REACTION. EMBO REP. V. 9 802 2008
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3B82 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 3B8H - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 3B78 - 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 6 families.
1 3B82 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 3B8H - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 3B78 - 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 5 families.
1 3B82 - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 3B8H - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
3 3B78 - 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 : 3B82; Ligand: NAD; Similar sites found: 57
This union binding pocket(no: 1) in the query (biounit: 3b82.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4BUY F37 0.0000000113 0.57594 2.08333
2 4J3L AJ5 0.0000003289 0.60482 2.38095
3 4Z9D NAD 0.0009171 0.41313 2.85714
4 4MSG 2C6 0.00000004143 0.63047 2.89855
5 1UC2 SUC 0.006044 0.4434 3.38164
6 4CJN QNZ 0.03999 0.40303 3.38164
7 5F7J ADE 0.02155 0.4132 3.4375
8 4FXQ G9L 0.00008992 0.5387 3.86473
9 3KL3 GCU 0.004518 0.48294 4.34783
10 3BRE C2E 0.001873 0.46891 4.46927
11 1KZL CRM 0.02207 0.40167 4.80769
12 3KJD 78P 0.000004968 0.5155 4.83092
13 3QPB URA 0.01054 0.43192 4.83092
14 4GK9 MAN BMA MAN MAN MAN 0.02572 0.4072 4.83092
15 2F6U CIT 0.02325 0.40863 5.31401
16 1OG1 TAD 0.00007277 0.48439 5.75221
17 5MX4 HPA 0.01427 0.42223 5.7971
18 1OJZ NAD 0.0001282 0.4886 6.28019
19 5MRH Q9Z 0.01217 0.41875 6.28019
20 1EFY BZC 0.00002059 0.51838 6.28571
21 4PJT 2YQ 0.000003643 0.47024 6.48649
22 1I1E DM2 0.02701 0.4052 6.76329
23 3BJE URA 0.0331 0.40213 6.76329
24 3UEC ALA ARG TPO LYS 0.02365 0.41699 6.84932
25 4YC0 5OF 0.00000801 0.50743 7.11297
26 3SAO DBH 0.01549 0.41988 7.5
27 4NFD SIA 0.02392 0.4162 7.5
28 2VDF OCT 0.004947 0.4204 7.50988
29 5LYH 7B8 0.0000001687 0.59859 7.77202
30 3QH2 3NM 0.02565 0.40638 8.1448
31 3LGS ADE 0.02659 0.40802 8.2397
32 1SC3 MLI 0.04498 0.40053 8.98876
33 4FK7 P34 0.00001317 0.59885 9.60699
34 2XG5 EC2 0.01989 0.41865 9.63303
35 2XG5 EC5 0.01989 0.41865 9.63303
36 4XSH NAI 0.0006243 0.43744 10.0457
37 4UI8 IY5 0.000001376 0.56999 10.4167
38 2W5P CL8 0.02138 0.41099 10.7383
39 4URG C2E 0.004734 0.44447 10.7784
40 1U9L ASN ARG PRO ILE LEU SER LEU 0.01939 0.41821 11.4286
41 5LX6 78P 0.000001326 0.45055 11.5183
42 1NW4 IMH 0.02245 0.40522 12.6812
43 4FGC PQ0 0.0116 0.42603 13.9394
44 4GV4 MEJ 0.0000001911 0.6154 14.0097
45 1GZF ADP 0.00005781 0.50411 15.942
46 1GZF NIR 0.0005637 0.49249 15.942
47 1GZF NAD 0.0001397 0.47704 15.942
48 2A9K NAD 0.0001276 0.45535 15.942
49 4F0E 0RU 0.0000009619 0.46004 16.5
50 1DTP APU 0.00000008976 0.61437 17.3684
51 1FMB HYB 0.01575 0.40507 20.1923
52 2P4T NAP 0.01851 0.40546 20.9677
53 4DSU BZI 0.006408 0.43853 26.9841
54 4H03 NAD 0.001516 0.44474 29.9517
55 3LQV ADE 0.01285 0.40286 30.7692
56 2WN6 NDP 0.0008524 0.46098 30.9179
57 2G30 ALA ALA PHE 0.0006398 0.49575 37.5
Pocket No.: 2; Query (leader) PDB : 3B82; Ligand: NAD; Similar sites found: 4
This union binding pocket(no: 2) in the query (biounit: 3b82.bio3) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3UDG TMP 0.01001 0.44004 5.64784
2 3KFF ZBT 0.03265 0.4023 8.02469
3 3KFF XBT 0.03265 0.4023 8.02469
4 5E6O TRP GLU GLU LEU 0.02634 0.40312 16.9492
Pocket No.: 3; Query (leader) PDB : 3B82; Ligand: NAD; Similar sites found: 3
This union binding pocket(no: 3) in the query (biounit: 3b82.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BTM PGA 0.02604 0.40043 3.57143
2 3VCA PRO 0.03421 0.41458 3.86473
3 3IHB GLU 0.02507 0.40667 16.886
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