Receptor
PDB id Resolution Class Description Source Keywords
1IFX 2.25 Å EC: 6.3.5.1 CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH TWO MOLECULES DEAMIDO-NAD BACILLUS SUBTILIS LYASE AMIDOTRANSFERASE NH3 DEPENDENT ATP PYROPHOSPHATASE LIGASE
Ref.: STABILIZATION OF ACTIVE-SITE LOOPS IN NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS. ACTA CRYSTALLOGR.,SECT.D V. 57 806 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DND A:8000;
B:7000;
Valid;
Valid;
none;
none;
submit data
665.418 C21 H27 N6 O15 P2 c1cc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1KQP 1.03 Å EC: 6.3.5.1 NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A BACILLUS SUBTILIS LIGASE AMIDOTRANSFERASE ATP PYROPHOSPHATASE NAD-ADENYLATE
Ref.: NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILI RESOLUTION. ACTA CRYSTALLOGR.,SECT.D V. 58 1138 2002
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1EE1 - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
2 1IH8 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
3 2NSY - AMP NAD n/a n/a
4 1NSY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 1IFX - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
6 1FYD - AMP C10 H14 N5 O7 P c1nc(c2c(n....
7 1KQP - ADJ C31 H44 N11 O21 P3 c1nc(c2c(n....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1EE1 - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
2 1IH8 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
3 2NSY - AMP NAD n/a n/a
4 1NSY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 1IFX - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
6 1FYD - AMP C10 H14 N5 O7 P c1nc(c2c(n....
7 1KQP - ADJ C31 H44 N11 O21 P3 c1nc(c2c(n....
8 2PZA - AMP C10 H14 N5 O7 P c1nc(c2c(n....
9 2PZ8 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1EE1 - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
2 1IH8 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
3 2NSY - AMP NAD n/a n/a
4 1NSY - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 1IFX - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
6 1FYD - AMP C10 H14 N5 O7 P c1nc(c2c(n....
7 1KQP - ADJ C31 H44 N11 O21 P3 c1nc(c2c(n....
8 1WXI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
9 1WXG - DND C21 H27 N6 O15 P2 c1cc(c[n+]....
10 1WXH - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
11 1WXE - AMP C10 H14 N5 O7 P c1nc(c2c(n....
12 2PZA - AMP C10 H14 N5 O7 P c1nc(c2c(n....
13 2PZ8 - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DND; Similar ligands found: 260
No: Ligand ECFP6 Tc MDL keys Tc
1 NXX 1 1
2 DND 1 1
3 NAD 0.765766 0.972603
4 A3D 0.752212 0.959459
5 NAD IBO 0.695652 0.909091
6 NAJ PYZ 0.663934 0.8875
7 A2D 0.659574 0.958904
8 AMP NAD 0.645161 0.946667
9 CNA 0.644068 0.972973
10 BA3 0.628866 0.958904
11 AP5 0.622449 0.958904
12 B4P 0.622449 0.958904
13 NHD 0.619835 0.945946
14 NAP 0.619048 0.959459
15 ZID 0.619048 0.959459
16 AR6 0.613861 0.958904
17 APR 0.613861 0.958904
18 NAQ 0.611111 0.910256
19 NA0 0.609375 0.946667
20 ADP 0.606061 0.932432
21 ATP 0.60396 0.932432
22 NAE 0.603175 0.934211
23 TAP 0.601562 0.897436
24 AN2 0.6 0.92
25 AQP 0.598039 0.932432
26 5FA 0.598039 0.932432
27 NFD 0.596774 0.922078
28 8ID 0.596639 0.923077
29 CA0 0.594059 0.959459
30 M33 0.594059 0.92
31 OOB 0.592593 0.972603
32 AD9 0.592233 0.907895
33 SAP 0.592233 0.884615
34 AGS 0.592233 0.884615
35 N01 0.592 0.945946
36 OAD 0.590909 0.959459
37 ACP 0.588235 0.907895
38 A1R 0.587156 0.873418
39 3OD 0.580357 0.959459
40 NDE 0.578947 0.946667
41 WAQ 0.571429 0.897436
42 NDC 0.57037 0.910256
43 A22 0.568807 0.945946
44 00A 0.567568 0.922078
45 DLL 0.567568 0.972603
46 ACQ 0.566038 0.907895
47 ANP 0.566038 0.907895
48 ADX 0.563107 0.841463
49 A 0.561224 0.905405
50 AMP 0.561224 0.905405
51 NGD 0.560976 0.923077
52 5AL 0.560748 0.945946
53 NJP 0.56 0.96
54 ABM 0.56 0.881579
55 50T 0.557692 0.894737
56 ATF 0.555556 0.896104
57 PRX 0.552381 0.858974
58 NAJ 0.552 0.945946
59 SRP 0.550459 0.921053
60 3UK 0.548673 0.959459
61 ADQ 0.544643 0.959459
62 AMO 0.544643 0.946667
63 4AD 0.544643 0.96
64 9SN 0.543103 0.910256
65 NAX 0.540984 0.8875
66 FYA 0.53913 0.894737
67 1ZZ 0.53913 0.853659
68 FA5 0.538462 0.946667
69 SON 0.538462 0.921053
70 GAP 0.537037 0.933333
71 TXE 0.536585 0.922078
72 8QN 0.535714 0.945946
73 AMP MG 0.534653 0.881579
74 AP2 0.533981 0.896104
75 A12 0.533981 0.896104
76 48N 0.532787 0.910256
77 PAJ 0.530973 0.898734
78 PR8 0.530435 0.864198
79 NCN 0.53 0.808219
80 NAI 0.528455 0.922078
81 TXD 0.528455 0.922078
82 6V0 0.528455 0.910256
83 AHX 0.526316 0.886076
84 TXA 0.525862 0.946667
85 BIS 0.525862 0.873418
86 YAP 0.525424 0.934211
87 G3A 0.525 0.910256
88 SRA 0.524752 0.858974
89 OMR 0.524194 0.865854
90 APC 0.523364 0.896104
91 TAT 0.522936 0.896104
92 25L 0.521368 0.945946
93 G5P 0.520661 0.910256
94 ADP MG 0.518868 0.894737
95 AU1 0.518868 0.907895
96 LAD 0.517241 0.875
97 BEF ADP 0.514019 0.871795
98 ADP BEF 0.514019 0.871795
99 NB8 0.512821 0.910256
100 ME8 0.512821 0.853659
101 PTJ 0.512821 0.886076
102 LAQ 0.512195 0.853659
103 25A 0.508772 0.932432
104 5SV 0.508772 0.817073
105 139 0.507812 0.8875
106 ADP PO3 0.504587 0.931507
107 ADV 0.504587 0.921053
108 RBY 0.504587 0.921053
109 GTA 0.504065 0.9
110 NDO 0.503704 0.933333
111 EAD 0.50365 0.8875
112 NAD BBN 0.5 0.878049
113 IOT 0.5 0.823529
114 TYM 0.5 0.946667
115 ADP ALF 0.5 0.860759
116 ALF ADP 0.5 0.860759
117 ATP MG 0.5 0.894737
118 T5A 0.496124 0.855422
119 AP0 0.496063 0.886076
120 4UU 0.495935 0.934211
121 AFH 0.495935 0.898734
122 XAH 0.495868 0.831325
123 ANP MG 0.495575 0.884615
124 NAD CJ3 0.493243 0.847059
125 A4P 0.492188 0.835294
126 UP5 0.492063 0.934211
127 4UV 0.491803 0.934211
128 DAL AMP 0.486957 0.945946
129 MAP 0.486957 0.884615
130 COD 0.484848 0.804598
131 ADJ 0.484615 0.865854
132 VO4 ADP 0.482456 0.92
133 ADP VO4 0.482456 0.92
134 DZD 0.481203 0.898734
135 BT5 0.481203 0.823529
136 4UW 0.480315 0.898734
137 M24 0.477941 0.8875
138 AOC 0.47619 0.789474
139 4TC 0.472868 0.910256
140 YLP 0.472441 0.833333
141 7MD 0.472 0.876543
142 TYR AMP 0.471545 0.946667
143 NBP 0.471429 0.898734
144 MYR AMP 0.471074 0.853659
145 P1H 0.468531 0.865854
146 AMP DBH 0.467742 0.933333
147 A A 0.466667 0.932432
148 ODP 0.466165 0.923077
149 DSZ 0.466102 0.813953
150 A2R 0.465517 0.945946
151 NAD NDT 0.464968 0.739583
152 PAP 0.464286 0.918919
153 ATP A A A 0.463415 0.945205
154 NAJ PZO 0.463235 0.886076
155 YLA 0.462121 0.833333
156 YLC 0.461538 0.853659
157 NMN 0.461538 0.851351
158 YLB 0.461538 0.833333
159 G5A 0.460177 0.772727
160 5AS 0.458716 0.752809
161 NA7 0.458333 0.896104
162 ADP BMA 0.458333 0.959459
163 AVV 0.457627 0.8625
164 2A5 0.455357 0.858974
165 P5A 0.454545 0.73913
166 VMS 0.452991 0.781609
167 54H 0.452991 0.781609
168 ATR 0.451327 0.905405
169 7D4 0.45045 0.846154
170 ITT 0.45045 0.88
171 UPA 0.450382 0.922078
172 LPA AMP 0.449612 0.853659
173 TSB 0.449153 0.811765
174 A5A 0.448276 0.8
175 AYB 0.447761 0.823529
176 NAD TDB 0.447205 0.68932
177 TAD 0.445312 0.875
178 SSA 0.444444 0.793103
179 6FA 0.442953 0.855422
180 LA8 ALF 3PG 0.442748 0.875
181 ALF ADP 3PG 0.442748 0.875
182 GSU 0.442623 0.793103
183 FB0 0.442177 0.777778
184 ARG AMP 0.44186 0.843373
185 AHZ 0.44186 0.853659
186 NSS 0.441667 0.813953
187 0WD 0.441176 0.910256
188 BTX 0.441176 0.811765
189 52H 0.440678 0.772727
190 7D3 0.440367 0.846154
191 5CD 0.44 0.773333
192 6AD 0.439655 0.851852
193 7MC 0.439394 0.855422
194 JB6 0.439024 0.873418
195 RAB 0.438776 0.810811
196 XYA 0.438776 0.810811
197 ADN 0.438776 0.810811
198 53H 0.436975 0.772727
199 5CA 0.436975 0.793103
200 N0B 0.43662 0.855422
201 YSA 0.436508 0.793103
202 A3P 0.436364 0.905405
203 FDA 0.436242 0.825581
204 YLY 0.435714 0.823529
205 4YB 0.434109 0.795455
206 AF3 ADP 3PG 0.431818 0.875
207 3AT 0.431034 0.906667
208 5N5 0.43 0.786667
209 LSS 0.429752 0.755556
210 NPW 0.42963 0.876543
211 FAD 0.427632 0.865854
212 SFD 0.427632 0.747368
213 FAS 0.427632 0.865854
214 PPS 0.42735 0.819277
215 EP4 0.427184 0.725
216 AR6 AR6 0.426357 0.958904
217 NVA LMS 0.42623 0.775281
218 FNK 0.425806 0.797753
219 A4D 0.425743 0.786667
220 DTA 0.423077 0.779221
221 LEU LMS 0.422764 0.775281
222 P5F 0.42236 0.858824
223 649 0.421053 0.758242
224 WSA 0.421053 0.802326
225 5X8 0.421053 0.779221
226 3AM 0.420561 0.866667
227 4TA 0.42029 0.843373
228 G A A A 0.42029 0.886076
229 KAA 0.419355 0.747253
230 NDP 0.419118 0.910256
231 MTA 0.419048 0.74359
232 U A G G 0.417266 0.897436
233 F2N 0.417178 0.806818
234 NZQ 0.416058 0.898734
235 TXP 0.416058 0.910256
236 7D5 0.415094 0.820513
237 ARU 0.414634 0.807229
238 6RE 0.412844 0.731707
239 AV2 0.411765 0.857143
240 A A A 0.41129 0.894737
241 3DH 0.411215 0.74359
242 A2P 0.410714 0.891892
243 M2T 0.409524 0.728395
244 SFG 0.408696 0.766234
245 62F 0.407643 0.853659
246 DTP 0.40678 0.846154
247 FA9 0.406061 0.855422
248 PUA 0.405594 0.875
249 J7C 0.405405 0.719512
250 A3N 0.405405 0.75641
251 FAY 0.405063 0.876543
252 DG1 0.40411 0.910256
253 1DG 0.40411 0.910256
254 ZAS 0.40367 0.759494
255 RFL 0.402516 0.835294
256 SA8 0.401709 0.722892
257 A5D 0.401709 0.779221
258 CMX 0.401361 0.816092
259 SCO 0.401361 0.816092
260 XNP 0.4 0.864198
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1KQP; Ligand: ADJ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1kqp.bio1) has 40 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1KQP; Ligand: ADJ; Similar sites found: 34
This union binding pocket(no: 2) in the query (biounit: 1kqp.bio1) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3DOO SKM 0.03895 0.41303 1.84502
2 1C3X 8IG 0.04803 0.41155 1.8797
3 4IRP UDP 0.04957 0.41243 1.99203
4 5MX4 HPA 0.04762 0.41248 2.21402
5 2FFU UDP 0.02299 0.40907 2.58303
6 1K97 CIR 0.003055 0.40174 2.95203
7 1K97 ASP 0.003055 0.40174 2.95203
8 3RK1 ATP 0.000495 0.49952 2.95359
9 3UDG TMP 0.01352 0.44588 3.32103
10 1Q19 APC 0.0000326 0.53055 3.69004
11 2C5S AMP 0.0003999 0.52145 3.69004
12 1U6R IOM 0.01349 0.43687 3.69004
13 4OCV ANP 0.02595 0.40359 3.69004
14 2D2F ADP 0.01641 0.43011 4
15 5UDS ATP 0.00005272 0.5616 4.05904
16 2AWN ADP 0.006532 0.45783 4.79705
17 3B9Q MLI 0.009745 0.43458 4.79705
18 5F7J ADE 0.02645 0.42901 4.79705
19 2OQ2 A3P 0.004907 0.43133 4.98084
20 3GP3 SEP 0.04796 0.40902 5.05837
21 1JGT CMA 0.001055 0.43593 5.53506
22 1JGT APC 0.001258 0.43019 5.53506
23 4P86 5GP 0.03828 0.40737 6.01093
24 4UZI IMD 0.01375 0.42164 6.64207
25 4F8L AES 0.04985 0.41214 6.89655
26 3S6X SIA GAL BGC 0.03143 0.43294 7.74908
27 3KTA AP5 0.03297 0.40436 9.24856
28 3X27 TRP 0.04609 0.41394 11.4391
29 1GPM AMP 0.000003805 0.65829 12.5461
30 2BOS GLA GAL GLC 0.0155 0.44195 16.1765
31 2BOS GLA GAL GLC NBU 0.01798 0.43625 16.1765
32 1IH7 GMP 0.01783 0.4325 18.0812
33 1XNG ATP 0.000000000009129 0.85104 38.806
34 1XNG DND 0.0000000001838 0.72685 38.806
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