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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;
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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: 271
No: Ligand ECFP6 Tc MDL keys Tc
1 DND 1 1
2 NXX 1 1
3 NAD 0.765766 0.972603
4 A3D 0.752212 0.959459
5 AMP NAD 0.689655 0.972603
6 A2D 0.659574 0.958904
7 CNA 0.644068 0.972973
8 BA3 0.628866 0.958904
9 B4P 0.622449 0.958904
10 AP5 0.622449 0.958904
11 NHD 0.619835 0.945946
12 ZID 0.619048 0.959459
13 NAP 0.619048 0.959459
14 AR6 0.613861 0.958904
15 APR 0.613861 0.958904
16 NAQ 0.611111 0.910256
17 NA0 0.609375 0.946667
18 ADP 0.606061 0.932432
19 ATP 0.60396 0.932432
20 HEJ 0.60396 0.932432
21 NAE 0.603175 0.934211
22 TAP 0.601562 0.897436
23 AN2 0.6 0.92
24 AT4 0.6 0.896104
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 AGS 0.592233 0.884615
33 SAP 0.592233 0.884615
34 AD9 0.592233 0.907895
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 DQV 0.581197 0.972603
40 3OD 0.580357 0.959459
41 NDE 0.578947 0.946667
42 A3R 0.572727 0.873418
43 WAQ 0.571429 0.897436
44 NDC 0.57037 0.910256
45 A22 0.568807 0.945946
46 DLL 0.567568 0.972603
47 00A 0.567568 0.922078
48 ACQ 0.566038 0.907895
49 ANP 0.566038 0.907895
50 ADX 0.563107 0.841463
51 9X8 0.5625 0.909091
52 A 0.561224 0.905405
53 AMP 0.561224 0.905405
54 NGD 0.560976 0.923077
55 5AL 0.560748 0.945946
56 ABM 0.56 0.881579
57 NJP 0.56 0.96
58 50T 0.557692 0.894737
59 ATF 0.555556 0.896104
60 PRX 0.552381 0.858974
61 NAJ 0.552 0.945946
62 6YZ 0.550459 0.907895
63 SRP 0.550459 0.921053
64 3UK 0.548673 0.959459
65 4AD 0.544643 0.96
66 AMO 0.544643 0.946667
67 ADQ 0.544643 0.959459
68 B5V 0.54386 0.946667
69 9SN 0.543103 0.910256
70 NAX 0.540984 0.8875
71 FYA 0.53913 0.894737
72 1ZZ 0.53913 0.853659
73 SON 0.538462 0.921053
74 B5M 0.538462 0.934211
75 FA5 0.538462 0.946667
76 GAP 0.537037 0.933333
77 TXE 0.536585 0.922078
78 8QN 0.535714 0.945946
79 F2R 0.535433 0.855422
80 AP2 0.533981 0.896104
81 A12 0.533981 0.896104
82 9JJ 0.533784 0.9
83 48N 0.532787 0.910256
84 PAJ 0.530973 0.898734
85 PR8 0.530435 0.864198
86 NCN 0.53 0.808219
87 TXD 0.528455 0.922078
88 6V0 0.528455 0.910256
89 NAI 0.528455 0.922078
90 AHX 0.526316 0.886076
91 BIS 0.525862 0.873418
92 TXA 0.525862 0.946667
93 YAP 0.525424 0.934211
94 G3A 0.525 0.910256
95 SRA 0.524752 0.858974
96 OMR 0.524194 0.865854
97 APC 0.523364 0.896104
98 TAT 0.522936 0.896104
99 T99 0.522936 0.896104
100 25L 0.521368 0.945946
101 G5P 0.520661 0.910256
102 AU1 0.518868 0.907895
103 LAD 0.517241 0.875
104 ME8 0.512821 0.853659
105 NB8 0.512821 0.910256
106 PTJ 0.512821 0.886076
107 B5Y 0.512605 0.934211
108 LAQ 0.512195 0.853659
109 80F 0.51145 0.878049
110 5SV 0.508772 0.817073
111 9ZD 0.508772 0.897436
112 25A 0.508772 0.932432
113 9ZA 0.508772 0.897436
114 139 0.507812 0.8875
115 RBY 0.504587 0.921053
116 ADP PO3 0.504587 0.931507
117 ADV 0.504587 0.921053
118 GTA 0.504065 0.9
119 NDO 0.503704 0.933333
120 EAD 0.50365 0.8875
121 ALF ADP 0.5 0.860759
122 DAL AMP 0.5 0.945946
123 ADP ALF 0.5 0.860759
124 IOT 0.5 0.823529
125 TYM 0.5 0.946667
126 T5A 0.496124 0.855422
127 AP0 0.496063 0.886076
128 4UU 0.495935 0.934211
129 AFH 0.495935 0.898734
130 XAH 0.495868 0.831325
131 A4P 0.492188 0.835294
132 UP5 0.492063 0.934211
133 4UV 0.491803 0.934211
134 MAP 0.486957 0.884615
135 COD 0.484848 0.804598
136 ADJ 0.484615 0.865854
137 GA7 0.483871 0.896104
138 VO4 ADP 0.482456 0.92
139 ADP VO4 0.482456 0.92
140 DZD 0.481203 0.898734
141 BT5 0.481203 0.823529
142 4UW 0.480315 0.898734
143 TYR AMP 0.479675 0.934211
144 M24 0.477941 0.8875
145 AOC 0.47619 0.789474
146 4TC 0.472868 0.910256
147 YLP 0.472441 0.833333
148 7MD 0.472 0.876543
149 NBP 0.471429 0.898734
150 LMS 0.471154 0.797619
151 MYR AMP 0.471074 0.853659
152 P1H 0.468531 0.865854
153 AMP DBH 0.467742 0.933333
154 A A 0.466667 0.932432
155 ODP 0.466165 0.923077
156 DSZ 0.466102 0.813953
157 A2R 0.465517 0.945946
158 PAP 0.464286 0.918919
159 ATP A A A 0.463415 0.945205
160 NAJ PZO 0.463235 0.886076
161 YLA 0.462121 0.833333
162 YLC 0.461538 0.853659
163 YLB 0.461538 0.833333
164 8X1 0.461538 0.747253
165 NMN 0.461538 0.851351
166 ARG AMP 0.460317 0.843373
167 G5A 0.460177 0.772727
168 5AS 0.458716 0.752809
169 NA7 0.458333 0.896104
170 ADP BMA 0.458333 0.959459
171 AVV 0.457627 0.8625
172 2A5 0.455357 0.858974
173 P5A 0.454545 0.73913
174 VMS 0.452991 0.781609
175 54H 0.452991 0.781609
176 ATR 0.451327 0.905405
177 7D4 0.45045 0.846154
178 ITT 0.45045 0.88
179 UPA 0.450382 0.922078
180 LPA AMP 0.449612 0.853659
181 TSB 0.449153 0.811765
182 A5A 0.448276 0.8
183 AYB 0.447761 0.823529
184 HFD 0.447368 0.884615
185 TAD 0.445312 0.875
186 SSA 0.444444 0.793103
187 6FA 0.442953 0.855422
188 GSU 0.442623 0.793103
189 FB0 0.442177 0.777778
190 AHZ 0.44186 0.853659
191 NSS 0.441667 0.813953
192 0WD 0.441176 0.910256
193 BTX 0.441176 0.811765
194 52H 0.440678 0.772727
195 7D3 0.440367 0.846154
196 5CD 0.44 0.773333
197 8PZ 0.44 0.813953
198 6AD 0.439655 0.851852
199 7MC 0.439394 0.855422
200 9K8 0.439024 0.747253
201 JB6 0.439024 0.873418
202 XYA 0.438776 0.810811
203 RAB 0.438776 0.810811
204 ADN 0.438776 0.810811
205 NVA LMS 0.438017 0.766667
206 5CA 0.436975 0.793103
207 53H 0.436975 0.772727
208 N0B 0.43662 0.855422
209 YSA 0.436508 0.793103
210 A3P 0.436364 0.905405
211 FDA 0.436242 0.825581
212 YLY 0.435714 0.823529
213 LEU LMS 0.434426 0.766667
214 4YB 0.434109 0.795455
215 AF3 ADP 3PG 0.431818 0.875
216 3AT 0.431034 0.906667
217 5N5 0.43 0.786667
218 LSS 0.429752 0.755556
219 NPW 0.42963 0.876543
220 NAJ PYZ 0.429577 0.843373
221 SFD 0.427632 0.747368
222 FAS 0.427632 0.865854
223 FAD 0.427632 0.865854
224 PPS 0.42735 0.819277
225 EP4 0.427184 0.725
226 AR6 AR6 0.426357 0.958904
227 FNK 0.425806 0.797753
228 A4D 0.425743 0.786667
229 DTA 0.423077 0.779221
230 P5F 0.42236 0.858824
231 649 0.421053 0.758242
232 WSA 0.421053 0.802326
233 5X8 0.421053 0.779221
234 3AM 0.420561 0.866667
235 A G 0.42029 0.897436
236 G A A A 0.42029 0.886076
237 4TA 0.42029 0.843373
238 KAA 0.419355 0.747253
239 NDP 0.419118 0.910256
240 MTA 0.419048 0.74359
241 U A G G 0.417266 0.897436
242 F2N 0.417178 0.806818
243 TXP 0.416058 0.910256
244 NZQ 0.416058 0.898734
245 7D5 0.415094 0.820513
246 ARU 0.414634 0.807229
247 6RE 0.412844 0.731707
248 AV2 0.411765 0.857143
249 A A A 0.41129 0.894737
250 3DH 0.411215 0.74359
251 A2P 0.410714 0.891892
252 M2T 0.409524 0.728395
253 SFG 0.408696 0.766234
254 62F 0.407643 0.853659
255 8Q2 0.407407 0.786517
256 DTP 0.40678 0.846154
257 FA9 0.406061 0.855422
258 PUA 0.405594 0.875
259 J7C 0.405405 0.719512
260 A3N 0.405405 0.75641
261 FAY 0.405063 0.876543
262 1DG 0.40411 0.910256
263 DG1 0.40411 0.910256
264 ZAS 0.40367 0.759494
265 RFL 0.402516 0.835294
266 SA8 0.401709 0.722892
267 A5D 0.401709 0.779221
268 U A 0.401408 0.922078
269 SCO 0.401361 0.816092
270 CMX 0.401361 0.816092
271 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 with APoc: 45
This union binding pocket(no: 1) in the query (biounit: 1kqp.bio1) has 40 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 1C3X 8IG 1.8797
3 3ZF8 GDP 2.58303
4 3MKN DNB 2.58303
5 1DKQ IHP 2.58303
6 4WOE 3S5 2.95203
7 3RK1 ATP 2.95359
8 1BC5 ACE ASN TRP GLU THR PHE 2.97398
9 1OSS BEN 3.13901
10 2C5S AMP 3.69004
11 1Q19 APC 3.69004
12 1U6R IOM 3.69004
13 1VRP IOM 3.69004
14 6DZN AE3 3.75587
15 6B2M COA 4.05904
16 6AC9 ANP 4.42804
17 5LX9 OLB 4.57746
18 5NC1 NAG 4.64135
19 5F7J ADE 4.79705
20 5N6N SUC 4.79705
21 3TFC PEP 5.16605
22 4YSX MLI 5.16605
23 1V9A SAH 5.85774
24 4P86 5GP 6.01093
25 4UZI IMD 6.64207
26 4HAQ CTR 6.64207
27 4F8L AES 6.89655
28 1CT9 AMP 7.01107
29 2W5P CL8 7.38255
30 3S6X SIA GAL BGC 7.74908
31 2GAG FOA 8.11808
32 4TVD BGC 8.11808
33 4EKQ NPO 9.09091
34 5FAG PPI 9.9631
35 4URS C2E 12.234
36 1GPM AMP 12.5461
37 1DTL BEP 13.6646
38 4URG C2E 13.7725
39 2BOS GLA GAL GLC 16.1765
40 2BOS GLA GAL GLC NBU 16.1765
41 1MJH ATP 17.9012
42 3HGM ATP 18.3673
43 5AHW CMP 19.0476
44 1XNG ATP 38.806
45 1XNG DND 38.806
Pocket No.: 2; Query (leader) PDB : 1KQP; Ligand: ADJ; Similar sites found with APoc: 33
This union binding pocket(no: 2) in the query (biounit: 1kqp.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
1 3DOO SKM 1.84502
2 4NTO 1PW 1.93237
3 1VC9 ATP 2.38095
4 2FFU UDP 2.58303
5 1K97 ASP 2.95203
6 1K97 CIR 2.95203
7 3RK0 AMP 2.95359
8 1B0U ATP 3.05344
9 4R2M ANP 3.16456
10 3UDG TMP 3.32103
11 1Q19 SSC 3.69004
12 4OCV ANP 3.69004
13 2D2F ADP 4
14 1OXV ANP 4.05904
15 5URY PAM 4.10959
16 5NM7 GLY 4.51128
17 2AWN ADP 4.79705
18 3B9Q MLI 4.79705
19 1TKU 5RP 4.90196
20 2OQ2 A3P 4.98084
21 3GP3 SEP 5.05837
22 2VWT PYR 5.24345
23 1JGT CMA 5.53506
24 1JGT APC 5.53506
25 1KSK URA 5.98291
26 4L80 OXL 6.27306
27 2H04 4UN 6.64207
28 3KTA AP5 9.24856
29 1KOR ARG 9.5
30 5BSH PRO 10.7011
31 3X27 TRP 11.4391
32 1IH7 GMP 18.0812
33 3QF7 ANP 24
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