Receptor
PDB id Resolution Class Description Source Keywords
3DLA 2.35 Å EC: 6.3.5.1 X-RAY CRYSTAL STRUCTURE OF GLUTAMINE-DEPENDENT NAD+ SYNTHETA MYCOBACTERIUM TUBERCULOSIS BOUND TO NAAD+ AND DON MYCOBACTERIUM TUBERCULOSIS GLUTAMINASE NAD+ SYNTHETASE AMMONIA TUNNELING ENZYME GLUDEPENDENT NAD+ SYNTHETASE GLUTAMINE-AMIDO TRANSFERASE ATPLIGASE NAD NUCLEOTIDE-BINDING
Ref.: REGULATION OF ACTIVE SITE COUPLING IN GLUTAMINE-DEP NAD(+) SYNTHETASE. NAT.STRUCT.MOL.BIOL. V. 16 421 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:804;
A:805;
B:681;
B:682;
B:683;
B:684;
C:681;
C:682;
C:683;
C:684;
D:681;
D:682;
D:683;
D:684;
D:685;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NXX A:680;
B:680;
C:680;
D:680;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
665.418 C21 H27 N6 O15 P2 c1cc(...
ONL A:800;
A:801;
A:802;
A:803;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
145.156 C6 H11 N O3 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3DLA 2.35 Å EC: 6.3.5.1 X-RAY CRYSTAL STRUCTURE OF GLUTAMINE-DEPENDENT NAD+ SYNTHETA MYCOBACTERIUM TUBERCULOSIS BOUND TO NAAD+ AND DON MYCOBACTERIUM TUBERCULOSIS GLUTAMINASE NAD+ SYNTHETASE AMMONIA TUNNELING ENZYME GLUDEPENDENT NAD+ SYNTHETASE GLUTAMINE-AMIDO TRANSFERASE ATPLIGASE NAD NUCLEOTIDE-BINDING
Ref.: REGULATION OF ACTIVE SITE COUPLING IN GLUTAMINE-DEP NAD(+) SYNTHETASE. NAT.STRUCT.MOL.BIOL. V. 16 421 2009
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3DLA - NXX C21 H27 N6 O15 P2 c1cc(c[n+]....
2 3SZG - NXX C21 H27 N6 O15 P2 c1cc(c[n+]....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3DLA - NXX C21 H27 N6 O15 P2 c1cc(c[n+]....
2 3SZG - NXX C21 H27 N6 O15 P2 c1cc(c[n+]....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3DLA - NXX C21 H27 N6 O15 P2 c1cc(c[n+]....
2 3SZG - NXX C21 H27 N6 O15 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NXX; 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 : 3DLA; Ligand: NXX; Similar sites found: 74
This union binding pocket(no: 1) in the query (biounit: 3dla.bio1) has 40 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1UO5 PIH 0.02199 0.45223 None
2 1PEA ACM 0.002401 0.48015 1.55844
3 1K6M AGS 0.004445 0.40118 1.62037
4 1SQ5 PAU 0.03031 0.40363 1.62338
5 2NCD ADP 0.01582 0.42118 1.66667
6 1O9U ADZ 0.00716 0.46313 2
7 3ZPG 5GP 0.01453 0.44662 2.09424
8 4E28 9MZ 0.01517 0.42716 2.15385
9 4E28 0MZ 0.03503 0.40498 2.15385
10 1Y42 TYR 0.03574 0.40036 2.29592
11 1RZM E4P 0.02493 0.42194 2.36686
12 1RZM PEP 0.0315 0.40287 2.36686
13 1I0Z OXM 0.0284 0.43089 2.4024
14 3P3N AKG 0.01437 0.4283 2.5788
15 2WA4 069 0.01155 0.40973 2.5788
16 3ESS 18N 0.04362 0.40914 2.6087
17 2F2U M77 0.00206 0.44554 2.98507
18 2QCX PF1 0.01846 0.41805 3.04183
19 1XX4 BAM 0.0158 0.4188 3.06513
20 3LTW HLZ 0.04564 0.40393 3.21429
21 1B0U ATP 0.0101 0.40463 3.43511
22 1XE7 GUN 0.02171 0.43721 3.44828
23 4DYO SD4 0.02693 0.40188 3.50515
24 1V7R CIT 0.008459 0.46738 3.76344
25 4M5P MLA 0.01581 0.45215 3.9312
26 4M5P 23W 0.03003 0.42344 3.9312
27 3SHR CMP 0.01287 0.41176 4.01338
28 1Y9Q MED 0.03701 0.40838 4.16667
29 2Q8H TF4 0.01762 0.4421 4.1769
30 3QV9 QV7 0.01872 0.41777 4.20842
31 4KCT FDP 0.01594 0.40394 4.20842
32 3BY8 MLT 0.006932 0.44969 4.22535
33 1G8S MET 0.02704 0.41502 4.34783
34 1C1L GAL BGC 0.003337 0.46546 4.37956
35 4RJK PYR 0.004531 0.49246 4.55342
36 1SS4 GSH 0.0007602 0.5436 4.57516
37 1N9L FMN 0.003962 0.41298 4.58716
38 4JWX 1N4 0.02429 0.40801 4.64286
39 1F1V DHY 0.006324 0.4295 4.64396
40 1BTN I3P 0.0004898 0.55654 4.71698
41 2EB5 OXL 0.04952 0.40219 4.86891
42 3S9K CIT 0.0007209 0.55496 5.08475
43 3MAG 3MA 0.0007735 0.52537 5.53746
44 1QDS PGA 0.01304 0.41151 5.57769
45 3QDT A2G GAL 0.009227 0.45002 5.59441
46 1YOA FMN 0.03523 0.44013 5.66038
47 1YOA FAD 0.0006208 0.43069 5.66038
48 2Q37 3AL 0.0336 0.40584 6.07735
49 1ZJ6 G3D 0.005203 0.42404 6.41711
50 4COQ SAN 0.04381 0.4048 6.47773
51 2QLX RM4 0.001855 0.47812 6.48148
52 3OCZ SRA 0.009428 0.40231 6.48855
53 3F81 STT 0.007347 0.46253 6.55738
54 1EJE FMN 0.0004323 0.44867 6.77083
55 1ULE GLA GAL NAG 0.01204 0.44404 7.33333
56 1MXI SAH 0.005949 0.40642 7.5
57 2V5E SCR 0.03536 0.43243 7.92079
58 3KJQ B94 0.007881 0.4166 8.42105
59 3P7I P7I 0.0004818 0.48469 8.72274
60 4F4S EFO 0.0183 0.41359 9.21053
61 4M6T SAM 0.02275 0.41823 9.83607
62 2XDQ MGX 0.003895 0.4773 10.7632
63 3UEC ALA ARG TPO LYS 0.01623 0.43128 10.9589
64 4K30 NLG 0.005602 0.4368 11.25
65 1T0S BML 0.005554 0.46139 11.6279
66 3KMT SAH 0.004233 0.42346 11.7647
67 1MZV AMP 0.005307 0.42811 13.617
68 1QO0 BMD 0.007533 0.4418 13.7755
69 2C5S AMP 0.001568 0.48324 14.0436
70 2E1A MSE 0.02733 0.4016 16
71 3FIU AMP 0.000000264 0.67312 23.6948
72 1XNG ATP 0.000003182 0.58039 27.9851
73 1XNG DND 0.00004201 0.49561 27.9851
74 1WXI AMP 0.0000006319 0.52245 29.0909
Pocket No.: 2; Query (leader) PDB : 3DLA; Ligand: NXX; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3dla.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3DLA; Ligand: NXX; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3dla.bio1) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3DLA; Ligand: NXX; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3dla.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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