Receptor
PDB id Resolution Class Description Source Keywords
3DHV 2 Å EC: 6.1.1.13 CRYSTAL STRUCTURE OF DLTA PROTEIN IN COMPLEX WITH D-ALANINE ADENYLATE BACILLUS CEREUS DLTA AMP-FORMING DOMAIN D-ALANINE ADENYLATION D-ALANINE CARRIER PROTEIN LIGASE CYTOPLASM
Ref.: CRYSTAL STRUCTURE AND ENANTIOMER SELECTION BY D-ALANYL CARRIER PROTEIN LIGASE DLTA FROM BACILLUS CEREUS. BIOCHEMISTRY V. 47 11473 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DAL AMP A:701;
 Valid;
 none;
 submit data
418.303 n/a P(=O)...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3DHV 2 Å EC: 6.1.1.13 CRYSTAL STRUCTURE OF DLTA PROTEIN IN COMPLEX WITH D-ALANINE ADENYLATE BACILLUS CEREUS DLTA AMP-FORMING DOMAIN D-ALANINE ADENYLATION D-ALANINE CARRIER PROTEIN LIGASE CYTOPLASM
Ref.: CRYSTAL STRUCTURE AND ENANTIOMER SELECTION BY D-ALANYL CARRIER PROTEIN LIGASE DLTA FROM BACILLUS CEREUS. BIOCHEMISTRY V. 47 11473 2008
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3DHV - DAL AMP n/a n/a
2 3FCC - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 3FCE - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3DHV - DAL AMP n/a n/a
2 3FCC - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 3FCE - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3E7W - AMP C10 H14 N5 O7 P c1nc(c2c(n....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3DHV - DAL AMP n/a n/a
2 3FCC - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 3FCE - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3E7W - AMP C10 H14 N5 O7 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DAL AMP; Similar ligands found: 328
No: Ligand ECFP6 Tc MDL keys Tc
1 DAL AMP 1 1
2 GAP 0.77381 0.958904
3 TYR AMP 0.736842 0.933333
4 ARG AMP 0.721649 0.864198
5 ADP MG 0.702381 0.957747
6 5AL 0.685393 0.972222
7 MYR AMP 0.677083 0.898734
8 ADP PO3 0.670455 0.957747
9 ATP MG 0.670455 0.957747
10 8LH 0.67033 0.945946
11 A 0.658537 0.90411
12 AMP 0.658537 0.90411
13 8LQ 0.655914 0.945946
14 CA0 0.655172 0.932432
15 ABM 0.654762 0.905405
16 45A 0.654762 0.905405
17 A2D 0.654762 0.905405
18 ADP VO4 0.652174 0.918919
19 VO4 ADP 0.652174 0.918919
20 8QN 0.648936 0.972222
21 KG4 0.647727 0.932432
22 4AD 0.642105 0.933333
23 ADP ALF 0.641304 0.883117
24 ALF ADP 0.641304 0.883117
25 AP2 0.639535 0.87013
26 A12 0.639535 0.87013
27 BA3 0.639535 0.905405
28 SRP 0.634409 0.92
29 B4P 0.632184 0.905405
30 ADP 0.632184 0.905405
31 AP5 0.632184 0.905405
32 9ZA 0.631579 0.921053
33 9ZD 0.631579 0.921053
34 8LE 0.630435 0.933333
35 PAJ 0.625 0.897436
36 LPA AMP 0.619048 0.875
37 M33 0.617977 0.918919
38 PTJ 0.616162 0.909091
39 AGS 0.615385 0.858974
40 APC MG 0.615385 0.931507
41 SAP 0.615385 0.858974
42 SRA 0.611765 0.857143
43 ATP 0.611111 0.905405
44 HEJ 0.611111 0.905405
45 50T 0.611111 0.868421
46 AMO 0.608247 0.92
47 AN2 0.606742 0.893333
48 SON 0.606742 0.92
49 AT4 0.606742 0.87013
50 5FA 0.604396 0.905405
51 PRX 0.604396 0.881579
52 APC 0.604396 0.87013
53 AQP 0.604396 0.905405
54 AR6 0.604396 0.931507
55 APR 0.604396 0.931507
56 AU1 0.6 0.881579
57 ADX 0.6 0.817073
58 TXA 0.6 0.945946
59 ME8 0.6 0.875
60 RBY 0.597826 0.894737
61 AD9 0.597826 0.881579
62 ADV 0.597826 0.894737
63 ADP BMA 0.59596 0.932432
64 ACP 0.593407 0.881579
65 A A 0.59 0.905405
66 LAD 0.59 0.873418
67 AMP DBH 0.586538 0.906667
68 NB8 0.584158 0.884615
69 OOB 0.581633 0.945205
70 9X8 0.58 0.907895
71 OAD 0.58 0.958904
72 AHZ 0.579439 0.898734
73 AF3 ADP 3PG 0.577982 0.897436
74 00A 0.57 0.896104
75 AHX 0.57 0.860759
76 DLL 0.57 0.945205
77 1ZZ 0.568627 0.875
78 3OD 0.568627 0.958904
79 ANP 0.568421 0.881579
80 T99 0.568421 0.87013
81 TAT 0.568421 0.87013
82 ACQ 0.568421 0.881579
83 YAP 0.567308 0.907895
84 ATP A 0.567308 0.944444
85 FA5 0.567308 0.92
86 ATP A A A 0.567308 0.944444
87 5SV 0.565657 0.8375
88 3UK 0.564356 0.932432
89 LMS 0.563218 0.795181
90 HQG 0.561224 0.918919
91 A1R 0.56 0.848101
92 PR8 0.558824 0.8625
93 WAQ 0.558824 0.896104
94 B5V 0.558824 0.92
95 9SN 0.557692 0.884615
96 A5A 0.556701 0.819277
97 ATF 0.556701 0.87013
98 AMP NAD 0.556522 0.972222
99 TSB 0.555556 0.809524
100 A22 0.555556 0.893333
101 B5Y 0.552381 0.933333
102 B5M 0.552381 0.933333
103 6YZ 0.55102 0.881579
104 AOC 0.550562 0.810811
105 NAQ 0.55 0.909091
106 LEU LMS 0.54902 0.784091
107 A3D 0.547009 0.958904
108 GA7 0.546296 0.87013
109 AR6 AR6 0.546296 0.958333
110 VMS 0.545455 0.8
111 YLP 0.545455 0.853659
112 54H 0.545455 0.8
113 48N 0.545455 0.909091
114 ADQ 0.544554 0.906667
115 A3R 0.544554 0.848101
116 5AS 0.543478 0.770115
117 NAD 0.543103 0.945205
118 G5A 0.541667 0.770115
119 MAP 0.54 0.858974
120 NVA LMS 0.539216 0.784091
121 OZV 0.534653 0.905405
122 25A 0.534653 0.905405
123 XAH 0.53271 0.829268
124 YLB 0.530973 0.853659
125 YLC 0.530973 0.875
126 XYA 0.530864 0.808219
127 ADN 0.530864 0.808219
128 RAB 0.530864 0.808219
129 5CD 0.53012 0.794521
130 52H 0.53 0.790698
131 LSS 0.529412 0.772727
132 NAJ PZO 0.529412 0.884615
133 NSS 0.529412 0.790698
134 NAE 0.528926 0.933333
135 4UV 0.527778 0.907895
136 TAD 0.527273 0.85
137 DQV 0.527273 0.918919
138 AYB 0.525862 0.843373
139 53H 0.524752 0.790698
140 JB6 0.52381 0.848101
141 FYA 0.52381 0.868421
142 LAQ 0.522523 0.851852
143 TYM 0.522124 0.92
144 F2R 0.521368 0.831325
145 ZID 0.520325 0.932432
146 SSA 0.52 0.770115
147 25L 0.518868 0.893333
148 7MD 0.518182 0.851852
149 AFH 0.518182 0.85
150 4UU 0.518182 0.907895
151 5N5 0.518072 0.783784
152 AP0 0.517544 0.860759
153 YLA 0.517241 0.831325
154 4TA 0.516949 0.864198
155 TXD 0.513274 0.871795
156 4UW 0.513274 0.897436
157 NAI 0.513274 0.871795
158 NAJ PYZ 0.512195 0.841463
159 A4D 0.511905 0.783784
160 EP4 0.511628 0.766234
161 H1Q 0.510417 0.891892
162 5CA 0.509804 0.770115
163 BIS 0.509434 0.848101
164 9K8 0.509434 0.764045
165 OMR 0.508772 0.864198
166 TXE 0.508772 0.871795
167 M2T 0.505747 0.769231
168 DTA 0.505747 0.776316
169 3DH 0.505618 0.786667
170 7MC 0.504348 0.853659
171 COD 0.504202 0.802326
172 MTA 0.5 0.786667
173 DND 0.5 0.945946
174 DSZ 0.5 0.790698
175 NAX 0.5 0.839506
176 NXX 0.5 0.945946
177 6V0 0.5 0.860759
178 GTA 0.5 0.875
179 P5A 0.5 0.736264
180 NDE 0.496124 0.92
181 IOT 0.495726 0.821429
182 G3A 0.495495 0.860759
183 8X1 0.495146 0.744444
184 5X8 0.494845 0.8
185 SFG 0.494845 0.786667
186 U A 0.491803 0.896104
187 G A A A 0.491667 0.884615
188 T5A 0.491525 0.831325
189 G5P 0.491071 0.860759
190 SMM 0.490196 0.759036
191 SAM 0.49 0.765432
192 6RE 0.48913 0.75
193 NDC 0.48855 0.884615
194 CNA 0.487395 0.92
195 GSU 0.485981 0.790698
196 KAA 0.485981 0.744444
197 EEM 0.485149 0.765432
198 SA8 0.484848 0.7625
199 A3P 0.484211 0.90411
200 N0B 0.484127 0.831325
201 YLY 0.483871 0.843373
202 80F 0.483607 0.831325
203 A G 0.479339 0.896104
204 J7C 0.478723 0.7375
205 7D5 0.477778 0.818182
206 YSA 0.477477 0.770115
207 PO4 PO4 A A A A PO4 0.476636 0.916667
208 GEK 0.47619 0.794872
209 U A G G 0.47541 0.896104
210 A4P 0.474576 0.790698
211 UP5 0.474138 0.883117
212 S4M 0.473684 0.697674
213 M24 0.472 0.8625
214 PAP 0.47 0.891892
215 7C5 0.469027 0.831169
216 Z5A 0.46875 0.833333
217 A2P 0.46875 0.890411
218 MAO 0.46875 0.75
219 8PZ 0.468468 0.770115
220 NEC 0.468085 0.76
221 3AM 0.467391 0.864865
222 ADJ 0.466667 0.819277
223 139 0.466667 0.839506
224 SAI 0.465347 0.769231
225 SAH 0.465347 0.779221
226 A3T 0.464646 0.835616
227 B1U 0.464286 0.747253
228 DZD 0.463415 0.85
229 BT5 0.463415 0.821429
230 A3N 0.463158 0.753247
231 A A A 0.462963 0.918919
232 ZAS 0.462366 0.779221
233 S7M 0.461538 0.765432
234 2A5 0.46 0.833333
235 GJV 0.458333 0.740741
236 6MZ 0.458333 0.891892
237 7D3 0.458333 0.820513
238 NVA 2AD 0.455446 0.794872
239 ATR 0.455446 0.878378
240 NMN AMP PO4 0.455285 0.907895
241 7D4 0.454545 0.820513
242 EAD 0.453846 0.8625
243 UPA 0.453782 0.871795
244 4TC 0.453782 0.860759
245 A3G 0.452632 0.789474
246 DSH 0.452632 0.716049
247 5AD 0.452381 0.760563
248 P1H 0.451128 0.841463
249 A U 0.45 0.907895
250 IMO 0.447917 0.864865
251 6IA 0.446602 0.804878
252 V3L 0.446602 0.931507
253 J4G 0.445455 0.907895
254 WSA 0.445378 0.77907
255 N01 0.444444 0.972222
256 A7D 0.444444 0.766234
257 A3S 0.444444 0.8
258 0UM 0.444444 0.753086
259 FB0 0.444444 0.775281
260 BTX 0.443548 0.809524
261 A2R 0.443396 0.918919
262 6AD 0.442308 0.85
263 PPS 0.442308 0.795181
264 COA FLC 0.44186 0.823529
265 SXZ 0.441441 0.765432
266 A5D 0.441176 0.776316
267 2AM 0.44086 0.853333
268 62X 0.440367 0.717647
269 ITT 0.44 0.853333
270 MHZ 0.44 0.689655
271 2SA 0.438095 0.894737
272 K15 0.436364 0.73494
273 4YB 0.435897 0.772727
274 2VA 0.435644 0.813333
275 CNV FAD 0.434483 0.833333
276 A C A C 0.433071 0.884615
277 Y3J 0.431818 0.716216
278 NA0 0.431818 0.945946
279 7D7 0.430233 0.733333
280 8Q2 0.429752 0.744444
281 KOY 0.428571 0.84
282 NAP 0.427481 0.932432
283 OVE 0.427083 0.820513
284 AV2 0.424528 0.831169
285 JSQ 0.423077 0.858974
286 SO8 0.423077 0.802632
287 HFD 0.423077 0.858974
288 N5O 0.42268 0.753247
289 U A C C 0.421875 0.896104
290 FAD NBT 0.421769 0.76087
291 649 0.421488 0.736264
292 NHD 0.420635 0.918919
293 FNK 0.416667 0.775281
294 AAT 0.415094 0.698795
295 C2R 0.414894 0.866667
296 AMZ 0.414894 0.853333
297 ARU 0.414414 0.804878
298 N5A 0.414141 0.727273
299 TAP 0.413534 0.871795
300 NJP 0.412698 0.907895
301 KB1 0.412281 0.731707
302 PGS 0.411765 0.825
303 NA7 0.410714 0.87013
304 A6D 0.410714 0.73494
305 U A A U 0.410448 0.896104
306 71V 0.41 0.825
307 6C6 0.409524 0.822785
308 VRT 0.409524 0.782051
309 0WD 0.409449 0.860759
310 DAT 0.407767 0.820513
311 DCA 0.407692 0.793103
312 ETB 0.407692 0.802326
313 FAD NBA 0.407643 0.736842
314 FDA 0.407143 0.802326
315 ENQ 0.40708 0.930556
316 3NZ 0.40708 0.794872
317 NIA 0.40625 0.790123
318 DTP 0.40566 0.820513
319 3AT 0.40566 0.88
320 6FA 0.404255 0.831325
321 NO7 0.40367 0.846154
322 NFD 0.403101 0.896104
323 COA 0.401515 0.793103
324 0T1 0.401515 0.793103
325 FAD CNX 0.401316 0.736842
326 KH3 0.4 0.72619
327 APC G U 0.4 0.848101
328 D3Y 0.4 0.779221
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DHV; Ligand: DAL AMP; Similar sites found with APoc: 7
This union binding pocket(no: 1) in the query (biounit: 3dhv.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 5MSD AMP 29.8828
2 6IJB AMP 30.2734
3 6IJB A8C 30.2734
4 4OXI GAP 35.7422
5 6AKD A5A 38.6719
6 1AMU AMP 48.6328
7 1AMU AMP 48.6328
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