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)...
View in 3D viewer
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 (2D)
Ligand no: 1; Ligand: DAL AMP; Similar ligands found: 348
No: Ligand ECFP6 Tc MDL keys Tc
1 DAL AMP 1 1
2 GAP 0.77381 0.958904
3 ARG AMP 0.721649 0.864198
4 ADP BEF 0.702381 0.957747
5 ADP MG 0.702381 0.957747
6 AMP MG 0.691358 0.943662
7 5AL 0.685393 0.972222
8 MYR AMP 0.677083 0.898734
9 ADP PO3 0.670455 0.957747
10 ATP MG 0.670455 0.957747
11 8LH 0.67033 0.945946
12 BEF ADP 0.662921 0.931507
13 AMP 0.658537 0.90411
14 A 0.658537 0.90411
15 8LQ 0.655914 0.945946
16 CA0 0.655172 0.932432
17 A2D 0.654762 0.905405
18 ABM 0.654762 0.905405
19 45A 0.654762 0.905405
20 8QN 0.648936 0.972222
21 KG4 0.647727 0.932432
22 4AD 0.642105 0.933333
23 VO4 ADP 0.641304 0.906667
24 ANP MG 0.641304 0.918919
25 ALF ADP 0.641304 0.883117
26 A12 0.639535 0.87013
27 AP2 0.639535 0.87013
28 BA3 0.639535 0.905405
29 QA7 0.638298 0.933333
30 SRP 0.634409 0.92
31 B4P 0.632184 0.905405
32 ADP 0.632184 0.905405
33 AP5 0.632184 0.905405
34 9ZA 0.631579 0.921053
35 9ZD 0.631579 0.921053
36 8LE 0.630435 0.933333
37 PAJ 0.625 0.897436
38 LPA AMP 0.619048 0.875
39 M33 0.617977 0.918919
40 PTJ 0.616162 0.909091
41 APC MG 0.615385 0.931507
42 AGS 0.615385 0.858974
43 SRA 0.611765 0.857143
44 ATP 0.611111 0.905405
45 HEJ 0.611111 0.905405
46 50T 0.611111 0.868421
47 AMO 0.608247 0.92
48 ALF ADP 3PG 0.607477 0.897436
49 AT4 0.606742 0.87013
50 SON 0.606742 0.92
51 AN2 0.606742 0.893333
52 AR6 0.604396 0.931507
53 AQP 0.604396 0.905405
54 APC 0.604396 0.87013
55 PRX 0.604396 0.881579
56 5FA 0.604396 0.905405
57 APR 0.604396 0.931507
58 AU1 0.6 0.881579
59 TXA 0.6 0.945946
60 ME8 0.6 0.875
61 ADX 0.6 0.817073
62 RBY 0.597826 0.894737
63 AD9 0.597826 0.881579
64 ADV 0.597826 0.894737
65 ADP BMA 0.59596 0.932432
66 V2G 0.595745 0.884615
67 ACP 0.593407 0.881579
68 LAD 0.59 0.873418
69 AMP DBH 0.586538 0.906667
70 NB8 0.584158 0.884615
71 OOB 0.581633 0.945205
72 9X8 0.58 0.907895
73 LEU LMS 0.58 0.802326
74 OAD 0.58 0.958904
75 AHZ 0.579439 0.898734
76 AF3 ADP 3PG 0.577982 0.897436
77 AHX 0.57 0.860759
78 00A 0.57 0.896104
79 DLL 0.57 0.945205
80 3OD 0.568627 0.958904
81 1ZZ 0.568627 0.875
82 T99 0.568421 0.87013
83 ACQ 0.568421 0.881579
84 TAT 0.568421 0.87013
85 ANP 0.568421 0.881579
86 ATP A 0.567308 0.944444
87 FA5 0.567308 0.92
88 ATP A A A 0.567308 0.944444
89 5SV 0.565657 0.8375
90 3UK 0.564356 0.932432
91 LMS 0.563218 0.795181
92 HQG 0.561224 0.918919
93 A1R 0.56 0.848101
94 PR8 0.558824 0.8625
95 WAQ 0.558824 0.896104
96 B5V 0.558824 0.92
97 9SN 0.557692 0.884615
98 ATF 0.556701 0.87013
99 A5A 0.556701 0.819277
100 AMP NAD 0.556522 0.972222
101 TSB 0.555556 0.809524
102 A22 0.555556 0.893333
103 JNT 0.554455 0.881579
104 B5Y 0.552381 0.933333
105 B5M 0.552381 0.933333
106 6YZ 0.55102 0.881579
107 AOC 0.550562 0.810811
108 NAQ 0.55 0.909091
109 A3D 0.547009 0.958904
110 AR6 AR6 0.546296 0.958333
111 GA7 0.546296 0.87013
112 VMS 0.545455 0.8
113 54H 0.545455 0.8
114 YLP 0.545455 0.853659
115 48N 0.545455 0.909091
116 NAD IBO 0.544643 0.958333
117 NAD TDB 0.544643 0.958333
118 ADQ 0.544554 0.906667
119 A3R 0.544554 0.848101
120 5AS 0.543478 0.770115
121 NAD 0.543103 0.945205
122 G5A 0.541667 0.770115
123 MAP 0.54 0.858974
124 NVA LMS 0.539216 0.784091
125 OZV 0.534653 0.905405
126 25A 0.534653 0.905405
127 XAH 0.53271 0.829268
128 YLB 0.530973 0.853659
129 YLC 0.530973 0.875
130 XYA 0.530864 0.808219
131 RAB 0.530864 0.808219
132 ADN 0.530864 0.808219
133 5CD 0.53012 0.794521
134 52H 0.53 0.790698
135 NSS 0.529412 0.790698
136 LSS 0.529412 0.772727
137 NAJ PZO 0.529412 0.884615
138 NAE 0.528926 0.933333
139 4UV 0.527778 0.907895
140 TAD 0.527273 0.85
141 DQV 0.527273 0.918919
142 AYB 0.525862 0.843373
143 53H 0.524752 0.790698
144 FYA 0.52381 0.868421
145 JB6 0.52381 0.848101
146 KMQ 0.523364 0.92
147 LAQ 0.522523 0.851852
148 TYM 0.522124 0.92
149 F2R 0.521368 0.831325
150 ZID 0.520325 0.932432
151 SSA 0.52 0.770115
152 25L 0.518868 0.893333
153 AFH 0.518182 0.85
154 4UU 0.518182 0.907895
155 7MD 0.518182 0.851852
156 5N5 0.518072 0.783784
157 AP0 0.517544 0.860759
158 YLA 0.517241 0.831325
159 4TA 0.516949 0.864198
160 TXD 0.513274 0.871795
161 4UW 0.513274 0.897436
162 NAI 0.513274 0.871795
163 NAJ PYZ 0.512195 0.841463
164 A4D 0.511905 0.783784
165 EP4 0.511628 0.766234
166 H1Q 0.510417 0.891892
167 5CA 0.509804 0.770115
168 BIS 0.509434 0.848101
169 9K8 0.509434 0.764045
170 OMR 0.508772 0.864198
171 TXE 0.508772 0.871795
172 DTA 0.505747 0.776316
173 M2T 0.505747 0.769231
174 3DH 0.505618 0.786667
175 7MC 0.504348 0.853659
176 L3W 0.504348 0.894737
177 COD 0.504202 0.802326
178 DSZ 0.5 0.790698
179 GTA 0.5 0.875
180 P5A 0.5 0.736264
181 6V0 0.5 0.860759
182 DND 0.5 0.945946
183 MTA 0.5 0.786667
184 NAX 0.5 0.839506
185 NDE 0.496124 0.92
186 IOT 0.495726 0.821429
187 G3A 0.495495 0.860759
188 8X1 0.495146 0.744444
189 5X8 0.494845 0.8
190 SFG 0.494845 0.786667
191 T5A 0.491525 0.831325
192 G5P 0.491071 0.860759
193 SMM 0.490196 0.759036
194 SAM 0.49 0.765432
195 6RE 0.48913 0.75
196 NDC 0.48855 0.884615
197 CNA 0.487395 0.92
198 KAA 0.485981 0.744444
199 GSU 0.485981 0.790698
200 EEM 0.485149 0.765432
201 SA8 0.484848 0.7625
202 A3P 0.484211 0.90411
203 N0B 0.484127 0.831325
204 YLY 0.483871 0.843373
205 80F 0.483607 0.831325
206 J7C 0.478723 0.7375
207 7D5 0.477778 0.818182
208 YSA 0.477477 0.770115
209 NWW 0.476744 0.75
210 PO4 PO4 A A A A PO4 0.476636 0.916667
211 GEK 0.47619 0.794872
212 A4P 0.474576 0.790698
213 UP5 0.474138 0.883117
214 S4M 0.473684 0.697674
215 DAL FAD PER 0.472603 0.797753
216 M24 0.472 0.8625
217 PAP 0.47 0.891892
218 7C5 0.469027 0.831169
219 MAO 0.46875 0.75
220 Z5A 0.46875 0.833333
221 A2P 0.46875 0.890411
222 8PZ 0.468468 0.770115
223 NEC 0.468085 0.76
224 3AM 0.467391 0.864865
225 ADJ 0.466667 0.819277
226 139 0.466667 0.839506
227 SAI 0.465347 0.769231
228 SAH 0.465347 0.779221
229 A3T 0.464646 0.835616
230 B1U 0.464286 0.747253
231 BT5 0.463415 0.821429
232 DZD 0.463415 0.85
233 A3N 0.463158 0.753247
234 ZAS 0.462366 0.779221
235 V47 0.461538 0.821918
236 S7M 0.461538 0.765432
237 2A5 0.46 0.833333
238 7D3 0.458333 0.820513
239 GJV 0.458333 0.740741
240 6MZ 0.458333 0.891892
241 D4F 0.456693 0.851852
242 ATR 0.455446 0.878378
243 NVA 2AD 0.455446 0.794872
244 NMN AMP PO4 0.455285 0.907895
245 7D4 0.454545 0.820513
246 EAD 0.453846 0.8625
247 UPA 0.453782 0.871795
248 4TC 0.453782 0.860759
249 DSH 0.452632 0.716049
250 A3G 0.452632 0.789474
251 5AD 0.452381 0.760563
252 P1H 0.451128 0.841463
253 O02 0.45098 0.8375
254 IMO 0.447917 0.864865
255 6IA 0.446602 0.804878
256 V3L 0.446602 0.931507
257 J4G 0.445455 0.907895
258 WSA 0.445378 0.77907
259 A7D 0.444444 0.766234
260 N01 0.444444 0.972222
261 A3S 0.444444 0.8
262 0UM 0.444444 0.753086
263 FB0 0.444444 0.775281
264 BTX 0.443548 0.809524
265 A2R 0.443396 0.918919
266 PPS 0.442308 0.795181
267 6AD 0.442308 0.85
268 COA FLC 0.44186 0.823529
269 SXZ 0.441441 0.765432
270 A5D 0.441176 0.776316
271 2AM 0.44086 0.853333
272 NWQ 0.44086 0.753425
273 62X 0.440367 0.717647
274 MHZ 0.44 0.689655
275 ITT 0.44 0.853333
276 2SA 0.438095 0.894737
277 K15 0.436364 0.73494
278 QXG 0.436364 0.727273
279 4YB 0.435897 0.772727
280 2VA 0.435644 0.813333
281 QXP 0.435185 0.735632
282 NAD BBN 0.432624 0.831325
283 NA0 0.431818 0.945946
284 Y3J 0.431818 0.716216
285 7D7 0.430233 0.733333
286 K3K 0.429825 0.769231
287 8Q2 0.429752 0.744444
288 KOY 0.428571 0.84
289 NAP 0.427481 0.932432
290 OVE 0.427083 0.820513
291 NAD CJ3 0.426573 0.802326
292 CNV FAD 0.424658 0.804598
293 AV2 0.424528 0.831169
294 NDP DTT 0.423358 0.831325
295 JSQ 0.423077 0.858974
296 HFD 0.423077 0.858974
297 SO8 0.423077 0.802632
298 N5O 0.42268 0.753247
299 K3E 0.422414 0.759494
300 FAD NBT 0.421769 0.76087
301 649 0.421488 0.736264
302 NHD 0.420635 0.918919
303 R2V 0.419643 0.735632
304 FAD T2C 0.418301 0.78022
305 FNK 0.416667 0.775281
306 AAT 0.415094 0.698795
307 C2R 0.414894 0.866667
308 AMZ 0.414894 0.853333
309 K2H 0.414414 0.746835
310 ARU 0.414414 0.804878
311 N5A 0.414141 0.727273
312 TAP 0.413534 0.871795
313 NJP 0.412698 0.907895
314 KB1 0.412281 0.731707
315 PGS 0.411765 0.825
316 A6D 0.410714 0.73494
317 NA7 0.410714 0.87013
318 NAD NDT 0.410596 0.736842
319 71V 0.41 0.825
320 6C6 0.409524 0.822785
321 VRT 0.409524 0.782051
322 0WD 0.409449 0.860759
323 DAT 0.407767 0.820513
324 CUU 0.407767 0.88
325 ETB 0.407692 0.802326
326 DCA 0.407692 0.793103
327 FAD NBA 0.407643 0.736842
328 BUA COA 0.407143 0.804598
329 FDA 0.407143 0.802326
330 ENQ 0.40708 0.930556
331 3NZ 0.40708 0.794872
332 K2K 0.40708 0.707317
333 NIA 0.40625 0.790123
334 DTP 0.40566 0.820513
335 3AT 0.40566 0.88
336 6FA 0.404255 0.831325
337 NO7 0.40367 0.846154
338 NFD 0.403101 0.896104
339 6NA COA 0.402778 0.786517
340 KYE 0.401709 0.72619
341 0T1 0.401515 0.793103
342 COA 0.401515 0.793103
343 FAD CNX 0.401316 0.736842
344 KH3 0.4 0.72619
345 5AD NJS 0.4 0.78022
346 D3Y 0.4 0.779221
347 PLP AAD 0.4 0.764045
348 KY2 0.4 0.702381
Similar Ligands (3D)
Ligand no: 1; Ligand: DAL AMP; Similar ligands found: 4
No: Ligand Similarity coefficient
1 GDP 0.9209
2 UDP 0.8905
3 GDP MG 0.8686
4 GCQ 0.8644
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
APoc FAQ
Feedback