-->
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
Ligand no: 1; Ligand: DAL AMP; Similar ligands found: 307
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 5AL 0.685393 0.972222
6 MYR AMP 0.677083 0.898734
7 ADP PO3 0.670455 0.957747
8 AMP 0.658537 0.90411
9 A 0.658537 0.90411
10 CA0 0.655172 0.932432
11 ABM 0.654762 0.905405
12 A2D 0.654762 0.905405
13 VO4 ADP 0.652174 0.918919
14 ADP VO4 0.652174 0.918919
15 8QN 0.648936 0.972222
16 4AD 0.642105 0.933333
17 ADP ALF 0.641304 0.883117
18 ALF ADP 0.641304 0.883117
19 AP2 0.639535 0.87013
20 BA3 0.639535 0.905405
21 A12 0.639535 0.87013
22 SRP 0.634409 0.92
23 B4P 0.632184 0.905405
24 AP5 0.632184 0.905405
25 ADP 0.632184 0.905405
26 9ZD 0.631579 0.921053
27 9ZA 0.631579 0.921053
28 PAJ 0.625 0.897436
29 LPA AMP 0.619048 0.875
30 M33 0.617977 0.918919
31 PTJ 0.616162 0.909091
32 AGS 0.615385 0.858974
33 SAP 0.615385 0.858974
34 SRA 0.611765 0.857143
35 50T 0.611111 0.868421
36 HEJ 0.611111 0.905405
37 ATP 0.611111 0.905405
38 AMO 0.608247 0.92
39 AT4 0.606742 0.87013
40 SON 0.606742 0.92
41 AN2 0.606742 0.893333
42 APC 0.604396 0.87013
43 PRX 0.604396 0.881579
44 AR6 0.604396 0.931507
45 AQP 0.604396 0.905405
46 APR 0.604396 0.931507
47 5FA 0.604396 0.905405
48 ADX 0.6 0.817073
49 TXA 0.6 0.945946
50 AU1 0.6 0.881579
51 ME8 0.6 0.875
52 AD9 0.597826 0.881579
53 RBY 0.597826 0.894737
54 ADV 0.597826 0.894737
55 ADP BMA 0.59596 0.932432
56 ACP 0.593407 0.881579
57 A A 0.59 0.905405
58 LAD 0.59 0.873418
59 AMP DBH 0.586538 0.906667
60 NB8 0.584158 0.884615
61 OOB 0.581633 0.945205
62 OAD 0.58 0.958904
63 9X8 0.58 0.907895
64 AHZ 0.579439 0.898734
65 AF3 ADP 3PG 0.577982 0.897436
66 00A 0.57 0.896104
67 DLL 0.57 0.945205
68 AHX 0.57 0.860759
69 3OD 0.568627 0.958904
70 1ZZ 0.568627 0.875
71 ANP 0.568421 0.881579
72 TAT 0.568421 0.87013
73 T99 0.568421 0.87013
74 ACQ 0.568421 0.881579
75 FA5 0.567308 0.92
76 YAP 0.567308 0.907895
77 ATP A A A 0.567308 0.944444
78 5SV 0.565657 0.8375
79 3UK 0.564356 0.932432
80 LMS 0.563218 0.795181
81 A1R 0.56 0.848101
82 PR8 0.558824 0.8625
83 WAQ 0.558824 0.896104
84 B5V 0.558824 0.92
85 9SN 0.557692 0.884615
86 ATF 0.556701 0.87013
87 A5A 0.556701 0.819277
88 AMP NAD 0.556522 0.972222
89 A22 0.555556 0.893333
90 TSB 0.555556 0.809524
91 B5Y 0.552381 0.933333
92 B5M 0.552381 0.933333
93 6YZ 0.55102 0.881579
94 AOC 0.550562 0.810811
95 NAQ 0.55 0.909091
96 LEU LMS 0.54902 0.784091
97 A3D 0.547009 0.958904
98 AR6 AR6 0.546296 0.958333
99 GA7 0.546296 0.87013
100 54H 0.545455 0.8
101 48N 0.545455 0.909091
102 YLP 0.545455 0.853659
103 VMS 0.545455 0.8
104 ADQ 0.544554 0.906667
105 A3R 0.544554 0.848101
106 5AS 0.543478 0.770115
107 NAD 0.543103 0.945205
108 G5A 0.541667 0.770115
109 MAP 0.54 0.858974
110 NVA LMS 0.539216 0.784091
111 25A 0.534653 0.905405
112 XAH 0.53271 0.829268
113 YLC 0.530973 0.875
114 YLB 0.530973 0.853659
115 RAB 0.530864 0.808219
116 XYA 0.530864 0.808219
117 ADN 0.530864 0.808219
118 5CD 0.53012 0.794521
119 52H 0.53 0.790698
120 LSS 0.529412 0.772727
121 NAJ PZO 0.529412 0.884615
122 NSS 0.529412 0.790698
123 NAE 0.528926 0.933333
124 4UV 0.527778 0.907895
125 TAD 0.527273 0.85
126 DQV 0.527273 0.918919
127 AYB 0.525862 0.843373
128 53H 0.524752 0.790698
129 FYA 0.52381 0.868421
130 JB6 0.52381 0.848101
131 LAQ 0.522523 0.851852
132 TYM 0.522124 0.92
133 F2R 0.521368 0.831325
134 ZID 0.520325 0.932432
135 SSA 0.52 0.770115
136 25L 0.518868 0.893333
137 7MD 0.518182 0.851852
138 4UU 0.518182 0.907895
139 AFH 0.518182 0.85
140 5N5 0.518072 0.783784
141 AP0 0.517544 0.860759
142 YLA 0.517241 0.831325
143 4TA 0.516949 0.864198
144 TXD 0.513274 0.871795
145 4UW 0.513274 0.897436
146 NAI 0.513274 0.871795
147 NAJ PYZ 0.512195 0.841463
148 A4D 0.511905 0.783784
149 EP4 0.511628 0.766234
150 5CA 0.509804 0.770115
151 9K8 0.509434 0.764045
152 BIS 0.509434 0.848101
153 TXE 0.508772 0.871795
154 OMR 0.508772 0.864198
155 M2T 0.505747 0.769231
156 DTA 0.505747 0.776316
157 3DH 0.505618 0.786667
158 7MC 0.504348 0.853659
159 COD 0.504202 0.802326
160 GTA 0.5 0.875
161 P5A 0.5 0.736264
162 DND 0.5 0.945946
163 DSZ 0.5 0.790698
164 NAX 0.5 0.839506
165 NXX 0.5 0.945946
166 6V0 0.5 0.860759
167 MTA 0.5 0.786667
168 NDE 0.496124 0.92
169 IOT 0.495726 0.821429
170 G3A 0.495495 0.860759
171 8X1 0.495146 0.744444
172 SFG 0.494845 0.786667
173 5X8 0.494845 0.8
174 U A 0.491803 0.896104
175 G A A A 0.491667 0.884615
176 T5A 0.491525 0.831325
177 G5P 0.491071 0.860759
178 SMM 0.490196 0.759036
179 SAM 0.49 0.765432
180 6RE 0.48913 0.75
181 NDC 0.48855 0.884615
182 CNA 0.487395 0.92
183 KAA 0.485981 0.744444
184 GSU 0.485981 0.790698
185 EEM 0.485149 0.765432
186 SA8 0.484848 0.7625
187 A3P 0.484211 0.90411
188 N0B 0.484127 0.831325
189 YLY 0.483871 0.843373
190 80F 0.483607 0.831325
191 A G 0.479339 0.896104
192 J7C 0.478723 0.7375
193 7D5 0.477778 0.818182
194 YSA 0.477477 0.770115
195 PO4 PO4 A A A A PO4 0.476636 0.916667
196 GEK 0.47619 0.794872
197 U A G G 0.47541 0.896104
198 A4P 0.474576 0.790698
199 UP5 0.474138 0.883117
200 S4M 0.473684 0.697674
201 M24 0.472 0.8625
202 PAP 0.47 0.891892
203 7C5 0.469027 0.831169
204 Z5A 0.46875 0.833333
205 MAO 0.46875 0.75
206 A2P 0.46875 0.890411
207 8PZ 0.468468 0.770115
208 NEC 0.468085 0.76
209 3AM 0.467391 0.864865
210 139 0.466667 0.839506
211 ADJ 0.466667 0.819277
212 SAH 0.465347 0.779221
213 SAI 0.465347 0.769231
214 A3T 0.464646 0.835616
215 DZD 0.463415 0.85
216 BT5 0.463415 0.821429
217 A3N 0.463158 0.753247
218 A A A 0.462963 0.918919
219 ZAS 0.462366 0.779221
220 S7M 0.461538 0.765432
221 2A5 0.46 0.833333
222 GJV 0.458333 0.740741
223 7D3 0.458333 0.820513
224 ATR 0.455446 0.878378
225 NVA 2AD 0.455446 0.794872
226 NMN AMP PO4 0.455285 0.907895
227 7D4 0.454545 0.820513
228 EAD 0.453846 0.8625
229 4TC 0.453782 0.860759
230 UPA 0.453782 0.871795
231 A3G 0.452632 0.789474
232 DSH 0.452632 0.716049
233 5AD 0.452381 0.760563
234 P1H 0.451128 0.841463
235 A U 0.45 0.907895
236 IMO 0.447917 0.864865
237 6IA 0.446602 0.804878
238 V3L 0.446602 0.931507
239 WSA 0.445378 0.77907
240 0UM 0.444444 0.753086
241 A7D 0.444444 0.766234
242 N01 0.444444 0.972222
243 FB0 0.444444 0.775281
244 A3S 0.444444 0.8
245 BTX 0.443548 0.809524
246 A2R 0.443396 0.918919
247 6AD 0.442308 0.85
248 PPS 0.442308 0.795181
249 SXZ 0.441441 0.765432
250 A5D 0.441176 0.776316
251 2AM 0.44086 0.853333
252 62X 0.440367 0.717647
253 MHZ 0.44 0.689655
254 ITT 0.44 0.853333
255 2SA 0.438095 0.894737
256 K15 0.436364 0.73494
257 4YB 0.435897 0.772727
258 2VA 0.435644 0.813333
259 CNV FAD 0.434483 0.833333
260 A C A C 0.433071 0.884615
261 NA0 0.431818 0.945946
262 Y3J 0.431818 0.716216
263 7D7 0.430233 0.733333
264 8Q2 0.429752 0.744444
265 NAP 0.427481 0.932432
266 OVE 0.427083 0.820513
267 AV2 0.424528 0.831169
268 HFD 0.423077 0.858974
269 SO8 0.423077 0.802632
270 U A C C 0.421875 0.896104
271 FAD NBT 0.421769 0.76087
272 649 0.421488 0.736264
273 NHD 0.420635 0.918919
274 FNK 0.416667 0.775281
275 AAT 0.415094 0.698795
276 AMZ 0.414894 0.853333
277 C2R 0.414894 0.866667
278 ARU 0.414414 0.804878
279 TAP 0.413534 0.871795
280 NJP 0.412698 0.907895
281 KB1 0.412281 0.731707
282 PGS 0.411765 0.825
283 A6D 0.410714 0.73494
284 NA7 0.410714 0.87013
285 U A A U 0.410448 0.896104
286 71V 0.41 0.825
287 VRT 0.409524 0.782051
288 6C6 0.409524 0.822785
289 0WD 0.409449 0.860759
290 DAT 0.407767 0.820513
291 DCA 0.407692 0.793103
292 ETB 0.407692 0.802326
293 FAD NBA 0.407643 0.736842
294 FDA 0.407143 0.802326
295 3NZ 0.40708 0.794872
296 ENQ 0.40708 0.930556
297 NIA 0.40625 0.790123
298 DTP 0.40566 0.820513
299 3AT 0.40566 0.88
300 6FA 0.404255 0.831325
301 NFD 0.403101 0.896104
302 0T1 0.401515 0.793103
303 COA 0.401515 0.793103
304 FAD CNX 0.401316 0.736842
305 D3Y 0.4 0.779221
306 KH3 0.4 0.72619
307 APC G U 0.4 0.848101
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: 75
This union binding pocket(no: 1) in the query (biounit: 3dhv.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 4B2G V1N 1.75781
2 1UC2 SUC 2.079
3 1ZGS XMM 2.23714
4 5H4S RAM 2.46479
5 4TS1 TYR 2.82132
6 1O9W NAG 2.82486
7 5FPE 3TR 2.84238
8 5KOD AMP 2.92969
9 6EGU 43Y 3.125
10 2YLN CYS 3.18021
11 3KU0 ADE 3.18725
12 3CF6 SP1 3.59281
13 4B2D SER 3.71094
14 4LEB THR THR THR THR THR THR THR 4.33333
15 5W5R PYR 4.54545
16 2IZ1 ATR 4.64135
17 4EPM AMP 5.85938
18 3KCC CMP 6.15385
19 5VKM GAL SIA 6.48148
20 2JC9 ADN 7.02703
21 3GCM 5GP 7.31707
22 5ZQS XYP 7.42188
23 1XFF GLU 7.5
24 2BVE PH5 8.40336
25 2IV3 UDP 9.64912
26 4OKE AMP 10.119
27 6FX2 FUC C4W NAG BMA MAN NAG GAL 13.9535
28 3ZZL TRP 14.2857
29 4NYT PC 14.7465
30 5LKC FUC GLA A2G 14.9351
31 1RY2 AMP 16.0156
32 1JQY A32 16.5049
33 2D1S SLU 22.8516
34 4FUT ATP 27.0378
35 4GXQ ATP 27.2727
36 5MST AMP 28.3203
37 5MST FUM 28.3203
38 3IES M24 28.7109
39 3O84 HTJ 29.4922
40 5MSD AMP 29.8828
41 5MSD BEZ 29.8828
42 1MDB AMP DBH 30.2734
43 2Y4O DLL 31.6027
44 1V25 ANP 31.8359
45 4R0M FA5 32.2266
46 4OXI GAP 35.7422
47 5HM3 649 35.7422
48 5C5H 4YB 35.9823
49 5IE3 AMP 36.9141
50 5IE3 OXD 36.9141
51 2V7B BEZ 38.8672
52 3KXW 1ZZ 39.2578
53 1PG4 PRX 39.6484
54 1PG4 COA 39.6484
55 4RLQ 3SK 39.8438
56 5EY9 5SV 40.2344
57 5BSR AMP 40.4297
58 5BSR COA 40.4297
59 5D6J ATP 40.4297
60 5OE4 3UK 40.5405
61 5X8G S0N 41.2371
62 5WM2 AMP 41.4062
63 5WM2 SAL 41.4062
64 3NYQ MCA 41.5842
65 3NYQ AMP 41.5842
66 3C5E ATP 41.6016
67 3CW9 AMP 41.6667
68 3CW9 01A 41.6667
69 4GR5 APC 42.7734
70 4DG8 AMP 44.3359
71 5N9X 8QN 45.5078
72 5N9X ATP 45.5078
73 5N9X THR 45.5078
74 5N81 8Q2 45.6674
75 1AMU AMP 48.6328
APoc FAQ
Feedback