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+](...
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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: 285
No: Ligand ECFP6 Tc MDL keys Tc
1 DAL AMP 1 1
2 GAP 0.752941 0.958904
3 TYR AMP 0.744681 0.945946
4 ARG AMP 0.707071 0.864198
5 ADP MG 0.694118 0.918919
6 ADP BEF 0.686047 0.894737
7 BEF ADP 0.686047 0.894737
8 5AL 0.685393 0.972222
9 AMP MG 0.682927 0.905405
10 MYR AMP 0.677083 0.898734
11 ADP PO3 0.670455 0.957747
12 ATP MG 0.662921 0.918919
13 A 0.658537 0.90411
14 AMP 0.658537 0.90411
15 CA0 0.655172 0.932432
16 ABM 0.654762 0.905405
17 8QN 0.648936 0.972222
18 ALF ADP 0.641304 0.883117
19 ADP ALF 0.641304 0.883117
20 AP2 0.639535 0.87013
21 A12 0.639535 0.87013
22 A2D 0.635294 0.905405
23 VO4 ADP 0.634409 0.918919
24 ADP VO4 0.634409 0.918919
25 ANP MG 0.634409 0.883117
26 SRP 0.634409 0.92
27 ADP 0.632184 0.905405
28 PAJ 0.625 0.897436
29 BA3 0.62069 0.905405
30 M33 0.617977 0.918919
31 PTJ 0.616162 0.909091
32 B4P 0.613636 0.905405
33 AP5 0.613636 0.905405
34 ADP BMA 0.612245 0.932432
35 SRA 0.611765 0.857143
36 4AD 0.608247 0.933333
37 AMO 0.608247 0.92
38 ALF ADP 3PG 0.607477 0.897436
39 LA8 ALF 3PG 0.607477 0.897436
40 AN2 0.606742 0.893333
41 PRX 0.604396 0.881579
42 APC 0.604396 0.87013
43 LPA AMP 0.603774 0.875
44 TXA 0.6 0.945946
45 AU1 0.6 0.881579
46 ME8 0.6 0.875
47 ADX 0.6 0.817073
48 OOB 0.597938 0.945205
49 ADV 0.597826 0.894737
50 RBY 0.597826 0.894737
51 ACP 0.593407 0.881579
52 50T 0.593407 0.868421
53 ATP 0.593407 0.905405
54 LAD 0.59 0.873418
55 A A 0.59 0.905405
56 SON 0.588889 0.92
57 5FA 0.586957 0.905405
58 APR 0.586957 0.931507
59 AR6 0.586957 0.931507
60 AQP 0.586957 0.905405
61 00A 0.585859 0.896104
62 NB8 0.584158 0.884615
63 AGS 0.580645 0.858974
64 SAP 0.580645 0.858974
65 AD9 0.580645 0.881579
66 3UK 0.58 0.932432
67 AHZ 0.579439 0.898734
68 AF3 ADP 3PG 0.577982 0.897436
69 9SN 0.572816 0.884615
70 AMP DBH 0.571429 0.906667
71 AHX 0.57 0.860759
72 DLL 0.57 0.945205
73 1ZZ 0.568627 0.875
74 ACQ 0.568421 0.881579
75 TAT 0.568421 0.87013
76 ANP 0.568421 0.881579
77 FA5 0.567308 0.92
78 ATP A A A 0.567308 0.944444
79 YAP 0.567308 0.907895
80 OAD 0.564356 0.958904
81 NAD IBO 0.561404 0.933333
82 WAQ 0.558824 0.896104
83 PR8 0.558824 0.8625
84 A5A 0.556701 0.819277
85 ATF 0.556701 0.87013
86 TSB 0.555556 0.809524
87 3OD 0.553398 0.958904
88 5SV 0.55 0.8375
89 LEU LMS 0.54902 0.793103
90 AR6 AR6 0.546296 0.958333
91 YLP 0.545455 0.853659
92 54H 0.545455 0.8
93 VMS 0.545455 0.8
94 AMP NAD 0.545455 0.972603
95 A1R 0.544554 0.848101
96 5AS 0.543478 0.770115
97 A22 0.54 0.893333
98 MAP 0.54 0.858974
99 NVA LMS 0.539216 0.793103
100 TYM 0.535714 0.92
101 25A 0.534653 0.905405
102 AOC 0.533333 0.810811
103 XAH 0.53271 0.829268
104 48N 0.531532 0.909091
105 YLC 0.530973 0.875
106 YLB 0.530973 0.853659
107 XYA 0.530864 0.808219
108 ADN 0.530864 0.808219
109 RAB 0.530864 0.808219
110 5CD 0.53012 0.794521
111 52H 0.53 0.790698
112 ADQ 0.529412 0.906667
113 LSS 0.529412 0.772727
114 4UV 0.527778 0.907895
115 TAD 0.527273 0.85
116 G5A 0.525773 0.770115
117 53H 0.524752 0.790698
118 NAQ 0.52459 0.909091
119 JB6 0.52381 0.848101
120 FYA 0.52381 0.868421
121 A3D 0.521008 0.958904
122 SSA 0.52 0.770115
123 7MD 0.518182 0.851852
124 4UU 0.518182 0.907895
125 5N5 0.518072 0.783784
126 NAD 0.516949 0.945205
127 NAJ PZO 0.516667 0.884615
128 4UW 0.513274 0.897436
129 AYB 0.512821 0.843373
130 A4D 0.511905 0.783784
131 EP4 0.511628 0.766234
132 5CA 0.509804 0.770115
133 BIS 0.509434 0.848101
134 LAQ 0.508929 0.851852
135 M2T 0.505747 0.769231
136 DTA 0.505747 0.776316
137 3DH 0.505618 0.786667
138 SAM 0.50505 0.765432
139 SMM 0.504951 0.759036
140 25L 0.504673 0.893333
141 AP0 0.504348 0.860759
142 7MC 0.504348 0.853659
143 YLA 0.504274 0.831325
144 4TA 0.504202 0.864198
145 NAE 0.504065 0.933333
146 TXD 0.5 0.871795
147 NAI 0.5 0.871795
148 P5A 0.5 0.736264
149 GTA 0.5 0.875
150 MTA 0.5 0.786667
151 GSU 0.5 0.790698
152 NSS 0.5 0.790698
153 DSZ 0.5 0.790698
154 ZID 0.496 0.932432
155 IOT 0.495726 0.821429
156 OMR 0.495652 0.864198
157 TXE 0.495652 0.871795
158 5X8 0.494845 0.8
159 COD 0.491667 0.802326
160 G A A A 0.491667 0.884615
161 AFH 0.491071 0.85
162 S4M 0.489362 0.697674
163 6RE 0.48913 0.75
164 NAJ PYZ 0.488 0.8625
165 NXX 0.486957 0.945946
166 NAX 0.486957 0.839506
167 DND 0.486957 0.945946
168 6V0 0.486957 0.860759
169 KAA 0.485981 0.744444
170 EEM 0.485149 0.765432
171 SA8 0.484848 0.7625
172 NDE 0.484615 0.92
173 A3P 0.484211 0.90411
174 YLY 0.483871 0.843373
175 M24 0.483871 0.8625
176 G3A 0.482143 0.860759
177 Z5A 0.480315 0.833333
178 SFG 0.479592 0.786667
179 J7C 0.478723 0.7375
180 G5P 0.477876 0.860759
181 7D5 0.477778 0.818182
182 YSA 0.477477 0.770115
183 PO4 PO4 A A A A PO4 0.476636 0.916667
184 U A G G 0.47541 0.896104
185 DZD 0.47541 0.85
186 CNA 0.475 0.92
187 PAP 0.47 0.891892
188 A2P 0.46875 0.890411
189 MAO 0.46875 0.75
190 3AM 0.467391 0.864865
191 T5A 0.466667 0.831325
192 ADJ 0.466667 0.819277
193 NDC 0.466165 0.884615
194 SAI 0.465347 0.769231
195 SAH 0.465347 0.779221
196 DAL FAD PER 0.465278 0.865854
197 A3T 0.464646 0.835616
198 BT5 0.463415 0.821429
199 A3N 0.463158 0.753247
200 IMO 0.463158 0.864865
201 A A A 0.462963 0.918919
202 ZAS 0.462366 0.779221
203 GEK 0.462264 0.794872
204 A4P 0.462185 0.790698
205 UP5 0.461538 0.883117
206 S7M 0.461538 0.765432
207 N0B 0.460938 0.831325
208 2A5 0.46 0.833333
209 7D3 0.458333 0.820513
210 GJV 0.458333 0.740741
211 WSA 0.457627 0.77907
212 ATR 0.455446 0.878378
213 139 0.454545 0.839506
214 4TC 0.453782 0.860759
215 UPA 0.453782 0.871795
216 A3G 0.452632 0.789474
217 DSH 0.452632 0.716049
218 NEC 0.452632 0.76
219 5AD 0.452381 0.760563
220 A U 0.45 0.907895
221 V3L 0.446602 0.931507
222 6IA 0.446602 0.804878
223 0UM 0.444444 0.753086
224 A7D 0.444444 0.766234
225 N01 0.444444 0.972222
226 A3S 0.444444 0.8
227 NMN AMP PO4 0.443548 0.907895
228 7C5 0.443478 0.831169
229 EAD 0.442748 0.8625
230 6AD 0.442308 0.85
231 PPS 0.442308 0.795181
232 OVE 0.442105 0.820513
233 SXZ 0.441441 0.765432
234 2AM 0.44086 0.853333
235 62X 0.440367 0.717647
236 P1H 0.440298 0.841463
237 MHZ 0.44 0.689655
238 7D4 0.44 0.820513
239 AV2 0.438095 0.831169
240 2SA 0.438095 0.894737
241 K15 0.436364 0.73494
242 4YB 0.435897 0.772727
243 2VA 0.435644 0.813333
244 FB0 0.433824 0.775281
245 NAD BBN 0.432624 0.831325
246 BTX 0.432 0.809524
247 Y3J 0.431818 0.716216
248 A2R 0.429907 0.918919
249 A5D 0.427184 0.776316
250 NVA 2AD 0.427184 0.779221
251 NAD CJ3 0.426573 0.802326
252 ITT 0.425743 0.853333
253 CNV FAD 0.424658 0.804598
254 SO8 0.423077 0.802632
255 U A C C 0.421875 0.896104
256 FAD NBT 0.421769 0.76087
257 649 0.421488 0.736264
258 U G A 0.421429 0.851852
259 AAT 0.415094 0.698795
260 C2R 0.414894 0.866667
261 AMZ 0.414894 0.853333
262 ARU 0.414414 0.804878
263 PLP AAD 0.414062 0.772727
264 7D7 0.413793 0.733333
265 KB1 0.412281 0.731707
266 PGS 0.411765 0.825
267 A6D 0.410714 0.73494
268 NAD NDT 0.410596 0.736842
269 NA0 0.410448 0.945946
270 U A A U 0.410448 0.896104
271 71V 0.41 0.825
272 6C6 0.409524 0.822785
273 VRT 0.409524 0.782051
274 DAT 0.407767 0.820513
275 3NZ 0.40708 0.794872
276 ENQ 0.40708 0.930556
277 FNK 0.406897 0.775281
278 NIA 0.40625 0.790123
279 NAP 0.406015 0.932432
280 AAM 0.40404 0.90411
281 NAD TDB 0.402597 0.686275
282 NJP 0.401575 0.907895
283 FAD CNX 0.401316 0.736842
284 KH3 0.4 0.72619
285 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: 52
This union binding pocket(no: 1) in the query (biounit: 3dhv.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4B2G V1N 0.0005981 0.44393 1.75781
2 5KOD AMP 0.0001427 0.4416 2.92969
3 2YLN CYS 0.01504 0.41963 3.18021
4 3KU0 ADE 0.03056 0.40486 3.18725
5 2IZ1 ATR 0.01923 0.41019 4.64135
6 4EPM AMP 0.0003092 0.44071 5.85938
7 3GCM 5GP 0.0295 0.41238 7.31707
8 1XFF GLU 0.01026 0.4108 7.5
9 2BVE PH5 0.02411 0.42228 8.40336
10 2Y4N DLL 0.0000001304 0.61246 9.38215
11 2Y4N PAC 0.000002653 0.54003 9.38215
12 4NYT PC 0.02971 0.41369 14.7465
13 5LKC FUC GLA A2G 0.0227 0.41588 14.9351
14 1RY2 AMP 0.0000000121 0.59352 16.0156
15 2D1S SLU 0.000000024 0.64656 22.8516
16 4FUT ATP 0.00000006257 0.59894 27.0378
17 4GXQ ATP 0.00000004741 0.61288 27.2727
18 5MST FUM 0.000000006462 0.65813 28.3203
19 5MST AMP 0.000000001361 0.65619 28.3203
20 3IES M24 0.0000002514 0.61027 28.7109
21 3O84 HTJ 0.00002223 0.47145 29.4922
22 5MSD BEZ 0.000000004257 0.64718 29.8828
23 5MSD AMP 0.000000002174 0.6267 29.8828
24 1MDB AMP DBH 0.00000006358 0.59974 30.2734
25 2Y4O DLL 0.0000002924 0.58539 31.6027
26 1V25 ANP 0.00000004069 0.50626 31.8359
27 4R0M FA5 0.00000002371 0.6395 32.2266
28 4OXI GAP 0.00000000001278 0.76164 35.7422
29 5HM3 649 0.0000001478 0.51674 35.7422
30 5C5H 4YB 0.0000005079 0.58253 35.9823
31 5IE3 OXD 0.0000000003033 0.72624 36.9141
32 5IE3 AMP 0.0000000003033 0.72624 36.9141
33 3KXW 1ZZ 0.0000001163 0.60994 39.2578
34 1PG4 PRX 0.00000002483 0.4572 39.6484
35 1PG4 COA 0.00000002483 0.4572 39.6484
36 4RLQ 3SK 0.0000006411 0.45032 39.8438
37 5EY9 5SV 0.0000006205 0.52801 40.2344
38 5BSR AMP 0.0000006673 0.6031 40.4297
39 5BSR COA 0.000001576 0.60274 40.4297
40 5D6J ATP 0.0000005588 0.55335 40.4297
41 5OE4 3UK 0.000000057 0.60954 40.5405
42 5X8G S0N 0.00000003677 0.6708 41.2371
43 3NYQ AMP 0.00000006159 0.6352 41.5842
44 3NYQ MCA 0.00000005682 0.63466 41.5842
45 3C5E ATP 0.00000000524 0.44428 41.6016
46 3CW9 AMP 0.00000001225 0.66281 41.6667
47 4GR5 APC 0.00000001214 0.68217 42.7734
48 4DG8 AMP 0.00000008626 0.56723 44.3359
49 5N9X 8QN 0.0000000001892 0.71642 45.5078
50 5N9X ATP 0.0000000005329 0.69412 45.5078
51 5N9X THR 0.0000006259 0.44118 45.5078
52 1AMU AMP 0.000000000009744 0.71098 48.6328
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