Receptor
PDB id Resolution Class Description Source Keywords
1MDB 2.15 Å EC: 6.3.2.- CRYSTAL STRUCTURE OF DHBE IN COMPLEX WITH DHB-ADENYLATE BACILLUS SUBTILIS LIGASE ADENYLATION DOMAIN PEPTIDE SYNTHETASE ANTIBIOTIC BIOSYNTHESIS SIDEROPHORE FORMATION
Ref.: CRYSTAL STRUCTURE OF DHBE, AN ARCHETYPE FOR ARYL AC ACTIVATING DOMAINS OF MODULAR NONRIBOSOMAL PEPTIDE SYNTHETASES. PROC.NATL.ACAD.SCI.USA V. 99 12120 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AMP DBH A:600;
 Valid;
 none;
 submit data
484.338 n/a P(=O)...
SO4 A:997;
A:999;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1MDB 2.15 Å EC: 6.3.2.- CRYSTAL STRUCTURE OF DHBE IN COMPLEX WITH DHB-ADENYLATE BACILLUS SUBTILIS LIGASE ADENYLATION DOMAIN PEPTIDE SYNTHETASE ANTIBIOTIC BIOSYNTHESIS SIDEROPHORE FORMATION
Ref.: CRYSTAL STRUCTURE OF DHBE, AN ARCHETYPE FOR ARYL AC ACTIVATING DOMAINS OF MODULAR NONRIBOSOMAL PEPTIDE SYNTHETASES. PROC.NATL.ACAD.SCI.USA V. 99 12120 2002
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 41 families.
1 1MDB - AMP DBH n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 1MDB - AMP DBH n/a n/a
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 3O84 Kd = 58 nM HTJ C19 H14 N4 O2 c1ccc(cc1)....
2 3O83 - IXN C31 H43 N9 O8 S CCCCCCCCCC....
3 5WM2 - SAL C7 H6 O3 c1ccc(c(c1....
4 5WM3 - B5V C17 H18 N5 O9 P c1ccc(c(c1....
5 5WM7 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
6 5WM6 - OOB C17 H18 N5 O8 P c1ccc(cc1)....
7 5WM5 - B5Y C18 H20 N5 O9 P Cc1ccc(c(c....
8 5WM4 - B5M C18 H20 N5 O9 P Cc1cccc(c1....
9 1MDB - AMP DBH n/a n/a
10 6IYK Ki = 50 nM B1U C17 H17 N7 O9 S c1ccc(c(c1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: AMP DBH; Similar ligands found: 267
No: Ligand ECFP6 Tc MDL keys Tc
1 AMP DBH 1 1
2 ADP MG 0.621053 0.917808
3 ADP BEF 0.621053 0.917808
4 AMP MG 0.608696 0.930556
5 ATP MG 0.59596 0.917808
6 ADP PO3 0.59596 0.917808
7 BEF ADP 0.59 0.893333
8 ANP MG 0.588235 0.881579
9 ALF ADP 0.588235 0.848101
10 DAL AMP 0.586538 0.906667
11 GAP 0.584158 0.894737
12 AMP 0.580645 0.891892
13 A 0.580645 0.891892
14 VO4 ADP 0.572816 0.87013
15 A2D 0.5625 0.918919
16 ABM 0.5625 0.868421
17 45A 0.5625 0.868421
18 ADP 0.561224 0.893333
19 B5V 0.559633 0.933333
20 A12 0.55102 0.858974
21 AP2 0.55102 0.858974
22 BA3 0.55102 0.918919
23 AU1 0.55 0.87013
24 M33 0.55 0.881579
25 APC MG 0.54902 0.893333
26 AP5 0.545455 0.918919
27 B4P 0.545455 0.918919
28 SRA 0.541667 0.846154
29 DLL 0.541284 0.906667
30 AN2 0.54 0.881579
31 AT4 0.54 0.858974
32 APR 0.539216 0.918919
33 AR6 0.539216 0.918919
34 OOB 0.537037 0.906667
35 ADP BMA 0.536364 0.945946
36 ADX 0.534653 0.807229
37 CA0 0.534653 0.894737
38 ADV 0.533981 0.883117
39 RBY 0.533981 0.883117
40 5AL 0.533333 0.881579
41 PAJ 0.53211 0.839506
42 50T 0.529412 0.881579
43 HEJ 0.529412 0.893333
44 ACP 0.529412 0.87013
45 ATP 0.529412 0.893333
46 KG4 0.529412 0.894737
47 8LQ 0.527778 0.858974
48 AHX 0.527273 0.82716
49 FYA 0.526786 0.881579
50 B5M 0.526316 0.921053
51 ATP A A A 0.526316 0.931507
52 FA5 0.526316 0.883117
53 ATP A 0.526316 0.931507
54 AF3 ADP 3PG 0.525 0.839506
55 AQP 0.524272 0.893333
56 5FA 0.524272 0.893333
57 APC 0.524272 0.858974
58 PRX 0.524272 0.846154
59 ANP 0.52381 0.87013
60 8LH 0.523364 0.858974
61 SRP 0.523364 0.858974
62 9ZD 0.522936 0.8375
63 8QN 0.522936 0.881579
64 9ZA 0.522936 0.8375
65 3UK 0.522523 0.92
66 MYR AMP 0.522124 0.819277
67 ARG AMP 0.521368 0.809524
68 NAD TDB 0.520661 0.918919
69 NAD IBO 0.520661 0.918919
70 AOC 0.520408 0.8
71 AGS 0.519231 0.848101
72 AD9 0.519231 0.87013
73 V2G 0.518868 0.82716
74 8LE 0.518868 0.848101
75 9SN 0.517544 0.873418
76 MAP 0.513761 0.848101
77 QA7 0.513761 0.848101
78 JNT 0.513514 0.87013
79 ALF ADP 3PG 0.512397 0.839506
80 A3D 0.511811 0.894737
81 SON 0.509804 0.858974
82 ACQ 0.509434 0.87013
83 T99 0.509434 0.858974
84 TAT 0.509434 0.858974
85 AR6 AR6 0.508475 0.945205
86 NAD 0.507937 0.906667
87 AMO 0.504505 0.883117
88 4AD 0.504505 0.896104
89 WAQ 0.504425 0.8375
90 PTJ 0.5 0.82716
91 ATF 0.5 0.858974
92 1ZZ 0.5 0.797619
93 LMS 0.5 0.764706
94 TXA 0.5 0.883117
95 NB8 0.5 0.85
96 LPA AMP 0.495868 0.819277
97 XAH 0.495726 0.776471
98 6YZ 0.495413 0.87013
99 LAD 0.491228 0.817073
100 HQG 0.490909 0.906667
101 TYM 0.487805 0.883117
102 AHZ 0.487603 0.841463
103 B5Y 0.487179 0.921053
104 8PZ 0.487179 0.761364
105 JB6 0.486957 0.8375
106 ME8 0.486957 0.797619
107 3OD 0.486957 0.894737
108 00A 0.486726 0.860759
109 A22 0.486486 0.906667
110 TSB 0.486486 0.758621
111 5AS 0.485437 0.722222
112 AMP NAD 0.484375 0.932432
113 B1U 0.483051 0.73913
114 OAD 0.482456 0.894737
115 9X8 0.482456 0.871795
116 OZV 0.482143 0.893333
117 25A 0.482143 0.893333
118 5SV 0.482143 0.804878
119 PR8 0.478261 0.807229
120 A1R 0.477876 0.8375
121 ADQ 0.477876 0.92
122 A3R 0.477876 0.8375
123 52H 0.477477 0.722222
124 LAQ 0.47541 0.797619
125 4TA 0.472868 0.809524
126 A5A 0.472727 0.747126
127 G5A 0.472222 0.722222
128 H1Q 0.471698 0.88
129 GA7 0.471074 0.883117
130 NAQ 0.470149 0.873418
131 SSA 0.468468 0.741573
132 DND 0.467742 0.933333
133 XYA 0.467391 0.821918
134 RAB 0.467391 0.821918
135 ADN 0.467391 0.821918
136 DQV 0.467213 0.906667
137 3DH 0.464646 0.753247
138 VMS 0.464286 0.730337
139 54H 0.464286 0.730337
140 NAJ PZO 0.462121 0.85
141 BIS 0.461538 0.8375
142 NVA LMS 0.46087 0.717391
143 YLB 0.460317 0.77907
144 5CA 0.460177 0.741573
145 8X1 0.460177 0.698925
146 53H 0.460177 0.722222
147 YLP 0.459677 0.77907
148 48N 0.459677 0.85
149 7MD 0.459016 0.819277
150 AFH 0.459016 0.8625
151 YSA 0.458333 0.761364
152 25L 0.457627 0.906667
153 5N5 0.457447 0.797297
154 NDE 0.457143 0.907895
155 QXG 0.456897 0.758621
156 TAD 0.455285 0.817073
157 4UV 0.454545 0.871795
158 F2R 0.453846 0.8
159 IOT 0.453125 0.770115
160 GSU 0.452991 0.741573
161 P5A 0.452991 0.691489
162 5CD 0.452632 0.783784
163 A4D 0.452632 0.797297
164 Z5A 0.452555 0.781609
165 WSA 0.452381 0.75
166 LSS 0.452174 0.706522
167 DSZ 0.452174 0.761364
168 NSS 0.452174 0.761364
169 NAE 0.451852 0.896104
170 KMQ 0.45 0.883117
171 YLA 0.449612 0.77907
172 ADJ 0.449612 0.831325
173 AP0 0.448819 0.85
174 YLC 0.448819 0.797619
175 A3P 0.447619 0.866667
176 4UU 0.447154 0.871795
177 BT5 0.44697 0.770115
178 CNA 0.446154 0.907895
179 ZID 0.445255 0.92
180 TXD 0.444444 0.860759
181 NAX 0.444444 0.829268
182 GTA 0.443548 0.864198
183 4YB 0.443548 0.764045
184 QXP 0.443478 0.747126
185 J7C 0.442308 0.728395
186 A3N 0.442308 0.766234
187 TXE 0.440945 0.860759
188 649 0.440945 0.728261
189 KAA 0.440678 0.698925
190 COD 0.439394 0.752809
191 NAD BBN 0.439189 0.843373
192 G3A 0.439024 0.873418
193 EP4 0.438776 0.734177
194 8Q2 0.4375 0.755556
195 7MC 0.4375 0.8
196 9K8 0.436975 0.736264
197 6RE 0.436893 0.740741
198 PAP 0.436364 0.88
199 G5P 0.435484 0.873418
200 AYB 0.435115 0.770115
201 DTA 0.434343 0.789474
202 M2T 0.434343 0.7375
203 M24 0.433824 0.851852
204 NAD CJ3 0.433333 0.813953
205 UP5 0.433071 0.871795
206 PO4 PO4 A A A A PO4 0.432203 0.90411
207 LEU LMS 0.432203 0.752809
208 3AM 0.431373 0.853333
209 5X8 0.431193 0.766234
210 MTA 0.43 0.753247
211 N01 0.42963 0.906667
212 R2V 0.428571 0.747126
213 SAM 0.428571 0.714286
214 BTX 0.428571 0.758621
215 NAJ PYZ 0.427536 0.809524
216 T5A 0.427481 0.8
217 NAD NDT 0.426752 0.71134
218 4TC 0.426357 0.85
219 K3K 0.42623 0.828947
220 A7D 0.425926 0.75641
221 7D5 0.425743 0.807692
222 DZD 0.425373 0.839506
223 KOY 0.425197 0.853333
224 S4M 0.424528 0.670455
225 GJV 0.424528 0.731707
226 A5D 0.423423 0.789474
227 6V0 0.421875 0.85
228 4UW 0.421875 0.839506
229 NAI 0.421875 0.860759
230 NDC 0.42069 0.873418
231 A2P 0.420561 0.853333
232 O02 0.419643 0.82716
233 K3E 0.419355 0.818182
234 DSH 0.419048 0.707317
235 OMR 0.418605 0.809524
236 V47 0.417391 0.786667
237 SMM 0.417391 0.709302
238 139 0.416667 0.829268
239 V3L 0.415929 0.893333
240 L3W 0.415385 0.858974
241 UPA 0.415385 0.860759
242 2A5 0.414414 0.822785
243 ZAS 0.413462 0.769231
244 YLY 0.413043 0.770115
245 CNV FAD 0.412903 0.795455
246 PPS 0.412281 0.785714
247 A4P 0.412214 0.781609
248 6FA 0.412162 0.843373
249 7D3 0.411215 0.810127
250 6MZ 0.411215 0.855263
251 ATR 0.410714 0.866667
252 FAD NBT 0.410256 0.752688
253 D4F 0.410072 0.841463
254 MHZ 0.409091 0.662921
255 NA0 0.408451 0.883117
256 NHD 0.407407 0.906667
257 MAO 0.407407 0.72093
258 SAH 0.40708 0.746835
259 6K6 0.40678 0.855263
260 SFG 0.405405 0.753247
261 7C5 0.404762 0.820513
262 NAP 0.404255 0.894737
263 N0B 0.404255 0.8
264 DJ0 FAD 0.403409 0.816092
265 IMO 0.401869 0.853333
266 A2R 0.401709 0.906667
267 80F 0.40146 0.821429
Similar Ligands (3D)
Ligand no: 1; Ligand: AMP DBH; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1MDB; Ligand: AMP DBH; Similar sites found with APoc: 3
This union binding pocket(no: 1) in the query (biounit: 1mdb.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 6K4D D4F 43.0427
2 6K4D ESJ 43.0427
3 6IJB AMP 44.7124
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