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 36 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 24 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 = 0.099 uM 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
Ligand no: 1; Ligand: AMP DBH; Similar ligands found: 257
No: Ligand ECFP6 Tc MDL keys Tc
1 AMP DBH 1 1
2 ADP MG 0.621053 0.917808
3 ADP PO3 0.59596 0.917808
4 ATP MG 0.59596 0.917808
5 ADP ALF 0.588235 0.848101
6 ALF ADP 0.588235 0.848101
7 DAL AMP 0.586538 0.906667
8 GAP 0.584158 0.894737
9 AMP 0.580645 0.891892
10 A 0.580645 0.891892
11 VO4 ADP 0.567308 0.881579
12 ADP VO4 0.567308 0.881579
13 ABM 0.5625 0.868421
14 45A 0.5625 0.868421
15 A2D 0.5625 0.918919
16 ADP 0.561224 0.893333
17 B5V 0.559633 0.933333
18 BA3 0.55102 0.918919
19 A12 0.55102 0.858974
20 AP2 0.55102 0.858974
21 AU1 0.55 0.87013
22 M33 0.55 0.881579
23 APC MG 0.54902 0.893333
24 A A 0.545455 0.918919
25 AP5 0.545455 0.918919
26 B4P 0.545455 0.918919
27 TYR AMP 0.54386 0.921053
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 CA0 0.534653 0.894737
37 ADX 0.534653 0.807229
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 ACP 0.529412 0.87013
43 HEJ 0.529412 0.893333
44 KG4 0.529412 0.894737
45 ATP 0.529412 0.893333
46 50T 0.529412 0.881579
47 8LQ 0.527778 0.858974
48 AHX 0.527273 0.82716
49 FYA 0.526786 0.881579
50 FA5 0.526316 0.883117
51 B5M 0.526316 0.921053
52 ATP A A A 0.526316 0.931507
53 ATP A 0.526316 0.931507
54 AF3 ADP 3PG 0.525 0.839506
55 AQP 0.524272 0.893333
56 PRX 0.524272 0.846154
57 5FA 0.524272 0.893333
58 APC 0.524272 0.858974
59 ANP 0.52381 0.87013
60 8LH 0.523364 0.858974
61 SRP 0.523364 0.858974
62 9ZA 0.522936 0.8375
63 9ZD 0.522936 0.8375
64 8QN 0.522936 0.881579
65 3UK 0.522523 0.92
66 MYR AMP 0.522124 0.819277
67 ARG AMP 0.521368 0.809524
68 AOC 0.520408 0.8
69 AGS 0.519231 0.848101
70 SAP 0.519231 0.848101
71 AD9 0.519231 0.87013
72 8LE 0.518868 0.848101
73 9SN 0.517544 0.873418
74 MAP 0.513761 0.848101
75 A3D 0.511811 0.894737
76 SON 0.509804 0.858974
77 T99 0.509434 0.858974
78 TAT 0.509434 0.858974
79 ACQ 0.509434 0.87013
80 AR6 AR6 0.508475 0.945205
81 NAD 0.507937 0.906667
82 4AD 0.504505 0.896104
83 AMO 0.504505 0.883117
84 WAQ 0.504425 0.8375
85 TXA 0.5 0.883117
86 1ZZ 0.5 0.797619
87 LMS 0.5 0.764706
88 ATF 0.5 0.858974
89 NB8 0.5 0.85
90 PTJ 0.5 0.82716
91 YAP 0.5 0.896104
92 LPA AMP 0.495868 0.819277
93 XAH 0.495726 0.776471
94 6YZ 0.495413 0.87013
95 LAD 0.491228 0.817073
96 HQG 0.490909 0.906667
97 TYM 0.487805 0.883117
98 AHZ 0.487603 0.841463
99 8PZ 0.487179 0.761364
100 B5Y 0.487179 0.921053
101 3OD 0.486957 0.894737
102 JB6 0.486957 0.8375
103 ME8 0.486957 0.797619
104 00A 0.486726 0.860759
105 TSB 0.486486 0.758621
106 A22 0.486486 0.906667
107 5AS 0.485437 0.722222
108 AMP NAD 0.484375 0.932432
109 B1U 0.483051 0.73913
110 9X8 0.482456 0.871795
111 OAD 0.482456 0.894737
112 25A 0.482143 0.893333
113 OZV 0.482143 0.893333
114 5SV 0.482143 0.804878
115 PR8 0.478261 0.807229
116 A1R 0.477876 0.8375
117 A3R 0.477876 0.8375
118 ADQ 0.477876 0.92
119 52H 0.477477 0.722222
120 LAQ 0.47541 0.797619
121 4TA 0.472868 0.809524
122 A5A 0.472727 0.747126
123 G5A 0.472222 0.722222
124 H1Q 0.471698 0.88
125 GA7 0.471074 0.883117
126 NAQ 0.470149 0.873418
127 SSA 0.468468 0.741573
128 DND 0.467742 0.933333
129 NXX 0.467742 0.933333
130 XYA 0.467391 0.821918
131 ADN 0.467391 0.821918
132 RAB 0.467391 0.821918
133 DQV 0.467213 0.906667
134 3DH 0.464646 0.753247
135 VMS 0.464286 0.730337
136 54H 0.464286 0.730337
137 NAJ PZO 0.462121 0.85
138 G A A A 0.461538 0.873418
139 BIS 0.461538 0.8375
140 NVA LMS 0.46087 0.717391
141 YLB 0.460317 0.77907
142 5CA 0.460177 0.741573
143 8X1 0.460177 0.698925
144 53H 0.460177 0.722222
145 48N 0.459677 0.85
146 YLP 0.459677 0.77907
147 AFH 0.459016 0.8625
148 7MD 0.459016 0.819277
149 YSA 0.458333 0.761364
150 25L 0.457627 0.906667
151 5N5 0.457447 0.797297
152 NDE 0.457143 0.907895
153 TAD 0.455285 0.817073
154 4UV 0.454545 0.871795
155 F2R 0.453846 0.8
156 IOT 0.453125 0.770115
157 P5A 0.452991 0.691489
158 GSU 0.452991 0.741573
159 A4D 0.452632 0.797297
160 5CD 0.452632 0.783784
161 Z5A 0.452555 0.781609
162 WSA 0.452381 0.75
163 DSZ 0.452174 0.761364
164 LSS 0.452174 0.706522
165 NSS 0.452174 0.761364
166 NAE 0.451852 0.896104
167 U A 0.451128 0.860759
168 A G 0.450382 0.884615
169 YLA 0.449612 0.77907
170 ADJ 0.449612 0.831325
171 YLC 0.448819 0.797619
172 AP0 0.448819 0.85
173 A3P 0.447619 0.866667
174 4UU 0.447154 0.871795
175 BT5 0.44697 0.770115
176 U A G G 0.44697 0.884615
177 CNA 0.446154 0.907895
178 ZID 0.445255 0.92
179 TXD 0.444444 0.860759
180 LEU LMS 0.444444 0.717391
181 A A A 0.444444 0.881579
182 NAX 0.444444 0.829268
183 4YB 0.443548 0.764045
184 GTA 0.443548 0.864198
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 G3A 0.439024 0.873418
192 EP4 0.438776 0.734177
193 7MC 0.4375 0.8
194 8Q2 0.4375 0.755556
195 9K8 0.436975 0.736264
196 6RE 0.436893 0.740741
197 PAP 0.436364 0.88
198 G5P 0.435484 0.873418
199 AYB 0.435115 0.770115
200 DTA 0.434343 0.789474
201 M2T 0.434343 0.7375
202 A U 0.434109 0.871795
203 M24 0.433824 0.851852
204 UP5 0.433071 0.871795
205 PO4 PO4 A A A A PO4 0.432203 0.90411
206 3AM 0.431373 0.853333
207 5X8 0.431193 0.766234
208 MTA 0.43 0.753247
209 N01 0.42963 0.906667
210 SAM 0.428571 0.714286
211 BTX 0.428571 0.758621
212 NAJ PYZ 0.427536 0.809524
213 T5A 0.427481 0.8
214 4TC 0.426357 0.85
215 A7D 0.425926 0.75641
216 7D5 0.425743 0.807692
217 DZD 0.425373 0.839506
218 KOY 0.425197 0.853333
219 S4M 0.424528 0.670455
220 GJV 0.424528 0.731707
221 A5D 0.423423 0.789474
222 CNV FAD 0.422078 0.802326
223 NAI 0.421875 0.860759
224 4UW 0.421875 0.839506
225 6V0 0.421875 0.85
226 NDC 0.42069 0.873418
227 A2P 0.420561 0.853333
228 DSH 0.419048 0.707317
229 OMR 0.418605 0.809524
230 SMM 0.417391 0.709302
231 139 0.416667 0.829268
232 V3L 0.415929 0.893333
233 UPA 0.415385 0.860759
234 2A5 0.414414 0.822785
235 ZAS 0.413462 0.769231
236 YLY 0.413043 0.770115
237 PPS 0.412281 0.785714
238 A4P 0.412214 0.781609
239 6FA 0.412162 0.843373
240 6MZ 0.411215 0.855263
241 7D3 0.411215 0.810127
242 ATR 0.410714 0.866667
243 FAD NBT 0.410256 0.752688
244 MHZ 0.409091 0.662921
245 A C A C 0.408759 0.85
246 NA0 0.408451 0.883117
247 MAO 0.407407 0.72093
248 NHD 0.407407 0.906667
249 SAH 0.40708 0.746835
250 6K6 0.40678 0.855263
251 SFG 0.405405 0.753247
252 7C5 0.404762 0.820513
253 NAP 0.404255 0.894737
254 N0B 0.404255 0.8
255 IMO 0.401869 0.853333
256 A2R 0.401709 0.906667
257 80F 0.40146 0.821429
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: 1
This union binding pocket(no: 1) in the query (biounit: 1mdb.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 6IJB AMP 44.7124
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