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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 (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 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
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AMP DBH; Similar ligands found: 242
No: Ligand ECFP6 Tc MDL keys Tc
1 AMP DBH 1 1
2 ADP PO3 0.59596 0.917808
3 ALF ADP 0.588235 0.848101
4 ADP ALF 0.588235 0.848101
5 DAL AMP 0.586538 0.906667
6 GAP 0.584158 0.894737
7 A 0.580645 0.891892
8 AMP 0.580645 0.891892
9 VO4 ADP 0.567308 0.881579
10 ADP VO4 0.567308 0.881579
11 ABM 0.5625 0.868421
12 A2D 0.5625 0.918919
13 ADP 0.561224 0.893333
14 B5V 0.559633 0.933333
15 BA3 0.55102 0.918919
16 AP2 0.55102 0.858974
17 A12 0.55102 0.858974
18 AU1 0.55 0.87013
19 M33 0.55 0.881579
20 AP5 0.545455 0.918919
21 B4P 0.545455 0.918919
22 A A 0.545455 0.918919
23 TYR AMP 0.54386 0.921053
24 SRA 0.541667 0.846154
25 DLL 0.541284 0.906667
26 AT4 0.54 0.858974
27 AN2 0.54 0.881579
28 AR6 0.539216 0.918919
29 APR 0.539216 0.918919
30 OOB 0.537037 0.906667
31 ADP BMA 0.536364 0.945946
32 ADX 0.534653 0.807229
33 CA0 0.534653 0.894737
34 ADV 0.533981 0.883117
35 RBY 0.533981 0.883117
36 5AL 0.533333 0.881579
37 PAJ 0.53211 0.839506
38 HEJ 0.529412 0.893333
39 ATP 0.529412 0.893333
40 50T 0.529412 0.881579
41 ACP 0.529412 0.87013
42 AHX 0.527273 0.82716
43 FYA 0.526786 0.881579
44 B5M 0.526316 0.921053
45 FA5 0.526316 0.883117
46 ATP A A A 0.526316 0.931507
47 AF3 ADP 3PG 0.525 0.839506
48 PRX 0.524272 0.846154
49 AQP 0.524272 0.893333
50 5FA 0.524272 0.893333
51 APC 0.524272 0.858974
52 ANP 0.52381 0.87013
53 SRP 0.523364 0.858974
54 8QN 0.522936 0.881579
55 9ZD 0.522936 0.8375
56 9ZA 0.522936 0.8375
57 3UK 0.522523 0.92
58 MYR AMP 0.522124 0.819277
59 ARG AMP 0.521368 0.809524
60 AOC 0.520408 0.8
61 AGS 0.519231 0.848101
62 SAP 0.519231 0.848101
63 AD9 0.519231 0.87013
64 9SN 0.517544 0.873418
65 MAP 0.513761 0.848101
66 A3D 0.511811 0.894737
67 SON 0.509804 0.858974
68 ACQ 0.509434 0.87013
69 T99 0.509434 0.858974
70 TAT 0.509434 0.858974
71 AR6 AR6 0.508475 0.945205
72 NAD 0.507937 0.906667
73 4AD 0.504505 0.896104
74 AMO 0.504505 0.883117
75 WAQ 0.504425 0.8375
76 TXA 0.5 0.883117
77 LMS 0.5 0.764706
78 ATF 0.5 0.858974
79 PTJ 0.5 0.82716
80 1ZZ 0.5 0.797619
81 YAP 0.5 0.896104
82 NB8 0.5 0.85
83 LPA AMP 0.495868 0.819277
84 XAH 0.495726 0.776471
85 6YZ 0.495413 0.87013
86 LAD 0.491228 0.817073
87 TYM 0.487805 0.883117
88 AHZ 0.487603 0.841463
89 B5Y 0.487179 0.921053
90 8PZ 0.487179 0.761364
91 ME8 0.486957 0.797619
92 3OD 0.486957 0.894737
93 JB6 0.486957 0.8375
94 00A 0.486726 0.860759
95 TSB 0.486486 0.758621
96 A22 0.486486 0.906667
97 5AS 0.485437 0.722222
98 AMP NAD 0.484375 0.932432
99 OAD 0.482456 0.894737
100 9X8 0.482456 0.871795
101 5SV 0.482143 0.804878
102 25A 0.482143 0.893333
103 PR8 0.478261 0.807229
104 A3R 0.477876 0.8375
105 A1R 0.477876 0.8375
106 ADQ 0.477876 0.92
107 52H 0.477477 0.722222
108 LAQ 0.47541 0.797619
109 4TA 0.472868 0.809524
110 A5A 0.472727 0.747126
111 G5A 0.472222 0.722222
112 GA7 0.471074 0.883117
113 NAQ 0.470149 0.873418
114 SSA 0.468468 0.741573
115 DND 0.467742 0.933333
116 NXX 0.467742 0.933333
117 RAB 0.467391 0.821918
118 XYA 0.467391 0.821918
119 ADN 0.467391 0.821918
120 DQV 0.467213 0.906667
121 3DH 0.464646 0.753247
122 54H 0.464286 0.730337
123 VMS 0.464286 0.730337
124 NAJ PZO 0.462121 0.85
125 BIS 0.461538 0.8375
126 G A A A 0.461538 0.873418
127 NVA LMS 0.46087 0.717391
128 YLB 0.460317 0.77907
129 8X1 0.460177 0.698925
130 53H 0.460177 0.722222
131 5CA 0.460177 0.741573
132 48N 0.459677 0.85
133 YLP 0.459677 0.77907
134 AFH 0.459016 0.8625
135 7MD 0.459016 0.819277
136 YSA 0.458333 0.761364
137 25L 0.457627 0.906667
138 5N5 0.457447 0.797297
139 NDE 0.457143 0.907895
140 TAD 0.455285 0.817073
141 4UV 0.454545 0.871795
142 F2R 0.453846 0.8
143 IOT 0.453125 0.770115
144 GSU 0.452991 0.741573
145 P5A 0.452991 0.691489
146 A4D 0.452632 0.797297
147 5CD 0.452632 0.783784
148 Z5A 0.452555 0.781609
149 WSA 0.452381 0.75
150 DSZ 0.452174 0.761364
151 NSS 0.452174 0.761364
152 LSS 0.452174 0.706522
153 NAE 0.451852 0.896104
154 U A 0.451128 0.860759
155 A G 0.450382 0.884615
156 ADJ 0.449612 0.831325
157 YLA 0.449612 0.77907
158 YLC 0.448819 0.797619
159 AP0 0.448819 0.85
160 A3P 0.447619 0.866667
161 4UU 0.447154 0.871795
162 U A G G 0.44697 0.884615
163 BT5 0.44697 0.770115
164 CNA 0.446154 0.907895
165 ZID 0.445255 0.92
166 TXD 0.444444 0.860759
167 NAX 0.444444 0.829268
168 LEU LMS 0.444444 0.717391
169 A A A 0.444444 0.881579
170 4YB 0.443548 0.764045
171 GTA 0.443548 0.864198
172 A3N 0.442308 0.766234
173 J7C 0.442308 0.728395
174 649 0.440945 0.728261
175 TXE 0.440945 0.860759
176 KAA 0.440678 0.698925
177 COD 0.439394 0.752809
178 G3A 0.439024 0.873418
179 EP4 0.438776 0.734177
180 7MC 0.4375 0.8
181 8Q2 0.4375 0.755556
182 9K8 0.436975 0.736264
183 6RE 0.436893 0.740741
184 PAP 0.436364 0.88
185 G5P 0.435484 0.873418
186 AYB 0.435115 0.770115
187 DTA 0.434343 0.789474
188 M2T 0.434343 0.7375
189 A U 0.434109 0.871795
190 M24 0.433824 0.851852
191 UP5 0.433071 0.871795
192 PO4 PO4 A A A A PO4 0.432203 0.90411
193 3AM 0.431373 0.853333
194 5X8 0.431193 0.766234
195 MTA 0.43 0.753247
196 N01 0.42963 0.906667
197 BTX 0.428571 0.758621
198 SAM 0.428571 0.714286
199 NAJ PYZ 0.427536 0.809524
200 T5A 0.427481 0.8
201 4TC 0.426357 0.85
202 A7D 0.425926 0.75641
203 7D5 0.425743 0.807692
204 DZD 0.425373 0.839506
205 S4M 0.424528 0.670455
206 GJV 0.424528 0.731707
207 A5D 0.423423 0.789474
208 CNV FAD 0.422078 0.802326
209 4UW 0.421875 0.839506
210 6V0 0.421875 0.85
211 NAI 0.421875 0.860759
212 NDC 0.42069 0.873418
213 A2P 0.420561 0.853333
214 DSH 0.419048 0.707317
215 OMR 0.418605 0.809524
216 SMM 0.417391 0.709302
217 139 0.416667 0.829268
218 V3L 0.415929 0.893333
219 UPA 0.415385 0.860759
220 2A5 0.414414 0.822785
221 ZAS 0.413462 0.769231
222 YLY 0.413043 0.770115
223 PPS 0.412281 0.785714
224 A4P 0.412214 0.781609
225 6FA 0.412162 0.843373
226 7D3 0.411215 0.810127
227 ATR 0.410714 0.866667
228 FAD NBT 0.410256 0.752688
229 MHZ 0.409091 0.662921
230 A C A C 0.408759 0.85
231 NA0 0.408451 0.883117
232 MAO 0.407407 0.72093
233 NHD 0.407407 0.906667
234 SAH 0.40708 0.746835
235 6K6 0.40678 0.855263
236 SFG 0.405405 0.753247
237 7C5 0.404762 0.820513
238 N0B 0.404255 0.8
239 NAP 0.404255 0.894737
240 IMO 0.401869 0.853333
241 A2R 0.401709 0.906667
242 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: 106
This union binding pocket(no: 1) in the query (biounit: 1mdb.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1PTR PRB None
2 4AP3 NAP 1.2987
3 4AP3 FAD 1.2987
4 1GPM AMP 1.33333
5 6EGU 43Y 1.50659
6 1COY FAD 1.57791
7 1COY AND 1.57791
8 4B2G V1N 1.66976
9 3Q9T FAY 1.66976
10 1V6A TRE 1.80723
11 6F5W KG1 1.89702
12 3QVP FAD 2.04082
13 2XQ0 BES 2.04082
14 3LTW HLZ 2.14286
15 2IZ1 ATR 2.32068
16 2CUN 3PG 2.43902
17 3G5N PB2 2.52101
18 1VJ7 GPX 3.05344
19 1I9Z 2IP 3.17003
20 1RL4 BRR 3.19149
21 2QJT AMP 3.40909
22 3CV2 COA 3.57143
23 5JY4 ISC 3.58056
24 3UCL NAP 3.8961
25 3UCL CYH 3.8961
26 3UCL FAD 3.8961
27 4D04 FAD 3.8961
28 4D04 NAP 3.8961
29 1QDS PGA 3.98406
30 1KQF MGD 4.14747
31 4Z7X 3CX 4.20168
32 6ER9 NAP 4.26716
33 4DS0 A2G GAL NAG FUC 4.29448
34 3UOY NAP 4.45269
35 3UOY FAD 4.45269
36 2Z6J TUI 4.51807
37 3KP6 SAL 4.63576
38 1H0H MGD 4.6729
39 3ZOD HQE 4.71204
40 3ZOD FMN 4.71204
41 4RF7 ARG 4.82375
42 2HJR CIT 4.87805
43 5JIB OIA 5.04451
44 3CYQ AMU 5.07246
45 5C9P FUC 5.24934
46 1USF FMN 5.61798
47 4AIA ADK 5.85106
48 3E1T FAD 6.05469
49 1LOJ URI 6.89655
50 2Y4O DLL 6.99774
51 3W68 4PT 7.14286
52 6AA8 NAD 7.28477
53 1SOW OXL 7.31707
54 1H8P PC 7.33945
55 2PKA BEN 8.75
56 3IWD M2T 8.82353
57 3GD8 GOL 8.96861
58 5A9A UTP 9.46502
59 1WDI CIT 10.7246
60 5HM3 649 11.1317
61 5ABU GTG 11.4286
62 5EY9 5SV 11.6883
63 2WMC MGP 12.3596
64 4OXI GAP 12.8015
65 5YRJ BGC GLC 14.0845
66 5MST AMP 14.2857
67 5MST FUM 14.2857
68 5BXV MGP 16.6667
69 5T46 MGP 18.1818
70 3KXW 1ZZ 20.7792
71 3NYQ MCA 24.3564
72 3NYQ AMP 24.3564
73 4DG8 AMP 28.757
74 5MSD AMP 29.8701
75 5MSD BEZ 29.8701
76 3DHV DAL AMP 30.2734
77 5D6J ATP 31.7254
78 5OE4 3UK 34.6437
79 4GR5 APC 38.0334
80 1RY2 AMP 38.7755
81 3C5E ATP 39.5176
82 4D57 ARG AMP 39.5176
83 5N81 8Q2 39.5785
84 3E7W AMP 40.1174
85 2V7B BEZ 40.2646
86 4FUT ATP 40.3579
87 4R0M FA5 40.4453
88 5N9X ATP 40.4537
89 5N9X 8QN 40.4537
90 5N9X THR 40.4537
91 1PG4 COA 40.8163
92 1PG4 PRX 40.8163
93 1AMU AMP 41.0019
94 3IES M24 41.0019
95 4RLQ 3SK 41.0405
96 2D1S SLU 41.3729
97 4GXQ ATP 41.6996
98 5BSR COA 42.6716
99 5BSR AMP 42.6716
100 3CW9 AMP 44.246
101 3CW9 01A 44.246
102 5X8G S0N 45.1546
103 5IE3 AMP 45.9144
104 5IE3 OXD 45.9144
105 1V25 ANP 46.0111
106 5C5H 4YB 47.0199
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