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 ACID 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+](...
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 ACID 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 34 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 23 families.
1 1MDB - AMP DBH n/a n/a
50% Homology Family (3)
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 1MDB - AMP DBH n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AMP DBH; Similar ligands found: 232
No: Ligand ECFP6 Tc MDL keys Tc
1 AMP DBH 1 1
2 ADP MG 0.614583 0.881579
3 BEF ADP 0.608247 0.858974
4 ADP BEF 0.608247 0.858974
5 AMP MG 0.602151 0.893333
6 ADP PO3 0.59596 0.917808
7 ATP MG 0.59 0.881579
8 ADP ALF 0.588235 0.848101
9 ALF ADP 0.588235 0.848101
10 GAP 0.584158 0.894737
11 ANP MG 0.582524 0.848101
12 A 0.580645 0.891892
13 AMP 0.580645 0.891892
14 DAL AMP 0.571429 0.906667
15 ADP VO4 0.567308 0.881579
16 VO4 ADP 0.567308 0.881579
17 A2D 0.5625 0.918919
18 ABM 0.5625 0.868421
19 ADP 0.561224 0.893333
20 AP2 0.55102 0.858974
21 BA3 0.55102 0.918919
22 A12 0.55102 0.858974
23 AU1 0.55 0.87013
24 M33 0.55 0.881579
25 TYR AMP 0.548673 0.933333
26 B4P 0.545455 0.918919
27 AP5 0.545455 0.918919
28 A A 0.545455 0.918919
29 SRA 0.541667 0.846154
30 DLL 0.541284 0.906667
31 AN2 0.54 0.881579
32 AR6 0.539216 0.918919
33 APR 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 ACP 0.529412 0.87013
43 ATP 0.529412 0.893333
44 50T 0.529412 0.881579
45 AHX 0.527273 0.82716
46 FYA 0.526786 0.881579
47 ATP A A A 0.526316 0.931507
48 FA5 0.526316 0.883117
49 AF3 ADP 3PG 0.525 0.839506
50 PRX 0.524272 0.846154
51 5FA 0.524272 0.893333
52 APC 0.524272 0.858974
53 AQP 0.524272 0.893333
54 ANP 0.52381 0.87013
55 SRP 0.523364 0.858974
56 8QN 0.522936 0.881579
57 3UK 0.522523 0.92
58 MYR AMP 0.522124 0.819277
59 AOC 0.520408 0.8
60 SAP 0.519231 0.848101
61 AGS 0.519231 0.848101
62 AD9 0.519231 0.87013
63 9SN 0.517544 0.873418
64 MAP 0.513761 0.848101
65 ARG AMP 0.512605 0.809524
66 ALF ADP 3PG 0.512397 0.839506
67 LA8 ALF 3PG 0.512397 0.839506
68 NAD IBO 0.512 0.871795
69 A3D 0.511811 0.894737
70 SON 0.509804 0.858974
71 ACQ 0.509434 0.87013
72 TAT 0.509434 0.858974
73 AR6 AR6 0.508475 0.945205
74 NAD 0.507937 0.906667
75 AMO 0.504505 0.883117
76 4AD 0.504505 0.896104
77 WAQ 0.504425 0.8375
78 TXA 0.5 0.883117
79 ATF 0.5 0.858974
80 PTJ 0.5 0.82716
81 YAP 0.5 0.896104
82 NB8 0.5 0.85
83 1ZZ 0.5 0.797619
84 LPA AMP 0.495868 0.819277
85 XAH 0.495726 0.776471
86 LAD 0.491228 0.817073
87 TYM 0.487805 0.883117
88 AHZ 0.487603 0.841463
89 JB6 0.486957 0.8375
90 ME8 0.486957 0.797619
91 3OD 0.486957 0.894737
92 00A 0.486726 0.860759
93 A22 0.486486 0.906667
94 TSB 0.486486 0.758621
95 5AS 0.485437 0.722222
96 OAD 0.482456 0.894737
97 5SV 0.482143 0.804878
98 25A 0.482143 0.893333
99 PR8 0.478261 0.807229
100 A1R 0.477876 0.8375
101 ADQ 0.477876 0.92
102 52H 0.477477 0.722222
103 LAQ 0.47541 0.797619
104 4TA 0.472868 0.809524
105 A5A 0.472727 0.747126
106 G5A 0.472222 0.722222
107 NAJ PYZ 0.470149 0.829268
108 NAQ 0.470149 0.873418
109 LEU LMS 0.469565 0.725275
110 SSA 0.468468 0.741573
111 DND 0.467742 0.933333
112 NXX 0.467742 0.933333
113 XYA 0.467391 0.821918
114 ADN 0.467391 0.821918
115 RAB 0.467391 0.821918
116 3DH 0.464646 0.753247
117 54H 0.464286 0.730337
118 VMS 0.464286 0.730337
119 NAJ PZO 0.462121 0.85
120 G A A A 0.461538 0.873418
121 BIS 0.461538 0.8375
122 NVA LMS 0.46087 0.725275
123 YLB 0.460317 0.77907
124 5CA 0.460177 0.741573
125 53H 0.460177 0.722222
126 YLP 0.459677 0.77907
127 48N 0.459677 0.85
128 AFH 0.459016 0.8625
129 7MD 0.459016 0.819277
130 YSA 0.458333 0.761364
131 25L 0.457627 0.906667
132 5N5 0.457447 0.797297
133 NDE 0.457143 0.907895
134 AMP NAD 0.455882 0.907895
135 TAD 0.455285 0.817073
136 4UV 0.454545 0.871795
137 IOT 0.453125 0.770115
138 P5A 0.452991 0.691489
139 GSU 0.452991 0.741573
140 5CD 0.452632 0.783784
141 A4D 0.452632 0.797297
142 Z5A 0.452555 0.781609
143 WSA 0.452381 0.75
144 NSS 0.452174 0.761364
145 DSZ 0.452174 0.761364
146 LSS 0.452174 0.706522
147 NAE 0.451852 0.896104
148 YLA 0.449612 0.77907
149 ADJ 0.449612 0.831325
150 AP0 0.448819 0.85
151 YLC 0.448819 0.797619
152 A3P 0.447619 0.866667
153 4UU 0.447154 0.871795
154 BT5 0.44697 0.770115
155 U A G G 0.44697 0.884615
156 CNA 0.446154 0.907895
157 ZID 0.445255 0.92
158 TXD 0.444444 0.860759
159 A A A 0.444444 0.881579
160 NAX 0.444444 0.829268
161 4YB 0.443548 0.764045
162 GTA 0.443548 0.864198
163 A3N 0.442308 0.766234
164 J7C 0.442308 0.728395
165 649 0.440945 0.728261
166 TXE 0.440945 0.860759
167 KAA 0.440678 0.698925
168 COD 0.439394 0.752809
169 NAD BBN 0.439189 0.843373
170 G3A 0.439024 0.873418
171 EP4 0.438776 0.734177
172 7MC 0.4375 0.8
173 6RE 0.436893 0.740741
174 PAP 0.436364 0.88
175 G5P 0.435484 0.873418
176 AYB 0.435115 0.770115
177 DTA 0.434343 0.789474
178 M2T 0.434343 0.7375
179 A U 0.434109 0.871795
180 M24 0.433824 0.851852
181 NAD CJ3 0.433333 0.813953
182 UP5 0.433071 0.871795
183 PO4 PO4 A A A A PO4 0.432203 0.90411
184 3AM 0.431373 0.853333
185 5X8 0.431193 0.766234
186 MTA 0.43 0.753247
187 N01 0.42963 0.906667
188 SAM 0.428571 0.714286
189 BTX 0.428571 0.758621
190 T5A 0.427481 0.8
191 NAD NDT 0.426752 0.71134
192 4TC 0.426357 0.85
193 A7D 0.425926 0.75641
194 7D5 0.425743 0.807692
195 DZD 0.425373 0.839506
196 S4M 0.424528 0.670455
197 GJV 0.424528 0.731707
198 A5D 0.423423 0.789474
199 NAI 0.421875 0.860759
200 6V0 0.421875 0.85
201 4UW 0.421875 0.839506
202 NDC 0.42069 0.873418
203 A2P 0.420561 0.853333
204 DSH 0.419048 0.707317
205 OMR 0.418605 0.809524
206 SMM 0.417391 0.709302
207 139 0.416667 0.829268
208 V3L 0.415929 0.893333
209 UPA 0.415385 0.860759
210 2A5 0.414414 0.822785
211 ZAS 0.413462 0.769231
212 YLY 0.413043 0.770115
213 CNV FAD 0.412903 0.795455
214 PPS 0.412281 0.785714
215 A4P 0.412214 0.781609
216 6FA 0.412162 0.843373
217 7D3 0.411215 0.810127
218 ATR 0.410714 0.866667
219 FAD NBT 0.410256 0.752688
220 U G A 0.409396 0.841463
221 MHZ 0.409091 0.662921
222 NA0 0.408451 0.883117
223 NHD 0.407407 0.906667
224 MAO 0.407407 0.72093
225 SAH 0.40708 0.746835
226 6K6 0.40678 0.855263
227 SFG 0.405405 0.753247
228 7C5 0.404762 0.820513
229 NAP 0.404255 0.894737
230 N0B 0.404255 0.8
231 IMO 0.401869 0.853333
232 A2R 0.401709 0.906667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1MDB; Ligand: AMP DBH; Similar sites found: 72
This union binding pocket(no: 1) in the query (biounit: 1mdb.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1PTR PRB 0.02155 0.40935 None
2 1GPM AMP 0.0185 0.41925 1.33333
3 4B2G V1N 0.000234 0.46543 1.66976
4 3Q9T FAY 0.01234 0.4094 1.66976
5 2IZ1 ATR 0.01701 0.41244 2.32068
6 1VJ7 GPX 0.02708 0.40033 3.05344
7 1I9Z 2IP 0.01178 0.42361 3.17003
8 1RL4 BRR 0.02362 0.40352 3.19149
9 3CV2 COA 0.005279 0.44303 3.57143
10 3UCL FAD 0.0251 0.41391 3.8961
11 3UCL NAP 0.0272 0.41391 3.8961
12 3UCL CYH 0.0251 0.41391 3.8961
13 1QDS PGA 0.01888 0.40023 3.98406
14 4DS0 A2G GAL NAG FUC 0.02914 0.41082 4.29448
15 3UOY NAP 0.04233 0.40387 4.45269
16 3UOY FAD 0.04233 0.40387 4.45269
17 2Z6J TUI 0.01349 0.40736 4.51807
18 3ZOD HQE 0.00701 0.40837 4.71204
19 3CYQ AMU 0.02013 0.40208 5.07246
20 4AIA ADK 0.0313 0.40411 5.85106
21 2Y4O DLL 0.0000002016 0.55747 6.99774
22 3W68 4PT 0.01476 0.40688 7.14286
23 1SOW OXL 0.01709 0.40737 7.31707
24 1H8P PC 0.003847 0.42935 7.33945
25 2PKA BEN 0.02774 0.40245 8.75
26 3IWD M2T 0.0184 0.41709 8.82353
27 2Y4N PAC 0.000002049 0.53797 9.83982
28 2Y4N DLL 0.00000006003 0.53113 9.83982
29 1WDI CIT 0.01431 0.41614 10.7246
30 5HM3 649 0.0000005468 0.49438 11.1317
31 5ABU GTG 0.02201 0.40814 11.4286
32 5EY9 5SV 0.000001581 0.5083 11.6883
33 2WMC MGP 0.0221 0.40772 12.3596
34 4OXI GAP 0.0000001459 0.59971 12.8015
35 5MST AMP 0.00000007974 0.61555 14.2857
36 5MST FUM 0.0000000719 0.56497 14.2857
37 5BXV MGP 0.02051 0.4115 16.6667
38 5T46 MGP 0.02909 0.40156 18.1818
39 3KXW 1ZZ 0.0000001589 0.61127 20.7792
40 3NYQ MCA 0.0000005687 0.59755 24.3564
41 3NYQ AMP 0.0000006271 0.59755 24.3564
42 4DG8 AMP 0.000009402 0.53873 28.757
43 5MSD BEZ 0.00000003924 0.62084 29.8701
44 5MSD AMP 0.00000002897 0.59846 29.8701
45 3DHV DAL AMP 0.00000006358 0.59974 30.2734
46 5D6J ATP 0.000001912 0.54278 31.7254
47 5OE4 3UK 0.00000003062 0.61159 34.6437
48 4GR5 APC 0.000001186 0.58706 38.0334
49 1RY2 AMP 0.0000001648 0.56106 38.7755
50 4D57 ARG AMP 0.00000004727 0.49334 39.5176
51 3E7W AMP 0.000121 0.49433 40.1174
52 2V7B BEZ 0.00001883 0.42341 40.2646
53 4FUT ATP 0.000002684 0.54324 40.3579
54 4R0M FA5 0.00000005146 0.63265 40.4453
55 5N9X ATP 0.000000064 0.59908 40.4537
56 5N9X 8QN 0.0000001301 0.57604 40.4537
57 5N9X THR 0.0005713 0.48234 40.4537
58 1PG4 COA 0.000003324 0.40343 40.8163
59 1PG4 PRX 0.000003324 0.40343 40.8163
60 3IES M24 0.00000001977 0.66687 41.0019
61 1AMU AMP 0.00000006673 0.63568 41.0019
62 4RLQ 3SK 0.0000006514 0.43709 41.0405
63 2D1S SLU 0.000000003196 0.69315 41.3729
64 4GXQ ATP 0.0000008419 0.55332 41.6996
65 5BSR COA 0.000000237 0.64813 42.6716
66 5BSR AMP 0.00000009748 0.64813 42.6716
67 3CW9 AMP 0.0000007788 0.57999 44.246
68 5X8G S0N 0.000001659 0.60091 45.1546
69 5IE3 OXD 0.00000001079 0.66735 45.9144
70 5IE3 AMP 0.00000001079 0.66735 45.9144
71 1V25 ANP 0.000000104 0.49164 46.0111
72 5C5H 4YB 0.0000005152 0.58896 47.0199
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