Receptor
PDB id Resolution Class Description Source Keywords
6IYK 2.45 Å EC: 2.7.7.58 THE STRUCTURE OF ENTE WITH 2-NITROBENZOYL ADENYLATE ANALOG ESCHERICHIA COLI 1303 LIGASE ADENYLATION NON-RIBOSOMAL PEPTIDE BIOSYNTHESIS
Ref.: AN ENGINEERED ARYL ACID ADENYLATION DOMAIN WITH AN SUBSTRATE BINDING POCKET. ANGEW.CHEM.INT.ED.ENGL. V. 58 6906 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
B1U B:601;
A:601;
 Valid;
Valid;
 none;
none;
 Ki = 50 nM
495.423 C17 H17 N7 O9 S c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6IYK 2.45 Å EC: 2.7.7.58 THE STRUCTURE OF ENTE WITH 2-NITROBENZOYL ADENYLATE ANALOG ESCHERICHIA COLI 1303 LIGASE ADENYLATION NON-RIBOSOMAL PEPTIDE BIOSYNTHESIS
Ref.: AN ENGINEERED ARYL ACID ADENYLATION DOMAIN WITH AN SUBSTRATE BINDING POCKET. ANGEW.CHEM.INT.ED.ENGL. V. 58 6906 2019
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6IYK Ki = 50 nM B1U C17 H17 N7 O9 S c1ccc(c(c1....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6IYK Ki = 50 nM B1U C17 H17 N7 O9 S c1ccc(c(c1....
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: B1U; Similar ligands found: 228
No: Ligand ECFP6 Tc MDL keys Tc
1 B1U 1 1
2 G5A 0.645833 0.858696
3 A5A 0.626263 0.88764
4 8X1 0.623762 0.831579
5 TSB 0.623762 0.877778
6 SSA 0.62 0.858696
7 4YB 0.618182 0.880435
8 52H 0.613861 0.858696
9 VMS 0.613861 0.868132
10 54H 0.613861 0.868132
11 GSU 0.609524 0.858696
12 53H 0.607843 0.858696
13 5CA 0.607843 0.858696
14 NVA LMS 0.605769 0.851064
15 8PZ 0.601852 0.879121
16 5AS 0.6 0.83871
17 LSS 0.596154 0.840426
18 NSS 0.596154 0.879121
19 DSZ 0.596154 0.858696
20 KAA 0.59434 0.831579
21 P5A 0.59434 0.822917
22 LMS 0.586957 0.886364
23 YSA 0.581818 0.879121
24 QXP 0.556604 0.826087
25 WSA 0.555556 0.888889
26 649 0.555556 0.842105
27 SLU 0.536 0.869565
28 3UK 0.527273 0.777778
29 8Q2 0.525 0.851064
30 AMP MG 0.515464 0.741573
31 CA0 0.509804 0.73913
32 B5V 0.508929 0.769231
33 EU9 0.508333 0.787234
34 AMP 0.505155 0.733333
35 A 0.505155 0.733333
36 QXG 0.5 0.817204
37 LEU LMS 0.5 0.810526
38 SON 0.5 0.731183
39 ADX 0.495146 0.844444
40 AOC 0.494949 0.659341
41 DLL 0.491071 0.766667
42 KG4 0.490385 0.73913
43 ADP 0.490196 0.736264
44 A2D 0.49 0.755556
45 ABM 0.49 0.717391
46 45A 0.49 0.717391
47 OOB 0.486486 0.766667
48 GAP 0.485981 0.73913
49 ADP MG 0.485437 0.752809
50 ADP BEF 0.485437 0.752809
51 SRA 0.484848 0.758242
52 AMP DBH 0.483051 0.73913
53 9SN 0.482759 0.744681
54 8LE 0.481481 0.723404
55 V2G 0.481481 0.726316
56 APC MG 0.481132 0.736264
57 AU1 0.480769 0.758242
58 A12 0.480392 0.712766
59 BA3 0.480392 0.755556
60 AP2 0.480392 0.712766
61 5N5 0.478261 0.637363
62 QA7 0.477477 0.723404
63 B4P 0.475728 0.755556
64 AP5 0.475728 0.755556
65 KOY 0.47541 0.703297
66 A6D 0.473684 0.788889
67 9ZD 0.473214 0.734043
68 9ZA 0.473214 0.734043
69 5CD 0.473118 0.644444
70 RAB 0.472527 0.655556
71 ADN 0.472527 0.655556
72 XYA 0.472527 0.655556
73 AN2 0.471154 0.747253
74 AT4 0.471154 0.75
75 R2V 0.469565 0.806452
76 3DH 0.469388 0.641304
77 5AL 0.46789 0.747253
78 ATP MG 0.46729 0.752809
79 ADP PO3 0.46729 0.752809
80 M33 0.466667 0.728261
81 AHX 0.464912 0.763441
82 DAL AMP 0.464286 0.747253
83 A22 0.464286 0.747253
84 8LQ 0.464286 0.731183
85 ANP MG 0.463636 0.786517
86 BEF ADP 0.462963 0.736264
87 ATP 0.462264 0.736264
88 HEJ 0.462264 0.736264
89 50T 0.462264 0.709677
90 ACP 0.462264 0.72043
91 H1Q 0.462264 0.744444
92 5X8 0.462264 0.652174
93 IXN 0.459854 0.803922
94 NAX 0.459677 0.71134
95 8LH 0.459459 0.731183
96 SRP 0.459459 0.731183
97 V47 0.459459 0.666667
98 ANP 0.458716 0.758242
99 APR 0.457944 0.736264
100 APC 0.457944 0.712766
101 PRX 0.457944 0.702128
102 5FA 0.457944 0.736264
103 AR6 0.457944 0.736264
104 AQP 0.457944 0.736264
105 A4D 0.457447 0.655556
106 FA5 0.453782 0.75
107 B5M 0.453782 0.76087
108 AD9 0.453704 0.72043
109 AGS 0.453704 0.76087
110 RBY 0.453704 0.712766
111 ADV 0.453704 0.712766
112 DTA 0.453608 0.688889
113 TXA 0.452991 0.731183
114 9K8 0.452991 0.757576
115 FYA 0.452991 0.728261
116 00A 0.452174 0.734043
117 MAP 0.451327 0.741935
118 VO4 ADP 0.45045 0.73913
119 ALF ADP 0.45045 0.705263
120 ATF 0.45045 0.712766
121 OAD 0.448276 0.73913
122 8QN 0.447368 0.747253
123 25A 0.447368 0.755556
124 J7C 0.446602 0.625
125 ACQ 0.445455 0.72043
126 T99 0.445455 0.75
127 TAT 0.445455 0.75
128 TXE 0.444444 0.734043
129 WAQ 0.444444 0.715789
130 PR8 0.444444 0.693878
131 LAD 0.444444 0.701031
132 PAJ 0.443478 0.701031
133 AMO 0.443478 0.731183
134 4AD 0.443478 0.741935
135 EP4 0.443299 0.610526
136 GJV 0.442308 0.628866
137 NWW 0.442105 0.606742
138 B5Y 0.441667 0.76087
139 6RE 0.441176 0.635417
140 ME8 0.440678 0.704082
141 1ZZ 0.440678 0.686869
142 NB8 0.440678 0.763441
143 AR6 AR6 0.439024 0.755556
144 M2T 0.438776 0.648936
145 XAH 0.438017 0.739583
146 MYR AMP 0.436975 0.686869
147 NEC 0.436893 0.602151
148 ADP BMA 0.435897 0.73913
149 9X8 0.435897 0.741935
150 DQV 0.435484 0.766667
151 K3E 0.434426 0.659574
152 MTA 0.434343 0.641304
153 6YZ 0.433628 0.72043
154 S7M 0.433628 0.632653
155 A3N 0.432692 0.617021
156 ADQ 0.431034 0.73913
157 HQG 0.429825 0.728261
158 K3K 0.429752 0.666667
159 KMQ 0.429752 0.712766
160 NAD IBO 0.429688 0.775281
161 NAD TDB 0.429688 0.775281
162 3OD 0.428571 0.73913
163 PTJ 0.428571 0.708333
164 BIS 0.428571 0.697917
165 ARG AMP 0.427419 0.69697
166 A5D 0.427273 0.688889
167 6V0 0.425197 0.726316
168 DND 0.425197 0.769231
169 25L 0.425 0.747253
170 MAO 0.424528 0.673469
171 SAH 0.423423 0.638298
172 DSH 0.423077 0.608247
173 4UV 0.422764 0.741935
174 OZV 0.422414 0.736264
175 5SV 0.422414 0.673469
176 SFG 0.422018 0.623656
177 TYM 0.421875 0.75
178 SMM 0.421053 0.63
179 AHZ 0.420635 0.721649
180 LAQ 0.420635 0.721649
181 SAM 0.419643 0.632653
182 7C5 0.419355 0.717391
183 A1R 0.418803 0.697917
184 A3R 0.418803 0.697917
185 YLC 0.418605 0.686869
186 ATP A 0.418033 0.764045
187 ATP A A A 0.418033 0.764045
188 ZAS 0.417476 0.692308
189 YLP 0.417323 0.673267
190 LPA AMP 0.417323 0.721649
191 JB6 0.416667 0.752688
192 CNA 0.416667 0.769231
193 7MD 0.416 0.704082
194 JNT 0.415254 0.72043
195 EO7 0.415094 0.847826
196 NAI 0.414062 0.734043
197 TXD 0.414062 0.734043
198 KY2 0.413793 0.6
199 F2R 0.413534 0.69
200 KXW 0.412698 0.612245
201 TAD 0.412698 0.71875
202 IOT 0.412214 0.683168
203 NAJ PZO 0.411765 0.744681
204 A2P 0.411215 0.722222
205 ALF ADP 3PG 0.410853 0.701031
206 OMR 0.410853 0.68
207 SAI 0.410714 0.614583
208 NAD 0.410448 0.786517
209 AMP NAD 0.410448 0.766667
210 GEK 0.410256 0.670213
211 A3G 0.409524 0.645161
212 N5O 0.409524 0.617021
213 3AM 0.407767 0.703297
214 YLB 0.407692 0.673267
215 V3L 0.40708 0.736264
216 KYB 0.40678 0.6
217 48N 0.40625 0.726316
218 SXZ 0.404959 0.616162
219 4UU 0.404762 0.741935
220 GA7 0.404762 0.712766
221 A3D 0.404412 0.777778
222 A7D 0.40367 0.645161
223 EEM 0.403509 0.6
224 KYE 0.403226 0.60396
225 UP5 0.403101 0.741935
226 ATR 0.401786 0.714286
227 KY5 0.401639 0.608247
228 AF3 ADP 3PG 0.4 0.701031
Similar Ligands (3D)
Ligand no: 1; Ligand: B1U; 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 : 6IYK; Ligand: B1U; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6iyk.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6IYK; Ligand: B1U; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 6iyk.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 6IJB AMP 31.7254
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