Receptor
PDB id Resolution Class Description Source Keywords
6XI9 2.14 Å EC: 2.5.1.120 X-RAY CRYSTAL STRUCTURE OF MQNE FROM PEDOBACTER HEPARINUS IN WITH AMINOFUTALOSINE AND METHIONINE PEDOBACTER HEPARINUS (STRAIN ATCC 13122366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NR14731 / HIM 762-3) IRON-SULFUR CLUSTER RADICAL SAM MENAQUINONE BIOSYNTHESIS BIOSYNTHETIC PROTEIN
Ref.: NARROW-SPECTRUM ANTIBIOTIC TARGETING OF THE RADICAL ENZYME MQNE IN MENAQUINONE BIOSYNTHESIS. BIOCHEMISTRY V. 59 2562 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SF4 A:401;
B:401;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
351.64 Fe4 S4 [S]12...
V47 A:403;
B:403;
 Valid;
Valid;
 none;
none;
 submit data
413.384 C19 H19 N5 O6 c1cc(...
CL A:404;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6XI9 2.14 Å EC: 2.5.1.120 X-RAY CRYSTAL STRUCTURE OF MQNE FROM PEDOBACTER HEPARINUS IN WITH AMINOFUTALOSINE AND METHIONINE PEDOBACTER HEPARINUS (STRAIN ATCC 13122366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NR14731 / HIM 762-3) IRON-SULFUR CLUSTER RADICAL SAM MENAQUINONE BIOSYNTHESIS BIOSYNTHETIC PROTEIN
Ref.: NARROW-SPECTRUM ANTIBIOTIC TARGETING OF THE RADICAL ENZYME MQNE IN MENAQUINONE BIOSYNTHESIS. BIOCHEMISTRY V. 59 2562 2020
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6XI9 - V47 C19 H19 N5 O6 c1cc(cc(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 6XI9 - V47 C19 H19 N5 O6 c1cc(cc(c1....
50% 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 6XI9 - V47 C19 H19 N5 O6 c1cc(cc(c1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: V47; Similar ligands found: 234
No: Ligand ECFP6 Tc MDL keys Tc
1 V47 1 1
2 5CD 0.5625 0.876923
3 6RE 0.551724 0.794521
4 GJV 0.550562 0.783784
5 XYA 0.544304 0.863636
6 ADN 0.544304 0.863636
7 RAB 0.544304 0.863636
8 J7C 0.539326 0.805556
9 5N5 0.530864 0.863636
10 A4D 0.52439 0.863636
11 EP4 0.52381 0.814286
12 DTA 0.517647 0.852941
13 AOC 0.511111 0.838235
14 R2V 0.509615 0.731707
15 M2T 0.5 0.791667
16 SON 0.5 0.8
17 SA8 0.494845 0.833333
18 MTA 0.494253 0.838235
19 5X8 0.489583 0.880597
20 SFG 0.489583 0.923077
21 KG4 0.489583 0.810811
22 A3N 0.48913 0.826087
23 AMP 0.488889 0.780822
24 A 0.488889 0.780822
25 LMS 0.488889 0.707317
26 NWW 0.488095 0.857143
27 F0P 0.486957 0.885714
28 KB1 0.485981 0.847222
29 OOB 0.485437 0.847222
30 QXP 0.485437 0.731707
31 GAP 0.484848 0.810811
32 AMP MG 0.483516 0.791667
33 3DH 0.483146 0.838235
34 EEM 0.48 0.810811
35 CA0 0.479167 0.810811
36 DSH 0.478261 0.805556
37 SAI 0.474747 0.869565
38 SAH 0.474747 0.882353
39 OZP 0.473684 0.885714
40 KOY 0.473684 0.925373
41 ABM 0.473118 0.76
42 45A 0.473118 0.76
43 A2D 0.473118 0.808219
44 ZAS 0.472527 0.802817
45 A6D 0.471698 0.753247
46 DND 0.469565 0.824324
47 4YB 0.469027 0.729412
48 AN2 0.46875 0.773333
49 S4M 0.468085 0.734177
50 SRA 0.467391 0.74026
51 8LE 0.465347 0.789474
52 V2G 0.465347 0.769231
53 A5D 0.464646 0.852941
54 5AD 0.463415 0.84127
55 AP2 0.463158 0.753247
56 MAO 0.463158 0.725
57 A12 0.463158 0.753247
58 BA3 0.463158 0.808219
59 DAL AMP 0.461538 0.821918
60 G5A 0.46 0.686047
61 B1U 0.459459 0.666667
62 H1Q 0.459184 0.77027
63 AP5 0.458333 0.808219
64 B4P 0.458333 0.808219
65 5AS 0.458333 0.666667
66 ADP 0.458333 0.783784
67 K15 0.457944 0.8
68 3UK 0.457944 0.835616
69 QXG 0.457944 0.722892
70 S7M 0.456311 0.810811
71 DQV 0.45614 0.821918
72 SAM 0.455446 0.810811
73 9SN 0.454545 0.792208
74 B5V 0.453704 0.824324
75 WAQ 0.453704 0.802632
76 AT4 0.453608 0.753247
77 ADP MG 0.453608 0.805556
78 ADP BEF 0.453608 0.805556
79 N37 0.452991 0.925373
80 5AL 0.45098 0.821918
81 8PZ 0.45045 0.705882
82 AGS 0.45 0.74359
83 APC MG 0.45 0.783784
84 9K8 0.449541 0.701149
85 M33 0.44898 0.773333
86 ADX 0.44898 0.707317
87 MHZ 0.44898 0.725
88 AU1 0.44898 0.763158
89 00A 0.448598 0.802632
90 62X 0.448598 0.779221
91 DLL 0.448598 0.847222
92 5CA 0.447619 0.686047
93 8LQ 0.447619 0.8
94 8X1 0.447619 0.681818
95 NEC 0.446809 0.808824
96 A3G 0.446809 0.84058
97 A5A 0.446602 0.710843
98 3AM 0.445652 0.743243
99 EU9 0.444444 0.775
100 HEJ 0.444444 0.783784
101 ATP 0.444444 0.783784
102 ACP 0.444444 0.763158
103 50T 0.444444 0.75
104 KXW 0.443478 0.859155
105 8QN 0.443396 0.821918
106 SMM 0.442308 0.779221
107 SSA 0.442308 0.686047
108 SRP 0.442308 0.8
109 8LH 0.442308 0.8
110 ANP 0.441176 0.763158
111 7D7 0.440476 0.779412
112 KAA 0.440367 0.681818
113 LAD 0.440367 0.782051
114 GSU 0.440367 0.72619
115 APC 0.44 0.753247
116 AQP 0.44 0.783784
117 AR6 0.44 0.808219
118 5FA 0.44 0.783784
119 PRX 0.44 0.763158
120 APR 0.44 0.808219
121 PAJ 0.439252 0.759494
122 DSZ 0.439252 0.705882
123 0UM 0.439252 0.821918
124 AMO 0.439252 0.8
125 4AD 0.439252 0.789474
126 AMP NAD 0.439024 0.847222
127 A7D 0.438776 0.84058
128 52H 0.438095 0.686047
129 VMS 0.438095 0.694118
130 54H 0.438095 0.694118
131 B5M 0.4375 0.813333
132 NAD TDB 0.436975 0.833333
133 NAD IBO 0.436975 0.833333
134 AAT 0.436893 0.783784
135 JB6 0.436364 0.779221
136 1ZZ 0.436364 0.7625
137 RBY 0.435644 0.776316
138 ADV 0.435644 0.776316
139 AD9 0.435644 0.763158
140 ATP MG 0.435644 0.805556
141 ADP PO3 0.435644 0.805556
142 NVA LMS 0.435185 0.681818
143 NWQ 0.434783 0.830769
144 53H 0.433962 0.686047
145 TSB 0.433962 0.702381
146 QA7 0.433962 0.789474
147 KYE 0.433628 0.789474
148 A3P 0.43299 0.780822
149 ATF 0.432692 0.753247
150 ALF ADP 0.432692 0.74359
151 MYR AMP 0.432432 0.7625
152 KY5 0.432432 0.830986
153 N5O 0.431579 0.826087
154 BEF ADP 0.431373 0.783784
155 A3T 0.43 0.865672
156 9ZA 0.429907 0.779221
157 9ZD 0.429907 0.779221
158 GEK 0.429907 0.871429
159 PR8 0.427273 0.772152
160 P5A 0.427273 0.674157
161 TAT 0.427184 0.753247
162 T99 0.427184 0.753247
163 ACQ 0.427184 0.763158
164 LSS 0.425926 0.670455
165 NSS 0.425926 0.686047
166 KYB 0.425926 0.763158
167 Y3J 0.425287 0.815385
168 FA5 0.424779 0.824324
169 B5Y 0.424779 0.813333
170 A3S 0.424242 0.852941
171 PTJ 0.423423 0.769231
172 3OD 0.423423 0.810811
173 TXA 0.423423 0.8
174 SXZ 0.423423 0.835616
175 N5A 0.42268 0.823529
176 AHX 0.422018 0.746835
177 K2H 0.422018 0.816901
178 XAH 0.421053 0.740741
179 YSA 0.421053 0.705882
180 KY2 0.420561 0.763158
181 MAP 0.420561 0.74359
182 A22 0.420561 0.797297
183 2AM 0.419355 0.733333
184 VO4 ADP 0.419048 0.763158
185 ANP MG 0.419048 0.773333
186 KH3 0.418803 0.789474
187 LEU LMS 0.418182 0.678161
188 OAD 0.418182 0.810811
189 AMP DBH 0.417391 0.786667
190 WSA 0.416667 0.714286
191 OZV 0.416667 0.783784
192 TYM 0.416667 0.824324
193 Q2P 0.416 0.813333
194 2VA 0.415842 0.84058
195 LAQ 0.415254 0.7625
196 6YZ 0.415094 0.763158
197 KY8 0.414414 0.808219
198 7C5 0.413793 0.859155
199 Q2M 0.413223 0.810811
200 8Q2 0.413223 0.681818
201 L3W 0.413223 0.776316
202 Q34 0.413223 0.813333
203 DZD 0.412698 0.759494
204 LPA AMP 0.411765 0.7625
205 HQG 0.411215 0.797297
206 M24 0.410853 0.772152
207 FYA 0.410714 0.773333
208 ME8 0.410714 0.7625
209 NB8 0.410714 0.769231
210 7MD 0.410256 0.7625
211 NAI 0.408333 0.779221
212 NAX 0.408333 0.772152
213 NVA 2AD 0.407767 0.819444
214 PAP 0.407767 0.77027
215 D3Y 0.407407 0.855072
216 9X8 0.405405 0.766234
217 649 0.404959 0.693182
218 NAD 0.404762 0.821918
219 SO8 0.403846 0.828571
220 25A 0.40367 0.808219
221 5SV 0.40367 0.725
222 HZ2 0.403361 0.835616
223 YLA 0.403226 0.743902
224 Q2V 0.403226 0.847222
225 YLB 0.401639 0.743902
226 YLP 0.4 0.743902
227 CNA 0.4 0.8
228 ATP A A A 0.4 0.819444
229 K3K 0.4 0.816901
230 U4Y 0.4 0.898551
231 A3R 0.4 0.734177
232 ADQ 0.4 0.810811
233 A1R 0.4 0.734177
234 ATP A 0.4 0.819444
Similar Ligands (3D)
Ligand no: 1; Ligand: V47; 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 : 6XI9; Ligand: V47; 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: 6xi9.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6XI9; Ligand: V47; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 6xi9.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
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