Receptor
PDB id Resolution Class Description Source Keywords
6MFW 2.5 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF A 4-DOMAIN CONSTRUCT OF LGRA IN THE SUB DONATION STATE BREVIBACILLUS PARABREVIS NONRIBOSOMAL PEPTIDE SYNTHETASE TAILORING DOMAIN NRPS ENZNATURAL PRODUCT LINEAR GRAMICIDIN LIGASE
Ref.: STRUCTURES OF A DIMODULAR NONRIBOSOMAL PEPTIDE SYNT REVEAL CONFORMATIONAL FLEXIBILITY. SCIENCE V. 366 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:1305;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
VAL A:1304;
Valid;
none;
submit data
117.146 C5 H11 N O2 CC(C)...
FON A:1302;
Valid;
none;
submit data
473.439 C20 H23 N7 O7 c1cc(...
APC MG A:1303;
Valid;
none;
submit data
501.178 n/a [P+](...
MG A:1306;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
JQG A:1301;
Invalid;
none;
submit data
467.431 C17 H32 N4 O9 P CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6MFX 2.2 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF A 4-DOMAIN CONSTRUCT OF A MUTANT OF LGR SUBSTRATE DONATION STATE BREVIBACILLUS PARABREVIS NONRIBOSOMAL PEPTIDE SYNTHETASE TAILORING DOMAIN NRPS ENZNATURAL PRODUCT LINEAR GRAMICIDIN LIGASE
Ref.: STRUCTURES OF A DIMODULAR NONRIBOSOMAL PEPTIDE SYNT REVEAL CONFORMATIONAL FLEXIBILITY. SCIENCE V. 366 2019
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 311 families.
1 6MFW - VAL C5 H11 N O2 CC(C)[C@@H....
2 6MFX - VAL C5 H11 N O2 CC(C)[C@@H....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 families.
1 6MFW - VAL C5 H11 N O2 CC(C)[C@@H....
2 6MFX - VAL C5 H11 N O2 CC(C)[C@@H....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 218 families.
1 6MFW - VAL C5 H11 N O2 CC(C)[C@@H....
2 6MFX - VAL C5 H11 N O2 CC(C)[C@@H....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: VAL; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 VAL 1 1
2 ALO 0.65 0.714286
3 THR 0.65 0.714286
4 DAL 0.611111 0.882353
5 ALA 0.611111 0.882353
6 ILE 0.565217 0.727273
7 HGY 0.473684 0.608696
8 AKB 0.454545 0.681818
9 DBB 0.454545 0.681818
10 ABA 0.454545 0.681818
11 LEU 0.44 0.772727
12 CDV 0.407407 0.607143
Ligand no: 2; Ligand: FON; Similar ligands found: 23
No: Ligand ECFP6 Tc MDL keys Tc
1 FOZ 1 1
2 FON 1 1
3 FFO 0.683168 1
4 TLL 0.663551 0.931507
5 C2F 0.550459 0.957747
6 THF 0.536364 0.943662
7 MHF 0.535714 0.881579
8 DHF 0.523364 0.926471
9 THG 0.518182 0.926471
10 1YJ 0.518182 0.926471
11 THH 0.486726 0.8
12 DDF 0.469027 0.847222
13 21V 0.469027 0.847222
14 FGD 0.463636 0.785714
15 GUE 0.461538 0.917808
16 FOL 0.447368 0.802817
17 DZF 0.447368 0.788732
18 TMF 0.428571 0.866667
19 9L9 0.420561 0.855072
20 LYA 0.415929 0.72973
21 MEF 0.413223 0.881579
22 1YA 0.413223 0.970588
23 83A 0.40678 0.77027
Ligand no: 3; Ligand: APC MG ; Similar ligands found: 331
No: Ligand ECFP6 Tc MDL keys Tc
1 APC MG 1 1
2 ADP MG 0.74359 0.971429
3 AMP 0.72 0.916667
4 A 0.72 0.916667
5 BA3 0.717949 0.917808
6 A2D 0.714286 0.917808
7 ADP 0.708861 0.917808
8 B4P 0.708861 0.917808
9 AP5 0.708861 0.917808
10 ATP MG 0.707317 0.971429
11 ADP PO3 0.707317 0.971429
12 A12 0.696203 0.932432
13 AP2 0.696203 0.932432
14 45A 0.692308 0.891892
15 ABM 0.692308 0.891892
16 ATP 0.682927 0.917808
17 HEJ 0.682927 0.917808
18 ACP 0.682927 0.918919
19 AN2 0.679012 0.905405
20 AT4 0.679012 0.881579
21 5FA 0.674699 0.917808
22 APC 0.674699 0.932432
23 AQP 0.674699 0.917808
24 ADX 0.670732 0.82716
25 M33 0.670732 0.905405
26 ACQ 0.670588 0.918919
27 SRA 0.666667 0.868421
28 AGS 0.666667 0.87013
29 SAP 0.666667 0.87013
30 ALF ADP 0.655172 0.894737
31 ADP ALF 0.655172 0.894737
32 AR6 0.654762 0.917808
33 APR 0.654762 0.917808
34 GAP 0.651163 0.918919
35 AU1 0.650602 0.893333
36 CA0 0.650602 0.893333
37 6YZ 0.647727 0.918919
38 ADP VO4 0.647727 0.931507
39 VO4 ADP 0.647727 0.931507
40 AD9 0.647059 0.893333
41 ADV 0.647059 0.932432
42 RBY 0.647059 0.932432
43 KG4 0.642857 0.893333
44 50T 0.642857 0.88
45 PRX 0.635294 0.868421
46 TAT 0.632184 0.881579
47 ANP 0.632184 0.893333
48 T99 0.632184 0.881579
49 ATF 0.617977 0.881579
50 DAL AMP 0.615385 0.931507
51 LMS 0.6125 0.804878
52 OZV 0.608696 0.917808
53 5AL 0.606742 0.905405
54 8LE 0.606742 0.87013
55 ADP BMA 0.606383 0.918919
56 HQG 0.604396 0.905405
57 A3R 0.602151 0.883117
58 SON 0.6 0.906667
59 MAP 0.597826 0.87013
60 A22 0.597826 0.905405
61 SRP 0.593407 0.881579
62 8LH 0.593407 0.881579
63 ATP A A A 0.591837 0.957747
64 ATP A 0.591837 0.957747
65 OOB 0.591398 0.905405
66 MYR AMP 0.587629 0.8625
67 ADQ 0.585106 0.893333
68 A1R 0.585106 0.883117
69 4AD 0.585106 0.894737
70 A A 0.583333 0.917808
71 ADN 0.581081 0.819444
72 XYA 0.581081 0.819444
73 RAB 0.581081 0.819444
74 8LQ 0.580645 0.881579
75 00A 0.578947 0.858974
76 AOC 0.578313 0.821918
77 5SV 0.574468 0.848101
78 25A 0.574468 0.917808
79 8QN 0.574468 0.905405
80 9ZD 0.574468 0.858974
81 9ZA 0.574468 0.858974
82 9X8 0.572917 0.87013
83 OAD 0.572917 0.893333
84 AHZ 0.572816 0.839506
85 25L 0.571429 0.905405
86 5AS 0.569767 0.758621
87 M2T 0.56962 0.75641
88 AR6 AR6 0.568627 0.944444
89 PAJ 0.568421 0.8375
90 AMO 0.568421 0.881579
91 H1Q 0.568182 0.90411
92 WAQ 0.56701 0.883117
93 5N5 0.565789 0.794521
94 DLL 0.5625 0.905405
95 AHX 0.5625 0.848101
96 NB8 0.561224 0.848101
97 1ZZ 0.561224 0.839506
98 BIS 0.561224 0.858974
99 3OD 0.561224 0.893333
100 A4D 0.558442 0.794521
101 5CD 0.558442 0.805556
102 3UK 0.556701 0.893333
103 GA7 0.553398 0.857143
104 LAD 0.55102 0.860759
105 B5V 0.55102 0.881579
106 PR8 0.55102 0.85
107 TYR AMP 0.54902 0.894737
108 AMP DBH 0.54902 0.893333
109 JB6 0.545455 0.858974
110 ME8 0.545455 0.817073
111 PTJ 0.545455 0.848101
112 TXA 0.545455 0.881579
113 FYA 0.545455 0.88
114 G3A 0.543689 0.848101
115 ARG AMP 0.538462 0.829268
116 7MD 0.538462 0.817073
117 G5P 0.538462 0.848101
118 LPA AMP 0.537736 0.8625
119 EP4 0.5375 0.753247
120 7D5 0.536585 0.853333
121 9SN 0.534653 0.848101
122 TAD 0.533333 0.884615
123 GTA 0.533333 0.839506
124 UP5 0.53271 0.87013
125 G5A 0.532609 0.758621
126 DTA 0.530864 0.810811
127 3DH 0.53012 0.773333
128 B5Y 0.529412 0.87013
129 B5M 0.529412 0.87013
130 FA5 0.529412 0.881579
131 YAP 0.529412 0.87013
132 GJV 0.528736 0.75
133 7D3 0.528736 0.855263
134 AF3 ADP 3PG 0.527778 0.860759
135 MTA 0.52439 0.773333
136 XAH 0.524272 0.839506
137 AFH 0.52381 0.8375
138 4TC 0.522936 0.871795
139 A3P 0.522727 0.916667
140 7D4 0.522222 0.855263
141 PAP 0.521739 0.90411
142 4UV 0.519231 0.87013
143 DQV 0.518868 0.905405
144 NAX 0.518519 0.82716
145 A5A 0.515789 0.785714
146 TSB 0.515464 0.776471
147 8X1 0.515464 0.733333
148 LAQ 0.514019 0.839506
149 OMR 0.513761 0.829268
150 F2R 0.513274 0.797619
151 6RE 0.511628 0.759494
152 S4M 0.511364 0.705882
153 2A5 0.51087 0.844156
154 SSA 0.510417 0.758621
155 4UU 0.509434 0.87013
156 48N 0.509259 0.848101
157 7MC 0.509091 0.797619
158 T5A 0.508929 0.819277
159 4TA 0.508772 0.851852
160 AMP NAD 0.508772 0.931507
161 3AM 0.505882 0.876712
162 A2P 0.505618 0.902778
163 ITT 0.505495 0.864865
164 ATR 0.505376 0.890411
165 54H 0.505155 0.767442
166 52H 0.505155 0.758621
167 VMS 0.505155 0.767442
168 P5A 0.504951 0.744444
169 DND 0.504587 0.906667
170 TXD 0.504587 0.858974
171 NXX 0.504587 0.906667
172 6V0 0.504587 0.848101
173 NAI 0.504587 0.858974
174 A4P 0.504505 0.77907
175 5CA 0.5 0.758621
176 J7C 0.5 0.746835
177 IMO 0.5 0.876712
178 ZAS 0.5 0.789474
179 TXE 0.5 0.858974
180 A3N 0.5 0.763158
181 53H 0.5 0.758621
182 NAD 0.495652 0.931507
183 ADJ 0.495575 0.829268
184 AP0 0.495495 0.848101
185 YLP 0.495413 0.819277
186 PO4 PO4 A A A A PO4 0.49505 0.929577
187 DZD 0.491379 0.884615
188 CNA 0.491228 0.906667
189 4UW 0.490909 0.8375
190 DSZ 0.49 0.758621
191 LSS 0.49 0.741573
192 NSS 0.49 0.77907
193 PPS 0.489583 0.804878
194 MAO 0.488889 0.759036
195 DSH 0.488636 0.746835
196 A3D 0.487179 0.918919
197 TYM 0.486486 0.881579
198 9K8 0.485437 0.714286
199 NVA LMS 0.485149 0.752809
200 AV2 0.484536 0.842105
201 JSQ 0.484211 0.87013
202 HFD 0.484211 0.87013
203 5X8 0.483871 0.763158
204 SFG 0.483871 0.773333
205 NAJ PZO 0.483051 0.871795
206 G A A A 0.482759 0.871795
207 139 0.482456 0.85
208 UPA 0.482143 0.858974
209 YLB 0.482143 0.819277
210 YLC 0.482143 0.839506
211 B1U 0.481132 0.736264
212 LEU LMS 0.480392 0.752809
213 NAJ PYZ 0.479339 0.829268
214 SAM 0.479167 0.731707
215 V3L 0.479167 0.917808
216 6MZ 0.477778 0.878378
217 2AM 0.476744 0.864865
218 KAA 0.475728 0.752809
219 GSU 0.475728 0.758621
220 M24 0.475 0.82716
221 A2R 0.474747 0.905405
222 5AD 0.474359 0.746479
223 6AD 0.474227 0.8375
224 IOT 0.473684 0.809524
225 7C5 0.472222 0.794872
226 Z5A 0.471545 0.821429
227 NAE 0.471074 0.894737
228 U A 0.470588 0.883117
229 COD 0.470085 0.790698
230 A G 0.470085 0.883117
231 YLA 0.469565 0.819277
232 YSA 0.46729 0.758621
233 NAQ 0.467213 0.871795
234 U A G G 0.466102 0.883117
235 BT5 0.466102 0.809524
236 A A A 0.466019 0.958333
237 AYB 0.465517 0.809524
238 SMM 0.464646 0.72619
239 ZID 0.463415 0.918919
240 A7D 0.462366 0.8
241 80F 0.462185 0.797619
242 OVE 0.460674 0.831169
243 WSA 0.460177 0.767442
244 AAT 0.459184 0.728395
245 SA8 0.458333 0.728395
246 8PZ 0.457944 0.758621
247 BTX 0.457627 0.819277
248 MHZ 0.457447 0.697674
249 71V 0.456522 0.835443
250 NEC 0.455556 0.723684
251 A3G 0.455556 0.776316
252 SAI 0.453608 0.75641
253 SAH 0.453608 0.766234
254 A U 0.452174 0.894737
255 Y3J 0.451219 0.726027
256 GEK 0.45098 0.782051
257 S7M 0.45 0.731707
258 7D7 0.45 0.767123
259 3AT 0.44898 0.891892
260 APC G U 0.446281 0.883117
261 NO7 0.445545 0.857143
262 EEM 0.444444 0.731707
263 A5D 0.443299 0.810811
264 NDE 0.44186 0.906667
265 N0B 0.44 0.819277
266 N5O 0.43956 0.74026
267 YLY 0.439024 0.809524
268 6C6 0.438776 0.857143
269 NIA 0.438202 0.8
270 NA7 0.438095 0.906667
271 A6D 0.438095 0.765432
272 DAT 0.4375 0.855263
273 4YB 0.4375 0.741573
274 AVV 0.436893 0.871795
275 NDC 0.435115 0.896104
276 649 0.434783 0.744444
277 6IA 0.434343 0.792683
278 DTP 0.434343 0.855263
279 J4G 0.433962 0.87013
280 EAD 0.433071 0.82716
281 0UM 0.432692 0.719512
282 AMZ 0.431818 0.84
283 C2R 0.431818 0.828947
284 A3S 0.431579 0.786667
285 8Q2 0.431034 0.733333
286 N5A 0.430108 0.714286
287 KOY 0.429825 0.802632
288 ARU 0.428571 0.792683
289 GGZ 0.427184 0.780488
290 PGS 0.427083 0.835443
291 2SA 0.425743 0.857143
292 D5M 0.423913 0.853333
293 DA 0.423913 0.853333
294 6K6 0.423077 0.878378
295 SLU 0.422764 0.75
296 A3T 0.42268 0.797297
297 P1H 0.419847 0.807229
298 7RA 0.419355 0.90411
299 AAM 0.419355 0.916667
300 RGT 0.418182 0.881579
301 62X 0.415094 0.686047
302 EO7 0.414894 0.767442
303 LQJ 0.414414 0.891892
304 128 0.413793 0.735632
305 FB0 0.413534 0.784091
306 TM1 0.412844 0.752941
307 3AD 0.411765 0.805556
308 A C A C 0.41129 0.871795
309 N01 0.41129 0.931507
310 K15 0.411215 0.702381
311 V1N 0.410714 0.891892
312 NMN AMP PO4 0.409836 0.894737
313 S8M 0.409524 0.759494
314 SFD 0.408759 0.697917
315 FDA 0.407407 0.770115
316 62F 0.407143 0.817073
317 AIR 0.406977 0.849315
318 DDS 0.405941 0.828947
319 CNV FAD 0.405594 0.8
320 6FA 0.404412 0.797619
321 SXZ 0.40367 0.731707
322 FAD NBT 0.402778 0.731183
323 ACK 0.402174 0.835616
324 QQY 0.402174 0.792208
325 7DD 0.402062 0.90411
326 N6P 0.401869 0.863014
327 NJP 0.401639 0.894737
328 8BR 0.4 0.857143
329 U A C C 0.4 0.883117
330 KB1 0.4 0.719512
331 U A A U 0.4 0.883117
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6MFX; Ligand: APC; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 6mfx.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 6AKD A5A 42.3792
Pocket No.: 2; Query (leader) PDB : 6MFX; Ligand: VAL; 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: 6mfx.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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