Receptor
PDB id Resolution Class Description Source Keywords
5N82 1.71 Å EC: 5.1.1.11 CRYSTAL STRUCTURE OF AN ENGINEERED TYCA VARIANT IN COMPLEX W BETA-PHE-AMP ANALOG BREVIBACILLUS PARABREVIS NONRIBOSOMAL PEPTIDE SYNTHETASE ADENYLATION DOMAIN LIGASE
Ref.: NONRIBOSOMAL BIOSYNTHESIS OF BACKBONE-MODIFIED PEPT NAT CHEM V. 10 282 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:501;
 Invalid;
 none;
 submit data
96.063 O4 S [O-]S...
8PZ A:503;
 Valid;
 none;
 submit data
493.494 C19 H23 N7 O7 S c1ccc...
BTB A:502;
 Invalid;
 none;
 submit data
209.24 C8 H19 N O5 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5N81 1.6 Å EC: 5.1.1.11 CRYSTAL STRUCTURE OF AN ENGINEERED TYCA VARIANT IN COMPLEX W PROPARGYL-BETA-TYR-AMP ANALOG BREVIBACILLUS PARABREVIS NONRIBOSOMAL PEPTIDE SYNTHETASE ADENYLATION DOMAIN LIGASE
Ref.: NONRIBOSOMAL BIOSYNTHESIS OF BACKBONE-MODIFIED PEPT NAT CHEM V. 10 282 2018
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5N81 - 8Q2 C22 H25 N7 O8 S C#CCOc1ccc....
2 5N82 - 8PZ C19 H23 N7 O7 S c1ccc(cc1)....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5N81 - 8Q2 C22 H25 N7 O8 S C#CCOc1ccc....
2 5N82 - 8PZ C19 H23 N7 O7 S c1ccc(cc1)....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 4D4G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
2 4D56 - TYR AMP n/a n/a
3 4D57 - ARG AMP n/a n/a
4 4D4I - ARG C6 H15 N4 O2 C(C[C@@H](....
5 1AMU - AMP C10 H14 N5 O7 P c1nc(c2c(n....
6 5N81 - 8Q2 C22 H25 N7 O8 S C#CCOc1ccc....
7 5N82 - 8PZ C19 H23 N7 O7 S c1ccc(cc1)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 8PZ; Similar ligands found: 247
No: Ligand ECFP6 Tc MDL keys Tc
1 8PZ 1 1
2 8Q2 0.784314 0.965116
3 G5A 0.706522 0.952941
4 A5A 0.666667 0.940476
5 SSA 0.659794 0.97619
6 54H 0.653061 0.918605
7 VMS 0.653061 0.918605
8 LSS 0.65 0.931035
9 DSZ 0.65 0.97619
10 5CA 0.646465 0.97619
11 TSB 0.646465 0.952381
12 53H 0.646465 0.908046
13 52H 0.636364 0.908046
14 NSS 0.633663 0.97619
15 GSU 0.631068 0.952941
16 KAA 0.631068 0.920455
17 649 0.630631 0.931818
18 4YB 0.623853 0.953488
19 8X1 0.613861 0.920455
20 NVA LMS 0.61165 0.920455
21 5AS 0.606383 0.886364
22 YSA 0.601852 0.97619
23 B1U 0.601852 0.879121
24 WSA 0.587719 0.987952
25 P5A 0.584906 0.910112
26 LMS 0.576087 0.939759
27 OOB 0.53271 0.811765
28 QA7 0.523364 0.764045
29 DLL 0.522936 0.811765
30 SRA 0.520833 0.802326
31 AMP 0.510417 0.776471
32 A 0.510417 0.776471
33 FA5 0.508772 0.835294
34 AMP MG 0.505155 0.764706
35 ADP MG 0.504951 0.776471
36 SON 0.504951 0.793103
37 ADP BEF 0.504951 0.776471
38 LEU LMS 0.504505 0.855556
39 CA0 0.5 0.802326
40 5AL 0.5 0.790698
41 AOC 0.5 0.697674
42 FYA 0.495575 0.811765
43 NB8 0.495575 0.827586
44 AHX 0.495495 0.827586
45 8LQ 0.495413 0.793103
46 5X8 0.495146 0.729412
47 KG4 0.495146 0.802326
48 ABM 0.494949 0.758621
49 45A 0.494949 0.758621
50 A2D 0.494949 0.821429
51 SLU 0.492188 0.91954
52 3UK 0.491071 0.802326
53 QXP 0.490909 0.873563
54 SRP 0.490741 0.813953
55 AN2 0.490196 0.811765
56 AT4 0.490196 0.813953
57 AMP DBH 0.487179 0.761364
58 B5V 0.486726 0.793103
59 AMO 0.486486 0.835294
60 8LE 0.485981 0.764045
61 V2G 0.485981 0.786517
62 AGS 0.485714 0.825581
63 ADX 0.485437 0.916667
64 AU1 0.485437 0.802326
65 AP2 0.485149 0.793103
66 A12 0.485149 0.793103
67 BA3 0.485149 0.821429
68 50T 0.480769 0.770115
69 AP5 0.480392 0.821429
70 ADP 0.480392 0.8
71 B4P 0.480392 0.821429
72 XAH 0.478632 0.78022
73 5CD 0.478261 0.682353
74 RAB 0.477778 0.714286
75 ADN 0.477778 0.714286
76 XYA 0.477778 0.714286
77 9ZA 0.477477 0.775281
78 8QN 0.477477 0.790698
79 9ZD 0.477477 0.775281
80 8LH 0.477064 0.772727
81 GAP 0.476636 0.761364
82 3DH 0.474227 0.678161
83 R2V 0.473684 0.873563
84 4AD 0.473214 0.825581
85 ATP MG 0.471698 0.776471
86 ADP PO3 0.471698 0.776471
87 M33 0.471154 0.790698
88 TXA 0.469565 0.793103
89 DAL AMP 0.468468 0.770115
90 VO4 ADP 0.46789 0.761364
91 ANP MG 0.46789 0.790698
92 5N5 0.467391 0.694118
93 BEF ADP 0.46729 0.758621
94 HEJ 0.466667 0.8
95 ACP 0.466667 0.802326
96 H1Q 0.466667 0.767442
97 ATP 0.466667 0.8
98 QXG 0.464912 0.863636
99 OAD 0.464912 0.802326
100 TAT 0.462963 0.813953
101 ANP 0.462963 0.802326
102 T99 0.462963 0.813953
103 A4D 0.462366 0.714286
104 APR 0.462264 0.8
105 AR6 0.462264 0.8
106 APC 0.462264 0.793103
107 AQP 0.462264 0.8
108 PRX 0.462264 0.741573
109 5FA 0.462264 0.8
110 9SN 0.461538 0.766667
111 WAQ 0.46087 0.775281
112 LAD 0.46087 0.777778
113 PAJ 0.460177 0.758242
114 DTA 0.458333 0.729412
115 AD9 0.457944 0.781609
116 APC MG 0.457944 0.758621
117 RBY 0.457944 0.793103
118 SA8 0.457944 0.663043
119 ADV 0.457944 0.793103
120 A5D 0.457944 0.729412
121 B5M 0.457627 0.784091
122 1ZZ 0.456897 0.723404
123 9K8 0.456897 0.778947
124 ME8 0.456897 0.78022
125 00A 0.45614 0.775281
126 7MD 0.454545 0.8
127 ALF ADP 0.454545 0.725275
128 SAH 0.453704 0.712644
129 SFG 0.45283 0.697674
130 OZV 0.451327 0.8
131 V47 0.45045 0.705882
132 S7M 0.45045 0.684783
133 ACQ 0.449541 0.802326
134 TYM 0.448 0.835294
135 EP4 0.447917 0.644444
136 HQG 0.446429 0.790698
137 6RE 0.445545 0.67033
138 NAD IBO 0.444444 0.8
139 NAD TDB 0.444444 0.8
140 3OD 0.444444 0.802326
141 JB6 0.444444 0.816092
142 PTJ 0.444444 0.747253
143 YLP 0.443548 0.744681
144 KOY 0.443548 0.724138
145 M2T 0.443299 0.666667
146 A22 0.442478 0.811765
147 MAP 0.442478 0.784091
148 ATF 0.441441 0.772727
149 MYR AMP 0.440678 0.705263
150 SAI 0.440367 0.685393
151 DND 0.44 0.813953
152 ADP BMA 0.439655 0.781609
153 9X8 0.439655 0.804598
154 DQV 0.439024 0.833333
155 MTA 0.438776 0.678161
156 25A 0.438596 0.8
157 6YZ 0.4375 0.802326
158 SMM 0.4375 0.680851
159 A3N 0.436893 0.670455
160 J7C 0.436893 0.677778
161 TXE 0.436508 0.795455
162 SAM 0.436364 0.684783
163 PR8 0.435897 0.769231
164 LAQ 0.435484 0.76087
165 ADQ 0.434783 0.802326
166 A1R 0.434783 0.795455
167 Q2V 0.434109 0.673913
168 ATP A A A 0.433333 0.788235
169 B5Y 0.433333 0.784091
170 ATP A 0.433333 0.788235
171 YLB 0.433071 0.744681
172 594 0.432836 0.833333
173 GJV 0.432692 0.663043
174 EEM 0.432432 0.648936
175 SXZ 0.432203 0.684783
176 NWW 0.431579 0.662651
177 JNT 0.431034 0.802326
178 ARG AMP 0.430894 0.734043
179 AR6 AR6 0.430894 0.77907
180 67D 0.430769 0.931035
181 NAX 0.428571 0.808989
182 DSH 0.427184 0.677778
183 NEC 0.427184 0.655172
184 A3G 0.427184 0.741176
185 4UV 0.42623 0.784091
186 5SV 0.426087 0.709677
187 3AM 0.425743 0.744186
188 ALF ADP 3PG 0.425197 0.73913
189 AMP NAD 0.424242 0.790698
190 NAD 0.424242 0.811765
191 0UM 0.422414 0.655914
192 A3R 0.422414 0.795455
193 7MC 0.421875 0.782609
194 YLC 0.421875 0.76087
195 ZAS 0.421569 0.693182
196 K3K 0.421488 0.704545
197 48N 0.420635 0.786517
198 LPA AMP 0.420635 0.741935
199 A7D 0.420561 0.701149
200 A3S 0.420561 0.75
201 BIS 0.420168 0.755556
202 CNA 0.419847 0.835294
203 S4M 0.419048 0.645833
204 590 0.41844 0.84375
205 A3D 0.41791 0.802326
206 EU9 0.417323 0.715789
207 6V0 0.417323 0.786517
208 F2R 0.416667 0.763441
209 KB1 0.416667 0.673913
210 25L 0.416667 0.811765
211 KXW 0.416 0.681319
212 TAD 0.416 0.797753
213 IOT 0.415385 0.736842
214 K15 0.415254 0.642105
215 MAO 0.415094 0.709677
216 A3P 0.415094 0.776471
217 K3E 0.414634 0.696629
218 OMR 0.414062 0.734043
219 AF3 ADP 3PG 0.414062 0.73913
220 S8M 0.413793 0.727273
221 A3T 0.412844 0.717647
222 AHZ 0.412698 0.723404
223 YLA 0.412214 0.744681
224 J4G 0.411765 0.804598
225 7C5 0.41129 0.719101
226 BT5 0.410448 0.755319
227 KMQ 0.409836 0.772727
228 BS5 0.409091 0.819149
229 AYB 0.409091 0.736842
230 M24 0.408759 0.769231
231 4UU 0.408 0.784091
232 AFH 0.408 0.777778
233 62X 0.40678 0.628866
234 NAI 0.40625 0.795455
235 TXD 0.40625 0.795455
236 EO7 0.40566 0.896552
237 MHZ 0.40367 0.65625
238 N37 0.403101 0.704545
239 COD 0.402985 0.757895
240 NAQ 0.402878 0.766667
241 NWQ 0.401961 0.647059
242 GEK 0.401709 0.727273
243 F0P 0.4 0.7
244 DZD 0.4 0.797753
245 N5O 0.4 0.709302
246 UPA 0.4 0.795455
247 L3W 0.4 0.793103
Similar Ligands (3D)
Ligand no: 1; Ligand: 8PZ; Similar ligands found: 2
No: Ligand Similarity coefficient
1 4UW 0.8889
2 V1N 0.8764
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5N81; Ligand: 8Q2; 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: 5n81.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5N81; Ligand: 8Q2; 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: 5n81.bio2) has 26 residues
No: Leader PDB Ligand Sequence Similarity
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