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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 1039 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
Ligand no: 1; Ligand: 8PZ; Similar ligands found: 214
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 DSZ 0.65 0.97619
9 LSS 0.65 0.931035
10 TSB 0.646465 0.952381
11 53H 0.646465 0.908046
12 5CA 0.646465 0.97619
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 LEU LMS 0.621359 0.920455
20 8X1 0.613861 0.920455
21 NVA LMS 0.61165 0.920455
22 5AS 0.606383 0.886364
23 YSA 0.601852 0.97619
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 DLL 0.522936 0.811765
29 SRA 0.520833 0.802326
30 A 0.510417 0.776471
31 AMP 0.510417 0.776471
32 FA5 0.508772 0.835294
33 SON 0.504951 0.793103
34 AOC 0.5 0.697674
35 CA0 0.5 0.802326
36 5AL 0.5 0.790698
37 FYA 0.495575 0.811765
38 NB8 0.495575 0.827586
39 AHX 0.495495 0.827586
40 5X8 0.495146 0.729412
41 A2D 0.494949 0.821429
42 ABM 0.494949 0.758621
43 SLU 0.492188 0.91954
44 3UK 0.491071 0.802326
45 SRP 0.490741 0.813953
46 AN2 0.490196 0.811765
47 AT4 0.490196 0.813953
48 AMP DBH 0.487179 0.761364
49 B5V 0.486726 0.793103
50 AMO 0.486486 0.835294
51 AGS 0.485714 0.825581
52 SAP 0.485714 0.825581
53 AU1 0.485437 0.802326
54 ADX 0.485437 0.916667
55 A12 0.485149 0.793103
56 BA3 0.485149 0.821429
57 AP2 0.485149 0.793103
58 50T 0.480769 0.770115
59 AP5 0.480392 0.821429
60 ADP 0.480392 0.8
61 B4P 0.480392 0.821429
62 XAH 0.478632 0.78022
63 5CD 0.478261 0.682353
64 XYA 0.477778 0.714286
65 ADN 0.477778 0.714286
66 RAB 0.477778 0.714286
67 8QN 0.477477 0.790698
68 9ZD 0.477477 0.775281
69 9ZA 0.477477 0.775281
70 GAP 0.476636 0.761364
71 3DH 0.474227 0.678161
72 4AD 0.473214 0.825581
73 ADP PO3 0.471698 0.776471
74 M33 0.471154 0.790698
75 TXA 0.469565 0.793103
76 DAL AMP 0.468468 0.770115
77 5N5 0.467391 0.694118
78 ACP 0.466667 0.802326
79 ATP 0.466667 0.8
80 HEJ 0.466667 0.8
81 OAD 0.464912 0.802326
82 VO4 ADP 0.463636 0.770115
83 ADP VO4 0.463636 0.770115
84 ANP 0.462963 0.802326
85 T99 0.462963 0.813953
86 TAT 0.462963 0.813953
87 A4D 0.462366 0.714286
88 5FA 0.462264 0.8
89 AQP 0.462264 0.8
90 APC 0.462264 0.793103
91 AR6 0.462264 0.8
92 APR 0.462264 0.8
93 PRX 0.462264 0.741573
94 9SN 0.461538 0.766667
95 WAQ 0.46087 0.775281
96 LAD 0.46087 0.777778
97 PAJ 0.460177 0.758242
98 DTA 0.458333 0.729412
99 ADV 0.457944 0.793103
100 A5D 0.457944 0.729412
101 AD9 0.457944 0.781609
102 RBY 0.457944 0.793103
103 SA8 0.457944 0.663043
104 B5M 0.457627 0.784091
105 YAP 0.457627 0.825581
106 1ZZ 0.456897 0.723404
107 9K8 0.456897 0.778947
108 ME8 0.456897 0.78022
109 00A 0.45614 0.775281
110 ALF ADP 0.454545 0.725275
111 ADP ALF 0.454545 0.725275
112 7MD 0.454545 0.8
113 SAH 0.453704 0.712644
114 SFG 0.45283 0.697674
115 S7M 0.45045 0.684783
116 ACQ 0.449541 0.802326
117 A A 0.448276 0.77907
118 TYM 0.448 0.835294
119 EP4 0.447917 0.644444
120 6RE 0.445545 0.67033
121 JB6 0.444444 0.816092
122 3OD 0.444444 0.802326
123 PTJ 0.444444 0.747253
124 YLP 0.443548 0.744681
125 M2T 0.443299 0.666667
126 MAP 0.442478 0.784091
127 A22 0.442478 0.811765
128 ATF 0.441441 0.772727
129 MYR AMP 0.440678 0.705263
130 SAI 0.440367 0.685393
131 DND 0.44 0.813953
132 NXX 0.44 0.813953
133 9X8 0.439655 0.804598
134 ADP BMA 0.439655 0.781609
135 DQV 0.439024 0.833333
136 MTA 0.438776 0.678161
137 25A 0.438596 0.8
138 TYR AMP 0.438017 0.804598
139 6YZ 0.4375 0.802326
140 SMM 0.4375 0.680851
141 J7C 0.436893 0.677778
142 A3N 0.436893 0.670455
143 TXE 0.436508 0.795455
144 SAM 0.436364 0.684783
145 PR8 0.435897 0.769231
146 LAQ 0.435484 0.76087
147 A1R 0.434783 0.795455
148 ADQ 0.434783 0.802326
149 ATP A A A 0.433333 0.788235
150 B5Y 0.433333 0.784091
151 YLB 0.433071 0.744681
152 594 0.432836 0.833333
153 GJV 0.432692 0.663043
154 EEM 0.432432 0.648936
155 SXZ 0.432203 0.684783
156 ARG AMP 0.430894 0.734043
157 AR6 AR6 0.430894 0.77907
158 67D 0.430769 0.931035
159 NAX 0.428571 0.808989
160 DSH 0.427184 0.677778
161 A3G 0.427184 0.741176
162 NEC 0.427184 0.655172
163 4UV 0.42623 0.784091
164 5SV 0.426087 0.709677
165 3AM 0.425743 0.744186
166 NAD 0.424242 0.811765
167 AMP NAD 0.424242 0.790698
168 0UM 0.422414 0.655914
169 A3R 0.422414 0.795455
170 7MC 0.421875 0.782609
171 YLC 0.421875 0.76087
172 ZAS 0.421569 0.693182
173 LPA AMP 0.420635 0.741935
174 48N 0.420635 0.786517
175 A3S 0.420561 0.75
176 A7D 0.420561 0.701149
177 BIS 0.420168 0.755556
178 CNA 0.419847 0.835294
179 S4M 0.419048 0.645833
180 590 0.41844 0.84375
181 A3D 0.41791 0.802326
182 6V0 0.417323 0.786517
183 F2R 0.416667 0.763441
184 KB1 0.416667 0.673913
185 25L 0.416667 0.811765
186 TAD 0.416 0.797753
187 IOT 0.415385 0.736842
188 K15 0.415254 0.642105
189 MAO 0.415094 0.709677
190 A3P 0.415094 0.776471
191 AF3 ADP 3PG 0.414062 0.73913
192 OMR 0.414062 0.734043
193 S8M 0.413793 0.727273
194 A3T 0.412844 0.717647
195 AHZ 0.412698 0.723404
196 YLA 0.412214 0.744681
197 7C5 0.41129 0.719101
198 BT5 0.410448 0.755319
199 AYB 0.409091 0.736842
200 BS5 0.409091 0.819149
201 M24 0.408759 0.769231
202 4UU 0.408 0.784091
203 AFH 0.408 0.777778
204 62X 0.40678 0.628866
205 TXD 0.40625 0.795455
206 NAI 0.40625 0.795455
207 EO7 0.40566 0.896552
208 MHZ 0.40367 0.65625
209 COD 0.402985 0.757895
210 NAQ 0.402878 0.766667
211 GEK 0.401709 0.727273
212 F0P 0.4 0.7
213 UPA 0.4 0.795455
214 DZD 0.4 0.797753
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: 106
This union binding pocket(no: 1) in the query (biounit: 5n81.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 1XXR MAN None
2 3IVV ASP GLU VAL THR SER THR THR SER SER SER 1.37931
3 4L9Z OXL 1.47493
4 3KIF GDL 1.88679
5 1SJD NPG 1.90217
6 5W5R PYR 2.15311
7 5VKM GAL SIA 2.16049
8 5LFV SIA GAL NAG 2.2082
9 6E1Q CFA 2.34192
10 1LVW TYD 2.37288
11 5OVV ACE ILE GLU SER THR GLU ILE 2.43902
12 3E3U NVC 2.53807
13 6FOF LAT 2.55102
14 4B2G V1N 2.8103
15 2YLN CYS 2.82686
16 2IV3 UDP 2.92398
17 2YP9 SIA CMO 3.0445
18 3VSV XYP 3.0445
19 5FPE 3TR 3.10078
20 3ZOK GLY 3.1746
21 4TO8 FLC 3.42466
22 1I1E DM2 3.51288
23 5YRJ BGC GLC 3.52113
24 5YRG BGC GLC 3.52113
25 5YRM BGC GLC 3.52113
26 5YRL GLC GLC 3.52113
27 5YRI GLC GLC 3.52113
28 5YRF GLC GLC 3.52113
29 3F5A SIA GAL NAG 4.06504
30 1M5B BN1 4.18251
31 1ZQ9 SAM 4.21053
32 4GN8 ASO 4.34783
33 5MZI FYK 4.44965
34 5F90 GLA GAL BGC 5VQ 4.48718
35 1BW9 PPY 4.49438
36 4ODV GP1 Z9M 4.5045
37 1C1X HFA 4.50704
38 5UI2 SUC 4.73186
39 4G0P U5P 4.7619
40 3UEC ALA ARG TPO LYS 4.79452
41 3VY6 BGC BGC 4.96454
42 1RJW ETF 5.01475
43 6GNO XDI 5.18518
44 5KOD AMP 5.38642
45 1I7Q PYR 5.38642
46 2V2G BEZ 5.5794
47 1F9V ADP 5.76369
48 3EXS 5RP 5.88235
49 1R1Q ACE ARG GLU PTR VAL ASN VAL 6
50 3ITA AIC 7.38636
51 2RDG NDG FUC SIA GAL 7.65306
52 4LEB THR THR THR THR THR THR THR 8
53 4NAE 1GP 8.88889
54 1USF NAP 8.98876
55 2WBV SIA 8.99471
56 1QDS PGA 9.56175
57 2GNK ATP 9.82143
58 3TAO PGH 10.4869
59 5E6O TRP GLU GLU LEU 11.8644
60 3QH2 3NM 12.2172
61 2Y4O DLL 12.6464
62 1ZEI CRS 13.2075
63 5HM3 649 13.8173
64 2OFD NGA 14.7887
65 4RHS SIA SIA GAL 16.3934
66 5EY9 5SV 19.2037
67 5D6J ATP 19.6721
68 3KXW 1ZZ 22.0141
69 5MST FUM 25.7611
70 5MST AMP 25.7611
71 5MSD BEZ 29.274
72 5MSD AMP 29.274
73 5OE4 3UK 35.8722
74 3IES M24 36.0656
75 3NYQ MCA 36.6337
76 3NYQ AMP 36.6337
77 5C5H 4YB 37.2365
78 4GXQ ATP 37.4707
79 4FUT ATP 37.4707
80 4RLQ 3SK 37.7049
81 2D1S SLU 38.1733
82 1V25 ANP 39.3443
83 5BSR AMP 39.5785
84 5BSR COA 39.5785
85 3CW9 AMP 39.5785
86 1MDB AMP DBH 39.5785
87 3CW9 01A 39.5785
88 4R0M FA5 40.0468
89 3O84 HTJ 40.9836
90 3C5E ATP 41.2178
91 5IE3 OXD 41.6862
92 5IE3 AMP 41.6862
93 1PG4 PRX 41.9204
94 1PG4 COA 41.9204
95 5X8G S0N 43.3255
96 2V7B BEZ 43.3255
97 1RY2 AMP 43.7939
98 4OXI GAP 44.2623
99 5WM2 AMP 44.2623
100 5WM2 SAL 44.2623
101 4DG8 AMP 44.7307
102 3DHV DAL AMP 45.6674
103 5N9X 8QN 46.37
104 5N9X ATP 46.37
105 5N9X THR 46.37
106 3E7W AMP 46.8384
Pocket No.: 2; Query (leader) PDB : 5N81; Ligand: 8Q2; Similar sites found with APoc: 24
This union binding pocket(no: 2) in the query (biounit: 5n81.bio2) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 5OWC AYZ 1.63934
2 1J78 OLA 2.34192
3 2HYR BGC GLC 2.45902
4 2GUD MAN 2.45902
5 2NU5 NAG 2.45902
6 2GUC MAN 2.45902
7 2NUO BGC 2.45902
8 1UNQ 4IP 3.2
9 3RS8 ALA TRP LEU PHE GLU ALA 3.51288
10 3E70 GDP 3.65854
11 1TRD PGH 4
12 1C1D PHE 4.50704
13 6B74 BEN 4.52675
14 1SW0 PGA 4.83871
15 1W6F ISZ 5.39568
16 3FJG 3PG 5.57769
17 5TQZ GLC 6.66667
18 1C3M MAN MAN 6.80272
19 5URY PAM 6.84932
20 1T0S BML 6.97674
21 2F6D ACR 7.02576
22 3AB4 THR 9.55056
23 2D3Y DU 9.58904
24 5LWY OLB 10.9244
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