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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:503;
A:502;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
8Q2 A:501;
B:501;
Valid;
Valid;
none;
none;
submit data
547.541 C22 H25 N7 O8 S C#CCO...
BTB B: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: 8Q2; Similar ligands found: 154
No: Ligand ECFP6 Tc MDL keys Tc
1 8Q2 1 1
2 8PZ 0.784314 0.965116
3 G5A 0.637255 0.920455
4 A5A 0.603774 0.908046
5 53H 0.601852 0.877778
6 SSA 0.598131 0.942529
7 52H 0.592593 0.877778
8 54H 0.592593 0.88764
9 VMS 0.592593 0.88764
10 DSZ 0.590909 0.942529
11 LSS 0.590909 0.9
12 5CA 0.587156 0.942529
13 TSB 0.587156 0.91954
14 649 0.578512 0.922222
15 YSA 0.577586 0.965116
16 NSS 0.576577 0.942529
17 KAA 0.575221 0.89011
18 GSU 0.575221 0.920455
19 8X1 0.572727 0.89011
20 LEU LMS 0.566372 0.89011
21 4YB 0.558333 0.921348
22 NVA LMS 0.557522 0.89011
23 5AS 0.548077 0.857143
24 P5A 0.547826 0.880435
25 LMS 0.519608 0.906977
26 WSA 0.515873 0.953488
27 AOC 0.509615 0.712644
28 SLU 0.488889 0.910112
29 SRA 0.485714 0.775281
30 5X8 0.464286 0.704545
31 AMP 0.462264 0.75
32 A 0.462264 0.75
33 SON 0.459459 0.766667
34 5AL 0.456897 0.764045
35 SAP 0.45614 0.797753
36 AGS 0.45614 0.797753
37 CA0 0.455357 0.775281
38 NB8 0.455285 0.8
39 BA3 0.454545 0.793103
40 AHX 0.454545 0.8
41 AP5 0.45045 0.793103
42 B4P 0.45045 0.793103
43 OOB 0.45 0.784091
44 ABM 0.449541 0.733333
45 A2D 0.449541 0.793103
46 A3N 0.449541 0.685393
47 SRP 0.449153 0.786517
48 AT4 0.446429 0.786517
49 AN2 0.446429 0.784091
50 AMO 0.446281 0.806818
51 00A 0.442623 0.75
52 AU1 0.442478 0.775281
53 ADX 0.442478 0.885057
54 A12 0.441441 0.766667
55 AP2 0.441441 0.766667
56 XAH 0.440945 0.755319
57 50T 0.438596 0.744444
58 HEJ 0.438596 0.772727
59 ATP 0.438596 0.772727
60 8QN 0.438017 0.764045
61 9ZD 0.438017 0.75
62 9ZA 0.438017 0.75
63 ADP 0.4375 0.772727
64 AMP DBH 0.4375 0.755556
65 GAP 0.435897 0.736264
66 B5V 0.435484 0.786517
67 5FA 0.434783 0.772727
68 AQP 0.434783 0.772727
69 4AD 0.434426 0.797753
70 YLA 0.433824 0.757895
71 YAP 0.433071 0.818182
72 TXA 0.432 0.766667
73 5CD 0.431373 0.659091
74 DLL 0.430894 0.784091
75 XYA 0.43 0.689655
76 ADN 0.43 0.689655
77 RAB 0.43 0.689655
78 3DH 0.429907 0.655556
79 M33 0.429825 0.764045
80 DAL AMP 0.429752 0.744444
81 DTA 0.428571 0.704545
82 3UK 0.427419 0.775281
83 SFG 0.426087 0.674157
84 ACP 0.426087 0.775281
85 9SN 0.425197 0.741935
86 S7M 0.425 0.663158
87 WAQ 0.424 0.75
88 LAD 0.424 0.752688
89 T99 0.423729 0.786517
90 TAT 0.423729 0.786517
91 ANP 0.423729 0.775281
92 PAJ 0.422764 0.734043
93 AR6 0.422414 0.772727
94 APR 0.422414 0.772727
95 PRX 0.422414 0.717391
96 APC 0.422414 0.766667
97 FA5 0.421875 0.806818
98 5N5 0.421569 0.670455
99 9K8 0.420635 0.755102
100 ME8 0.420635 0.755319
101 1ZZ 0.420635 0.701031
102 7MD 0.419847 0.774194
103 AD9 0.418803 0.755556
104 ADV 0.418803 0.766667
105 SA8 0.418803 0.642105
106 ADP PO3 0.418803 0.75
107 RBY 0.418803 0.766667
108 A4D 0.417476 0.689655
109 OAD 0.416 0.775281
110 TYR AMP 0.415385 0.797753
111 SAH 0.415254 0.688889
112 M2T 0.415094 0.645161
113 VO4 ADP 0.413223 0.744444
114 ADP VO4 0.413223 0.744444
115 SMM 0.413223 0.659794
116 A A 0.412698 0.752809
117 ACQ 0.411765 0.775281
118 SAM 0.411765 0.663158
119 ADQ 0.41129 0.775281
120 MTA 0.411215 0.655556
121 B5M 0.410853 0.777778
122 YLP 0.410448 0.721649
123 JB6 0.409449 0.788889
124 PTJ 0.409449 0.723404
125 FYA 0.409449 0.784091
126 DND 0.407407 0.786517
127 NXX 0.407407 0.786517
128 MAP 0.406504 0.758242
129 A22 0.406504 0.784091
130 MYR AMP 0.40625 0.683673
131 DQV 0.406015 0.804598
132 EP4 0.40566 0.623656
133 6RE 0.405405 0.648936
134 ADP ALF 0.404959 0.702128
135 ATF 0.404959 0.747253
136 ALF ADP 0.404959 0.702128
137 ADP BMA 0.404762 0.755556
138 9X8 0.404762 0.777778
139 AF3 ADP 3PG 0.404412 0.715789
140 SAI 0.403361 0.663043
141 25A 0.403226 0.772727
142 5SV 0.403226 0.6875
143 LAQ 0.402985 0.736842
144 AHZ 0.402985 0.701031
145 594 0.402778 0.808081
146 6YZ 0.401639 0.775281
147 PR8 0.401575 0.744681
148 7MC 0.40146 0.757895
149 YLB 0.40146 0.721649
150 A1R 0.4 0.769231
151 0UM 0.4 0.635417
152 B5Y 0.4 0.777778
153 67D 0.4 0.9
154 48N 0.4 0.76087
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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