Receptor
PDB id Resolution Class Description Source Keywords
5EXK 1.86 Å EC: 2.8.1.8 CRYSTAL STRUCTURE OF M. TUBERCULOSIS LIPOYL SYNTHASE WITH 6- THIOOCTANOYL PEPTIDE INTERMEDIATE MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCH37RV) AUXILIARY IRON-SULFUR CLUSTER ADOMET RADICAL RADICAL SAM INSERTION TRANSFERASE
Ref.: CRYSTALLOGRAPHIC SNAPSHOTS OF SULFUR INSERTION BY L SYNTHASE. PROC.NATL.ACAD.SCI.USA V. 113 9446 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SF4 G:402;
K:402;
I:402;
C:402;
A:402;
E:402;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
351.64 Fe4 S4 [S]12...
GLU SER THR XOK SER VAL SER ASP B:599;
F:600;
H:600;
L:600;
D:599;
J:601;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data n/a n/a n/a n/a
5AD G:403;
C:403;
K:403;
E:403;
I:403;
A:403;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
251.242 C10 H13 N5 O3 C[C@@...
IMD A:405;
E:405;
Invalid;
Invalid;
none;
none;
submit data
69.085 C3 H5 N2 c1c[n...
MET C:404;
G:404;
K:404;
E:404;
A:404;
I:404;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
149.211 C5 H11 N O2 S CSCC[...
F3S A:401;
K:401;
C:401;
E:401;
G:401;
I:401;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
295.795 Fe3 S4 S1[Fe...
CL K:405;
A:406;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
IPA C:405;
Invalid;
none;
submit data
60.095 C3 H8 O CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5EXK 1.86 Å EC: 2.8.1.8 CRYSTAL STRUCTURE OF M. TUBERCULOSIS LIPOYL SYNTHASE WITH 6- THIOOCTANOYL PEPTIDE INTERMEDIATE MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCH37RV) AUXILIARY IRON-SULFUR CLUSTER ADOMET RADICAL RADICAL SAM INSERTION TRANSFERASE
Ref.: CRYSTALLOGRAPHIC SNAPSHOTS OF SULFUR INSERTION BY L SYNTHASE. PROC.NATL.ACAD.SCI.USA V. 113 9446 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5EXK - 5AD C10 H13 N5 O3 C[C@@H]1[C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5EXK - 5AD C10 H13 N5 O3 C[C@@H]1[C....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4U0P - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 4U0O - MTA C11 H15 N5 O3 S CSC[C@@H]1....
3 5EXK - 5AD C10 H13 N5 O3 C[C@@H]1[C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5AD; Similar ligands found: 196
No: Ligand ECFP6 Tc MDL keys Tc
1 5AD 1 1
2 XYA 0.672727 0.854839
3 ADN 0.672727 0.854839
4 RAB 0.672727 0.854839
5 5N5 0.649123 0.854839
6 Y3J 0.649123 0.929825
7 MTA 0.639344 0.857143
8 5CD 0.637931 0.868852
9 A4D 0.637931 0.854839
10 EP4 0.633333 0.830769
11 M2T 0.622951 0.80597
12 DTA 0.596774 0.815385
13 3DH 0.59375 0.857143
14 CC5 0.568965 0.883333
15 7D7 0.568965 0.793651
16 S4M 0.565217 0.72
17 NEC 0.558824 0.885246
18 AOC 0.558824 0.828125
19 AMP 0.552239 0.768116
20 ZAS 0.552239 0.791045
21 A 0.552239 0.768116
22 A3N 0.550725 0.815385
23 ABM 0.550725 0.771429
24 SRA 0.544118 0.726027
25 6RE 0.544118 0.757143
26 3AM 0.537313 0.753623
27 AMP MG 0.536232 0.746479
28 DSH 0.536232 0.768116
29 MAO 0.535211 0.710526
30 3AD 0.532258 0.83871
31 RP1 0.529412 0.722222
32 SP1 0.529412 0.722222
33 J7C 0.528571 0.768116
34 A2D 0.528571 0.746479
35 5AS 0.527778 0.650602
36 GJV 0.521127 0.746479
37 SON 0.520548 0.716216
38 A3G 0.514286 0.80303
39 AP2 0.513889 0.716216
40 BA3 0.513889 0.746479
41 A12 0.513889 0.716216
42 AU1 0.513514 0.726027
43 M33 0.513514 0.760563
44 MHZ 0.513514 0.710526
45 ADP 0.506849 0.746479
46 B4P 0.506849 0.746479
47 AP5 0.506849 0.746479
48 A7D 0.5 0.80303
49 AN2 0.5 0.736111
50 SAM 0.5 0.75
51 PRX 0.5 0.75
52 2AM 0.5 0.742857
53 SA8 0.493506 0.771429
54 AD9 0.493506 0.726027
55 CA0 0.493333 0.726027
56 ADP MG 0.493333 0.736111
57 ADX 0.493333 0.670886
58 CMP 0.493151 0.776119
59 A3P 0.493151 0.742857
60 2BA 0.493151 0.764706
61 ACP 0.486842 0.726027
62 BEF ADP 0.486842 0.716216
63 SFG 0.486842 0.828125
64 5X8 0.486842 0.815385
65 ATP 0.486842 0.746479
66 50T 0.486842 0.736111
67 A3T 0.486842 0.857143
68 ADP BEF 0.486842 0.716216
69 7D5 0.485294 0.684932
70 SMM 0.481481 0.72
71 ANP 0.481013 0.726027
72 AR6 0.480519 0.746479
73 5FA 0.480519 0.746479
74 AQP 0.480519 0.746479
75 APC 0.480519 0.716216
76 APR 0.480519 0.746479
77 A3S 0.48 0.815385
78 OVE 0.478873 0.712329
79 5AL 0.475 0.760563
80 EEM 0.475 0.75
81 AAT 0.475 0.746479
82 SAP 0.474359 0.706667
83 RBY 0.474359 0.716216
84 ADV 0.474359 0.716216
85 A5D 0.474359 0.815385
86 ADP PO3 0.474359 0.768116
87 AGS 0.474359 0.706667
88 QQX 0.471429 0.708333
89 5F1 0.469697 0.78125
90 A5A 0.469136 0.675
91 SAI 0.468354 0.779412
92 ATP MG 0.468354 0.736111
93 G5A 0.468354 0.630952
94 SAH 0.468354 0.791045
95 QQY 0.464789 0.71831
96 103 0.464789 0.764706
97 ACK 0.464789 0.761194
98 S7M 0.463415 0.75
99 ANP MG 0.463415 0.706667
100 GAP 0.4625 0.726027
101 TAT 0.4625 0.716216
102 ACQ 0.4625 0.726027
103 3L1 0.461538 0.772727
104 3D1 0.461538 0.772727
105 VMS 0.457831 0.658537
106 54H 0.457831 0.658537
107 52H 0.457831 0.650602
108 PAP 0.455696 0.732394
109 NVA 2AD 0.455696 0.791045
110 A2P 0.453333 0.753623
111 NOC 0.453125 0.790323
112 5I5 0.453125 0.913793
113 MAP 0.452381 0.706667
114 DAL AMP 0.452381 0.760563
115 53H 0.452381 0.650602
116 TSB 0.452381 0.666667
117 ATF 0.451219 0.716216
118 ALF ADP 0.451219 0.706667
119 ADP ALF 0.451219 0.706667
120 2VA 0.448718 0.830769
121 5SV 0.447059 0.710526
122 8QN 0.447059 0.760563
123 SSA 0.445783 0.630952
124 SRP 0.445783 0.716216
125 ADP VO4 0.445783 0.736111
126 VO4 ADP 0.445783 0.736111
127 LSS 0.44186 0.635294
128 PAJ 0.44186 0.701299
129 0UM 0.44186 0.760563
130 7D3 0.44 0.666667
131 PPS 0.439024 0.65
132 1ZZ 0.438202 0.683544
133 NVA LMS 0.436782 0.635294
134 62X 0.436782 0.72
135 A22 0.435294 0.736111
136 5CA 0.435294 0.630952
137 D3Y 0.435294 0.791045
138 KB1 0.433333 0.736111
139 MYR AMP 0.433333 0.683544
140 ARJ 0.432836 0.774194
141 VRT 0.432099 0.794118
142 SO8 0.432099 0.818182
143 OAD 0.431818 0.75
144 K15 0.431818 0.739726
145 LEU LMS 0.431818 0.635294
146 25A 0.430233 0.746479
147 GEK 0.430233 0.757143
148 S8M 0.430233 0.757143
149 OOB 0.430233 0.736111
150 WAQ 0.426966 0.697368
151 3NZ 0.426966 0.782609
152 GSU 0.426966 0.630952
153 ADZ 0.425926 0.618182
154 DSZ 0.425287 0.630952
155 ADQ 0.425287 0.726027
156 4AD 0.425287 0.706667
157 AMO 0.425287 0.716216
158 NSS 0.425287 0.630952
159 A1R 0.425287 0.697368
160 2A5 0.425 0.68
161 TXA 0.422222 0.739726
162 SXZ 0.422222 0.75
163 3OD 0.422222 0.75
164 ME8 0.422222 0.683544
165 PTJ 0.422222 0.710526
166 BIS 0.422222 0.697368
167 AHX 0.420455 0.688312
168 DLL 0.420455 0.736111
169 00A 0.420455 0.697368
170 ATR 0.419753 0.742857
171 7D4 0.417722 0.666667
172 TAD 0.416667 0.679487
173 A6D 0.41573 0.716216
174 ADP BMA 0.41573 0.726027
175 3UK 0.41573 0.726027
176 26A 0.411765 0.787879
177 AFX 0.411765 0.716418
178 P5A 0.411111 0.602273
179 LAD 0.411111 0.679487
180 PR8 0.411111 0.670886
181 A A 0.411111 0.746479
182 KAA 0.411111 0.609195
183 V3L 0.409639 0.746479
184 AMP NAD 0.409091 0.739726
185 YAP 0.408602 0.706667
186 0XU 0.407407 0.828125
187 NB8 0.406593 0.688312
188 FYA 0.406593 0.736111
189 JB6 0.406593 0.697368
190 YSA 0.404255 0.630952
191 TYR AMP 0.404255 0.716216
192 ZDA 0.402439 0.742857
193 25L 0.402174 0.736111
194 4UV 0.4 0.706667
195 A A A 0.4 0.736111
196 101 0.4 0.708333
Ligand no: 2; Ligand: MET; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 MET 1 1
2 MED 1 1
3 DBB 0.518519 0.655172
4 ABA 0.518519 0.655172
5 2FM 0.514286 0.666667
6 NVA 0.5 0.758621
7 MF3 0.5 0.647059
8 DAB 0.466667 0.636364
9 HSE 0.466667 0.617647
10 SME 0.457143 0.717949
11 MHO 0.457143 0.717949
12 HCS 0.451613 0.733333
13 API 0.451613 0.606061
14 CDT 0.447368 0.756757
15 2MM 0.444444 0.657143
16 NLE 0.441176 0.766667
17 ONL 0.441176 0.71875
18 UN1 0.428571 0.606061
19 11C 0.428571 0.606061
20 MSE 0.428571 0.9
21 GGL 0.424242 0.625
22 GLU 0.424242 0.625
23 DGL 0.424242 0.625
24 CBH 0.418605 0.685714
25 ORN 0.411765 0.65625
26 AME 0.410256 0.771429
27 FME 0.410256 0.84375
28 LEU 0.40625 0.666667
29 CYS 0.4 0.666667
30 C2N 0.4 0.633333
31 DCY 0.4 0.666667
32 JM6 0.4 0.7
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5EXK; Ligand: MET; Similar sites found: 17
This union binding pocket(no: 1) in the query (biounit: 5exk.bio6) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TRD PGH 0.01076 0.41474 1.2
2 4B0T ADP 0.02173 0.41282 1.81269
3 5AG3 3EB 0.01918 0.40219 2.1148
4 5DB3 58Q 0.02709 0.40515 2.41692
5 1NFS DED 0.01045 0.41696 3.27869
6 3KN5 ANP 0.01977 0.40512 3.38462
7 5KJW 53C 0.01431 0.40033 3.92749
8 3VC3 C6P 0.0335 0.40463 4.83384
9 4I8P NAD 0.04499 0.40587 6.64653
10 1X7D ORN 0.02672 0.42281 6.94864
11 1F76 FMN 0.03413 0.40271 7.55287
12 4NMC FAD 0.04866 0.40836 7.85498
13 4NMC 2OP 0.04685 0.40836 7.85498
14 3HNB 768 0.001928 0.43783 8.80503
15 2P3V SRT 0.004994 0.42278 10.5469
16 5A5W GUO 0.02385 0.42559 13.4387
17 4A2A ATP 0.0149 0.41569 37.5
Pocket No.: 2; Query (leader) PDB : 5EXK; Ligand: 5AD; Similar sites found: 43
This union binding pocket(no: 2) in the query (biounit: 5exk.bio6) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3DLS ADP 0.02107 0.40061 0.906344
2 5UL4 SAM 0.001026 0.46715 1.20846
3 1RE8 BD2 0.02767 0.42655 1.20846
4 4AZW ATP 0.0265 0.40266 1.51057
5 3PE2 E1B 0.01629 0.43953 1.81269
6 2W92 NGT 0.0004136 0.47373 2.1148
7 2WSB NAD 0.0295 0.42138 2.3622
8 4LH7 1X8 0.01159 0.40481 2.41692
9 1OLT SAM 0.000002892 0.46876 2.71903
10 3RFA SAM 0.00007267 0.4373 2.71903
11 3OTX AP5 0.02665 0.41744 2.71903
12 1S1D GP2 0.01749 0.40743 2.71903
13 4WCX SAM 0.00012 0.40383 2.91667
14 2QK4 ATP 0.01011 0.41046 3.02115
15 2VPQ ANP 0.01725 0.4155 3.32326
16 3TXO 07U 0.01827 0.40359 3.32326
17 3HAV ATP 0.00943 0.40661 3.34448
18 3AQV TAK 0.02038 0.40488 3.62319
19 4FHD EEM 0.01609 0.42677 4.07609
20 4FHD 0TT 0.01609 0.42677 4.07609
21 1Q8Y ADP 0.02242 0.40681 4.22961
22 4Q0L V14 0.03698 0.40068 4.53172
23 3ETH ATP 0.01506 0.41584 5.43807
24 5EY0 GTP 0.01458 0.40517 6.20438
25 5C4L SIS 0.01531 0.42857 6.54206
26 5C4L 4XR 0.01737 0.42543 6.54206
27 4OCJ NDG 0.003993 0.46756 6.64653
28 5TDF ADP 0.008671 0.42816 6.64653
29 4R78 AMP 0.0053 0.40253 6.79612
30 1NFQ NAI 0.0365 0.40914 7.69231
31 1MJT ITU 0.008705 0.40312 8.1571
32 5AHW CMP 0.02588 0.40012 10.2041
33 4U5I BXP 0.01563 0.40099 11.1663
34 4K39 SAM 0.0001015 0.52302 12.3867
35 4K37 SAM 0.0001505 0.43215 12.3867
36 4K38 SAM 0.00008988 0.42353 12.3867
37 5A5W GUO 0.01817 0.43319 13.4387
38 5DZT AMP 0.01055 0.40348 13.8973
39 5K2M ADP 0.004433 0.44789 16.9811
40 3T7V SAM 0.000005068 0.44436 20.5438
41 2FB3 GTP 0.0009665 0.49091 21.7523
42 2FB3 5AD 0.0004043 0.48746 21.7523
43 2FB3 MET 0.005699 0.42659 21.7523
Pocket No.: 3; Query (leader) PDB : 5EXK; Ligand: MET; Similar sites found: 7
This union binding pocket(no: 3) in the query (biounit: 5exk.bio3) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WK9 PLP 0.03099 0.41267 4.53172
2 5BSH PRO 0.02382 0.41948 4.69314
3 5L2Z 70C 0.03737 0.41108 5.51181
4 1O9J NAD 0.0284 0.4138 6.34441
5 2P1M IHP 0.03621 0.40207 6.64653
6 5J8O 6GZ 0.01063 0.41849 8.06452
7 3GGU 017 0.04243 0.40041 17.1717
Pocket No.: 4; Query (leader) PDB : 5EXK; Ligand: 5AD; Similar sites found: 3
This union binding pocket(no: 4) in the query (biounit: 5exk.bio3) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5KBF CMP 0.02163 0.401 2.32558
2 4A3U FMN 0.03114 0.40031 2.71903
3 4POO SAM 0.037 0.40241 5.5
Pocket No.: 5; Query (leader) PDB : 5EXK; Ligand: MET; Similar sites found: 9
This union binding pocket(no: 5) in the query (biounit: 5exk.bio4) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WCX MET 0.002446 0.40843 2.91667
2 1Y7P RIP 0.01446 0.40768 3.58744
3 4L2I NAD 0.03762 0.41899 4.56274
4 3GGO ENO 0.04955 0.40844 6.6879
5 3GGO NAI 0.04955 0.40844 6.6879
6 4LNU GTP 0.03361 0.40478 8
7 1MJH ATP 0.03049 0.40161 9.25926
8 3KRU FMN 0.04219 0.40588 9.91254
9 5XDT ZI7 0.04087 0.40072 11.039
Pocket No.: 6; Query (leader) PDB : 5EXK; Ligand: 5AD; Similar sites found: 15
This union binding pocket(no: 6) in the query (biounit: 5exk.bio4) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4L3L 5FI 0.01024 0.43434 1.81269
2 5WGG SAM 0.001656 0.40553 2.1148
3 2QCS ANP 0.01032 0.43004 2.4055
4 3FHQ BMA NGT MAN MAN 0.003691 0.43877 2.41692
5 4IJP 1EH 0.01628 0.41185 2.41692
6 1ZTH ADP 0.01398 0.40305 2.71318
7 1M0W ANP 0.01091 0.41296 2.71903
8 4GYI ADP 0.002369 0.40931 3.32326
9 1PHK ATP 0.01368 0.41395 4.02685
10 4DFU QUE 0.01237 0.40051 5.2795
11 3ZG6 APR 0.02326 0.40552 6.75676
12 5LXC 7AA 0.005327 0.42855 7.25076
13 4WW7 AMP 0.02669 0.40242 7.66284
14 5VSM MET 0.0004129 0.41084 8.1761
15 5VSM 5AD 0.0005556 0.40388 8.1761
Pocket No.: 7; Query (leader) PDB : 5EXK; Ligand: MET; Similar sites found: 3
This union binding pocket(no: 7) in the query (biounit: 5exk.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1WPQ NAD 0.03371 0.40176 3.02115
2 5X7Q GLC GLC 0.006238 0.40748 3.62538
3 5IXJ THR 0.04788 0.40027 4.22961
Pocket No.: 8; Query (leader) PDB : 5EXK; Ligand: 5AD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5exk.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 5EXK; Ligand: 5AD; Similar sites found: 7
This union binding pocket(no: 9) in the query (biounit: 5exk.bio5) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3CGD FAD 0.03202 0.44068 1.51057
2 3CGD COA 0.03202 0.44068 1.51057
3 3CGD NAD 0.03202 0.44068 1.51057
4 5JCM NAD 0.01051 0.46334 4.53172
5 5JCM FAD 0.01051 0.46334 4.53172
6 5JCM ISD 0.01103 0.46334 4.53172
7 4IRX INS 0.01155 0.40716 7.77027
Pocket No.: 10; Query (leader) PDB : 5EXK; Ligand: MET; Similar sites found: 3
This union binding pocket(no: 10) in the query (biounit: 5exk.bio5) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WK9 PLG 0.04476 0.40578 4.53172
2 2FXD DR7 0.04877 0.40076 6.06061
3 5HES 032 0.02989 0.4022 6.84039
Pocket No.: 11; Query (leader) PDB : 5EXK; Ligand: 5AD; Similar sites found: 1
This union binding pocket(no: 11) in the query (biounit: 5exk.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4JWH SAH 0.02521 0.4109 1.91693
Pocket No.: 12; Query (leader) PDB : 5EXK; Ligand: MET; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 5exk.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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