Receptor
PDB id Resolution Class Description Source Keywords
3IOE 1.95 Å EC: 6.3.2.1 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE SYNTHETASE AT 1.95 ANG RESOLUTION IN COMPLEX WITH 5'-DEOXY-4 -DIHYDROXYBUTYLTHIO)-ADENOSINE MYCOBACTERIUM TUBERCULOSIS MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE BIOSYNTHESIS ENZYMLIGASE INHIBITORS DRUG DESIGN FRAGMENT-BASED DYNAMIC COMBINATORIAL CHEMISTRY ATP-BINDING MAGNESIUM METAL-BINDNUCLEOTIDE-BINDING
Ref.: A FRAGMENT-BASED APPROACH TO PROBING ADENOSINE RECO SITES BY USING DYNAMIC COMBINATORIAL CHEMISTRY CHEMBIOCHEM V. 10 2772 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
A7D A:901;
B:902;
Valid;
Valid;
none;
none;
Kd = 540 uM
371.412 C14 H21 N5 O5 S c1nc(...
EOH A:710;
A:711;
Invalid;
Invalid;
none;
none;
submit data
46.068 C2 H6 O CCO
GOL A:701;
A:708;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:703;
B:704;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3COW 1.8 Å EC: 6.3.2.1 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE SYNTHETASE AT 1.8 ANG RESOLUTION- IN COMPLEX WITH SULPHONAMI NHIBITOR 2 MYCOBACTERIUM TUBERCULOSIS MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE BIOSYNTHESIS ENZYMLIGASE INHIBITORS DRUG DESIGN ATP-BINDING MAGNESIUM MEBINDING NUCLEOTIDE-BINDING
Ref.: INHIBITION OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENA SYNTHETASE BY ANALOGUES OF THE REACTION INTERMEDIAT CHEMBIOCHEM V. 9 2606 2008
Members (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3IVG Kd = 50 uM FG5 C20 H18 N2 O6 S COc1ccc2c(....
2 2A84 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 1N2O - BAL C3 H7 N O2 C(CN)C(=O)....
4 1N2E - PAF C6 H11 O4 CC(C)(CO)[....
5 3IMC Kd = 1100 uM BZ3 C9 H9 N O COc1ccc2c(....
6 4G5Y Kd = 1.69 mM 0OC C6 H9 N O2 S2 CN(C)S(=O)....
7 3IOD Kd = 80 uM A6D C17 H18 N6 O5 S2 c1cc(cc(c1....
8 3COY Kd = 0.96 uM 53H C16 H25 N7 O7 S CC(C)(C)[C....
9 3IUB Kd = 29 uM FG2 C16 H15 N3 O4 S Cc1ccc(nc1....
10 3LE8 Kd = 860 nM 2B5 C21 H18 N2 O5 COc1ccc2c(....
11 3ISJ Kd = 210 uM A8D C11 H12 N2 O4 S COc1ccc2c(....
12 2A86 - BAL C3 H7 N O2 C(CN)C(=O)....
13 3IOE Kd = 540 uM A7D C14 H21 N5 O5 S c1nc(c2c(n....
14 4G5F Kd = 0.88 mM 15N C9 H8 O4 c1ccc2c(c1....
15 4EFK Kd = 3.18 mM 0OC C6 H9 N O2 S2 CN(C)S(=O)....
16 1N2B - PAF C6 H11 O4 CC(C)(CO)[....
17 1N2G - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
18 4DDH Kd = 0.48 mM MS0 C11 H10 O4 COc1ccc2c(....
19 3COZ Kd = 2.7 uM 54H C15 H23 N7 O7 S CC(C)[C@H]....
20 1N2H - PAJ C16 H24 N5 O10 P CC(C)(CO)[....
21 3COW Kd = 0.125 uM 52H C16 H24 N6 O8 S CC(C)(C)[C....
22 3IOC Kd = 210 uM A5D C17 H19 N5 O3 S2 c1ccc(cc1)....
23 3IVC Kd = 76 uM FG4 C21 H17 N O6 COc1ccc2c(....
24 4EF6 Kd = 1.18 mM I2E C10 H10 O4 c1cc2c(cc1....
25 4DDK Kd = 5.13 mM 0HN C8 H6 O4 c1cc2c(cc1....
26 3IMG - BZ3 C9 H9 N O COc1ccc2c(....
27 4FZJ Kd = 0.74 mM 0W1 C8 H8 N2 O2 S Cc1c2cc(sc....
28 1N2I - PAJ C16 H24 N5 O10 P CC(C)(CO)[....
29 3IUE Kd = 1.5 uM FG3 C18 H17 N3 O6 S Cc1ccc(nc1....
30 3IVX Kd = 1.8 uM FG6 C20 H16 N2 O7 S COc1ccc2c(....
31 2A7X - AMP C10 H14 N5 O7 P c1nc(c2c(n....
32 4DE5 Kd = 0.67 mM 0JD C9 H8 O4 c1ccc2c(c1....
33 1N2J - PAF C6 H11 O4 CC(C)(CO)[....
34 3IME Kd = 1000 uM BZ2 C9 H6 O3 c1ccc2c(c1....
35 4DDM Kd = 3.48 mM 0HO C7 H4 N2 O2 S c1cc2c(cc1....
36 3IOB Kd = 380 uM A4D C10 H13 N5 O3 S c1nc(c2c(n....
70% Homology Family (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3IVG Kd = 50 uM FG5 C20 H18 N2 O6 S COc1ccc2c(....
2 2A84 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 1N2O - BAL C3 H7 N O2 C(CN)C(=O)....
4 1N2E - PAF C6 H11 O4 CC(C)(CO)[....
5 3IMC Kd = 1100 uM BZ3 C9 H9 N O COc1ccc2c(....
6 4G5Y Kd = 1.69 mM 0OC C6 H9 N O2 S2 CN(C)S(=O)....
7 3IOD Kd = 80 uM A6D C17 H18 N6 O5 S2 c1cc(cc(c1....
8 3COY Kd = 0.96 uM 53H C16 H25 N7 O7 S CC(C)(C)[C....
9 3IUB Kd = 29 uM FG2 C16 H15 N3 O4 S Cc1ccc(nc1....
10 3LE8 Kd = 860 nM 2B5 C21 H18 N2 O5 COc1ccc2c(....
11 3ISJ Kd = 210 uM A8D C11 H12 N2 O4 S COc1ccc2c(....
12 2A86 - BAL C3 H7 N O2 C(CN)C(=O)....
13 3IOE Kd = 540 uM A7D C14 H21 N5 O5 S c1nc(c2c(n....
14 4G5F Kd = 0.88 mM 15N C9 H8 O4 c1ccc2c(c1....
15 4EFK Kd = 3.18 mM 0OC C6 H9 N O2 S2 CN(C)S(=O)....
16 1N2B - PAF C6 H11 O4 CC(C)(CO)[....
17 1N2G - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
18 4DDH Kd = 0.48 mM MS0 C11 H10 O4 COc1ccc2c(....
19 3COZ Kd = 2.7 uM 54H C15 H23 N7 O7 S CC(C)[C@H]....
20 1N2H - PAJ C16 H24 N5 O10 P CC(C)(CO)[....
21 3COW Kd = 0.125 uM 52H C16 H24 N6 O8 S CC(C)(C)[C....
22 3IOC Kd = 210 uM A5D C17 H19 N5 O3 S2 c1ccc(cc1)....
23 3IVC Kd = 76 uM FG4 C21 H17 N O6 COc1ccc2c(....
24 4EF6 Kd = 1.18 mM I2E C10 H10 O4 c1cc2c(cc1....
25 4DDK Kd = 5.13 mM 0HN C8 H6 O4 c1cc2c(cc1....
26 3IMG - BZ3 C9 H9 N O COc1ccc2c(....
27 4FZJ Kd = 0.74 mM 0W1 C8 H8 N2 O2 S Cc1c2cc(sc....
28 1N2I - PAJ C16 H24 N5 O10 P CC(C)(CO)[....
29 3IUE Kd = 1.5 uM FG3 C18 H17 N3 O6 S Cc1ccc(nc1....
30 3IVX Kd = 1.8 uM FG6 C20 H16 N2 O7 S COc1ccc2c(....
31 2A7X - AMP C10 H14 N5 O7 P c1nc(c2c(n....
32 4DE5 Kd = 0.67 mM 0JD C9 H8 O4 c1ccc2c(c1....
33 1N2J - PAF C6 H11 O4 CC(C)(CO)[....
34 3IME Kd = 1000 uM BZ2 C9 H6 O3 c1ccc2c(c1....
35 4DDM Kd = 3.48 mM 0HO C7 H4 N2 O2 S c1cc2c(cc1....
36 3IOB Kd = 380 uM A4D C10 H13 N5 O3 S c1nc(c2c(n....
50% Homology Family (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3IVG Kd = 50 uM FG5 C20 H18 N2 O6 S COc1ccc2c(....
2 2A84 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 1N2O - BAL C3 H7 N O2 C(CN)C(=O)....
4 1N2E - PAF C6 H11 O4 CC(C)(CO)[....
5 3IMC Kd = 1100 uM BZ3 C9 H9 N O COc1ccc2c(....
6 4G5Y Kd = 1.69 mM 0OC C6 H9 N O2 S2 CN(C)S(=O)....
7 3IOD Kd = 80 uM A6D C17 H18 N6 O5 S2 c1cc(cc(c1....
8 3COY Kd = 0.96 uM 53H C16 H25 N7 O7 S CC(C)(C)[C....
9 3IUB Kd = 29 uM FG2 C16 H15 N3 O4 S Cc1ccc(nc1....
10 3LE8 Kd = 860 nM 2B5 C21 H18 N2 O5 COc1ccc2c(....
11 3ISJ Kd = 210 uM A8D C11 H12 N2 O4 S COc1ccc2c(....
12 2A86 - BAL C3 H7 N O2 C(CN)C(=O)....
13 3IOE Kd = 540 uM A7D C14 H21 N5 O5 S c1nc(c2c(n....
14 4G5F Kd = 0.88 mM 15N C9 H8 O4 c1ccc2c(c1....
15 4EFK Kd = 3.18 mM 0OC C6 H9 N O2 S2 CN(C)S(=O)....
16 1N2B - PAF C6 H11 O4 CC(C)(CO)[....
17 1N2G - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
18 4DDH Kd = 0.48 mM MS0 C11 H10 O4 COc1ccc2c(....
19 3COZ Kd = 2.7 uM 54H C15 H23 N7 O7 S CC(C)[C@H]....
20 1N2H - PAJ C16 H24 N5 O10 P CC(C)(CO)[....
21 3COW Kd = 0.125 uM 52H C16 H24 N6 O8 S CC(C)(C)[C....
22 3IOC Kd = 210 uM A5D C17 H19 N5 O3 S2 c1ccc(cc1)....
23 3IVC Kd = 76 uM FG4 C21 H17 N O6 COc1ccc2c(....
24 4EF6 Kd = 1.18 mM I2E C10 H10 O4 c1cc2c(cc1....
25 4DDK Kd = 5.13 mM 0HN C8 H6 O4 c1cc2c(cc1....
26 3IMG - BZ3 C9 H9 N O COc1ccc2c(....
27 4FZJ Kd = 0.74 mM 0W1 C8 H8 N2 O2 S Cc1c2cc(sc....
28 1N2I - PAJ C16 H24 N5 O10 P CC(C)(CO)[....
29 3IUE Kd = 1.5 uM FG3 C18 H17 N3 O6 S Cc1ccc(nc1....
30 3IVX Kd = 1.8 uM FG6 C20 H16 N2 O7 S COc1ccc2c(....
31 2A7X - AMP C10 H14 N5 O7 P c1nc(c2c(n....
32 4DE5 Kd = 0.67 mM 0JD C9 H8 O4 c1ccc2c(c1....
33 1N2J - PAF C6 H11 O4 CC(C)(CO)[....
34 3IME Kd = 1000 uM BZ2 C9 H6 O3 c1ccc2c(c1....
35 4DDM Kd = 3.48 mM 0HO C7 H4 N2 O2 S c1cc2c(cc1....
36 3IOB Kd = 380 uM A4D C10 H13 N5 O3 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: A7D; Similar ligands found: 219
No: Ligand ECFP6 Tc MDL keys Tc
1 A7D 1 1
2 DSH 0.763889 0.927536
3 SAH 0.734177 0.926471
4 3DH 0.708333 0.882353
5 DTA 0.690141 0.869565
6 S8M 0.674419 0.887324
7 MTA 0.657534 0.882353
8 SXZ 0.637363 0.851351
9 5X8 0.634146 0.897059
10 XYA 0.614286 0.909091
11 RAB 0.614286 0.909091
12 ADN 0.614286 0.909091
13 5N5 0.597222 0.880597
14 A4D 0.589041 0.909091
15 5CD 0.589041 0.865672
16 EP4 0.565789 0.830986
17 M2T 0.558442 0.833333
18 A5D 0.545455 0.869565
19 AAT 0.544444 0.875
20 AMP 0.54321 0.797297
21 LMS 0.54321 0.722892
22 A 0.54321 0.797297
23 ZAS 0.52439 0.794521
24 ABM 0.52381 0.776316
25 J7C 0.52381 0.847222
26 45A 0.52381 0.776316
27 SRA 0.518072 0.779221
28 6RE 0.518072 0.835616
29 S4M 0.517647 0.842105
30 AOC 0.511905 0.882353
31 TT8 0.510638 0.9
32 A3N 0.505882 0.869565
33 A2D 0.505882 0.776316
34 SFG 0.505618 0.882353
35 SSA 0.5 0.72093
36 5AD 0.5 0.80303
37 GJV 0.5 0.824324
38 EEM 0.494624 0.826667
39 SA8 0.494505 0.849315
40 ADX 0.494382 0.722892
41 MAO 0.494253 0.807692
42 A12 0.494253 0.792208
43 BA3 0.494253 0.776316
44 AP2 0.494253 0.792208
45 Y3J 0.493506 0.779412
46 5CA 0.489583 0.72093
47 SAI 0.48913 0.885714
48 AP5 0.488636 0.776316
49 B4P 0.488636 0.776316
50 5AS 0.488636 0.701149
51 ADP 0.488636 0.776316
52 A6D 0.484848 0.769231
53 SMM 0.484211 0.818182
54 SAM 0.483871 0.851351
55 AN2 0.483146 0.766234
56 SON 0.483146 0.792208
57 AT4 0.483146 0.769231
58 ADP MG 0.483146 0.797297
59 KAA 0.48 0.735632
60 52H 0.479167 0.681818
61 M33 0.477778 0.766234
62 AU1 0.477778 0.75641
63 MHZ 0.477778 0.807692
64 CA0 0.477778 0.75641
65 NVA LMS 0.474747 0.696629
66 TSB 0.474227 0.697674
67 7D7 0.473684 0.850746
68 A5A 0.473684 0.705882
69 G5A 0.473118 0.72093
70 HEJ 0.472527 0.776316
71 50T 0.472527 0.766234
72 H1Q 0.472527 0.786667
73 ACP 0.472527 0.779221
74 KG4 0.472527 0.75641
75 ATP 0.472527 0.776316
76 K15 0.47 0.815789
77 GEK 0.469388 0.887324
78 8QN 0.469388 0.766234
79 SRP 0.46875 0.792208
80 8LH 0.46875 0.769231
81 S7M 0.46875 0.851351
82 APC 0.467391 0.792208
83 5FA 0.467391 0.776316
84 AQP 0.467391 0.776316
85 AR6 0.467391 0.776316
86 PRX 0.467391 0.779221
87 APR 0.467391 0.776316
88 GSU 0.465347 0.72093
89 DSZ 0.464646 0.701149
90 LSS 0.464646 0.685393
91 VMS 0.463918 0.689655
92 54H 0.463918 0.689655
93 5AL 0.463158 0.766234
94 RBY 0.462366 0.792208
95 SAP 0.462366 0.759494
96 ADV 0.462366 0.792208
97 AD9 0.462366 0.75641
98 APC MG 0.462366 0.8
99 ATP MG 0.462366 0.797297
100 ADP PO3 0.462366 0.797297
101 AGS 0.462366 0.759494
102 ME8 0.460784 0.777778
103 62X 0.46 0.794872
104 AHX 0.46 0.7625
105 NEC 0.45977 0.8
106 8LQ 0.459184 0.769231
107 53H 0.459184 0.681818
108 3AM 0.458824 0.783784
109 ACQ 0.452632 0.779221
110 TAT 0.452632 0.769231
111 ANP 0.452632 0.75641
112 GAP 0.452632 0.779221
113 T99 0.452632 0.769231
114 LAD 0.45098 0.797468
115 A3S 0.450549 0.897059
116 NSS 0.45 0.701149
117 0UM 0.45 0.837838
118 PAJ 0.45 0.731707
119 N5A 0.449438 0.84058
120 8LE 0.447917 0.7375
121 DAL AMP 0.444444 0.766234
122 8X1 0.444444 0.715909
123 A3P 0.444444 0.773333
124 XAH 0.443396 0.777778
125 ATF 0.443299 0.746835
126 ALF ADP 0.443299 0.7375
127 ADP ALF 0.443299 0.7375
128 N5O 0.443182 0.869565
129 A3G 0.443182 0.884058
130 36A 0.441441 0.864865
131 LEU LMS 0.441176 0.677778
132 A3T 0.44086 0.882353
133 9ZA 0.44 0.728395
134 25A 0.44 0.776316
135 9ZD 0.44 0.728395
136 VO4 ADP 0.438776 0.766234
137 ADP VO4 0.438776 0.766234
138 6YZ 0.438776 0.779221
139 A1R 0.435644 0.794872
140 AMO 0.435644 0.769231
141 4AD 0.435644 0.759494
142 7D5 0.435294 0.763158
143 HQG 0.434343 0.766234
144 PTJ 0.432692 0.719512
145 NB8 0.432692 0.740741
146 TXA 0.432692 0.746835
147 JB6 0.432692 0.794872
148 3AD 0.432099 0.923077
149 NVA 2AD 0.431579 0.861111
150 DLL 0.431373 0.766234
151 2AM 0.430233 0.773333
152 MAP 0.43 0.7375
153 A22 0.43 0.766234
154 YSA 0.429907 0.701149
155 KB1 0.428571 0.837838
156 VRT 0.427083 0.873239
157 AMP DBH 0.425926 0.75641
158 OOB 0.425743 0.766234
159 OZV 0.425743 0.776316
160 5SV 0.425743 0.7625
161 P5A 0.423077 0.727273
162 WAQ 0.423077 0.794872
163 5F1 0.421687 0.811594
164 A3R 0.421569 0.794872
165 ADQ 0.421569 0.779221
166 8PZ 0.420561 0.701149
167 QQY 0.420455 0.75
168 YLP 0.419643 0.759036
169 OZP 0.419643 0.849315
170 FYA 0.419048 0.789474
171 AFH 0.418182 0.753086
172 GA7 0.418182 0.792208
173 CC5 0.417722 0.907692
174 00A 0.417476 0.728395
175 OVE 0.41573 0.766234
176 MTP 0.414634 0.805556
177 3L1 0.414634 0.882353
178 3D1 0.414634 0.882353
179 TAD 0.414414 0.775
180 IOT 0.413793 0.75
181 3UK 0.413462 0.75641
182 ADP BMA 0.413462 0.779221
183 9X8 0.413462 0.759494
184 OAD 0.413462 0.75641
185 A2P 0.413043 0.76
186 SO8 0.412371 0.84507
187 9SN 0.411215 0.719512
188 2VA 0.410526 0.857143
189 B5V 0.409524 0.746835
190 PR8 0.409524 0.7875
191 J4G 0.409524 0.782051
192 A A 0.409524 0.776316
193 QQX 0.409091 0.74026
194 F0P 0.408696 0.849315
195 B5M 0.407407 0.7375
196 B5Y 0.407407 0.7375
197 YAP 0.407407 0.759494
198 NOC 0.407407 0.820895
199 FA5 0.407407 0.769231
200 48N 0.40708 0.740741
201 BIS 0.40566 0.75
202 9K8 0.40566 0.659341
203 3OD 0.40566 0.75641
204 1ZZ 0.40566 0.73494
205 7MD 0.405405 0.756098
206 ARG AMP 0.405405 0.746988
207 SP1 0.404494 0.753247
208 RP1 0.404494 0.753247
209 ACK 0.404494 0.767123
210 PPS 0.40404 0.702381
211 B1U 0.40367 0.645161
212 HY8 0.403509 0.876712
213 PAP 0.402062 0.763158
214 MYR AMP 0.401869 0.73494
215 25L 0.401869 0.766234
216 KH3 0.401786 0.828947
217 WSA 0.4 0.709302
218 N37 0.4 0.833333
219 TYR AMP 0.4 0.759494
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3COW; Ligand: 52H; 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: 3cow.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3COW; Ligand: 52H; 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: 3cow.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
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