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 = 75 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 = 670 uM 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 = 75 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 = 670 uM 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 = 75 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 = 670 uM 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 (2D)
Ligand no: 1; Ligand: A7D; Similar ligands found: 238
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 RAB 0.614286 0.909091
11 XYA 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 U4Y 0.574257 0.887324
17 EP4 0.565789 0.830986
18 M2T 0.558442 0.833333
19 A5D 0.545455 0.869565
20 AAT 0.544444 0.875
21 AMP 0.54321 0.797297
22 LMS 0.54321 0.722892
23 A 0.54321 0.797297
24 ZAS 0.52439 0.794521
25 45A 0.52381 0.776316
26 J7C 0.52381 0.847222
27 ABM 0.52381 0.776316
28 SRA 0.518072 0.779221
29 6RE 0.518072 0.835616
30 AMP MG 0.518072 0.808219
31 S4M 0.517647 0.842105
32 AOC 0.511905 0.882353
33 TT8 0.510638 0.9
34 A2D 0.505882 0.776316
35 A3N 0.505882 0.869565
36 SFG 0.505618 0.882353
37 GJV 0.5 0.824324
38 5AD 0.5 0.80303
39 SSA 0.5 0.72093
40 EEM 0.494624 0.826667
41 SA8 0.494505 0.849315
42 ADX 0.494382 0.722892
43 AP2 0.494253 0.792208
44 MAO 0.494253 0.807692
45 A12 0.494253 0.792208
46 BA3 0.494253 0.776316
47 Y3J 0.493506 0.779412
48 5CA 0.489583 0.72093
49 SAI 0.48913 0.885714
50 B4P 0.488636 0.776316
51 AP5 0.488636 0.776316
52 ADP 0.488636 0.776316
53 5AS 0.488636 0.701149
54 NWW 0.487179 0.791045
55 A6D 0.484848 0.769231
56 SMM 0.484211 0.818182
57 SAM 0.483871 0.851351
58 AN2 0.483146 0.766234
59 SON 0.483146 0.792208
60 AT4 0.483146 0.769231
61 ADP BEF 0.483146 0.797297
62 ADP MG 0.483146 0.797297
63 KAA 0.48 0.735632
64 52H 0.479167 0.681818
65 AU1 0.477778 0.75641
66 MHZ 0.477778 0.807692
67 CA0 0.477778 0.75641
68 M33 0.477778 0.766234
69 NVA LMS 0.474747 0.696629
70 TSB 0.474227 0.697674
71 7D7 0.473684 0.850746
72 A5A 0.473684 0.705882
73 G5A 0.473118 0.72093
74 ATP 0.472527 0.776316
75 ACP 0.472527 0.779221
76 50T 0.472527 0.766234
77 H1Q 0.472527 0.786667
78 KG4 0.472527 0.75641
79 HEJ 0.472527 0.776316
80 K15 0.47 0.815789
81 8QN 0.469388 0.766234
82 GEK 0.469388 0.887324
83 8LH 0.46875 0.769231
84 SRP 0.46875 0.792208
85 S7M 0.46875 0.851351
86 APC 0.467391 0.792208
87 5FA 0.467391 0.776316
88 APR 0.467391 0.776316
89 PRX 0.467391 0.779221
90 AQP 0.467391 0.776316
91 AR6 0.467391 0.776316
92 GSU 0.465347 0.72093
93 LSS 0.464646 0.685393
94 DSZ 0.464646 0.701149
95 54H 0.463918 0.689655
96 VMS 0.463918 0.689655
97 5AL 0.463158 0.766234
98 AGS 0.462366 0.759494
99 APC MG 0.462366 0.8
100 RBY 0.462366 0.792208
101 ATP MG 0.462366 0.797297
102 ADV 0.462366 0.792208
103 ADP PO3 0.462366 0.797297
104 AD9 0.462366 0.75641
105 ME8 0.460784 0.777778
106 JNT 0.46 0.802632
107 AHX 0.46 0.7625
108 62X 0.46 0.794872
109 NEC 0.45977 0.8
110 8LQ 0.459184 0.769231
111 KY2 0.459184 0.851351
112 53H 0.459184 0.681818
113 3AM 0.458824 0.783784
114 BEF ADP 0.457447 0.776316
115 ACQ 0.452632 0.779221
116 GAP 0.452632 0.779221
117 T99 0.452632 0.769231
118 ANP 0.452632 0.75641
119 TAT 0.452632 0.769231
120 LAD 0.45098 0.797468
121 A3S 0.450549 0.897059
122 0UM 0.45 0.837838
123 NSS 0.45 0.701149
124 KYB 0.45 0.851351
125 PAJ 0.45 0.731707
126 N5A 0.449438 0.84058
127 V2G 0.447917 0.7625
128 8LE 0.447917 0.7375
129 A3P 0.444444 0.773333
130 DAL AMP 0.444444 0.766234
131 8X1 0.444444 0.715909
132 QA7 0.444444 0.7375
133 XAH 0.443396 0.777778
134 KYE 0.443396 0.828947
135 ANP MG 0.443299 0.766234
136 VO4 ADP 0.443299 0.75641
137 ALF ADP 0.443299 0.7375
138 ATF 0.443299 0.746835
139 N5O 0.443182 0.869565
140 A3G 0.443182 0.884058
141 36A 0.441441 0.864865
142 LEU LMS 0.441176 0.693182
143 A3T 0.44086 0.882353
144 9ZA 0.44 0.728395
145 25A 0.44 0.776316
146 QXP 0.44 0.705882
147 9ZD 0.44 0.728395
148 V47 0.438776 0.84058
149 6YZ 0.438776 0.779221
150 R2V 0.436893 0.705882
151 AMO 0.435644 0.769231
152 4AD 0.435644 0.759494
153 A1R 0.435644 0.794872
154 7D5 0.435294 0.763158
155 HQG 0.434343 0.766234
156 PTJ 0.432692 0.719512
157 TXA 0.432692 0.746835
158 NB8 0.432692 0.740741
159 JB6 0.432692 0.794872
160 3AD 0.432099 0.923077
161 NVA 2AD 0.431579 0.861111
162 DLL 0.431373 0.766234
163 2AM 0.430233 0.773333
164 NWQ 0.430233 0.768116
165 MAP 0.43 0.7375
166 A22 0.43 0.766234
167 YSA 0.429907 0.701149
168 KB1 0.428571 0.837838
169 QXG 0.427184 0.697674
170 VRT 0.427083 0.873239
171 AMP DBH 0.425926 0.75641
172 OZV 0.425743 0.776316
173 OOB 0.425743 0.766234
174 5SV 0.425743 0.7625
175 KL2 0.423529 0.746667
176 KY8 0.423077 0.875
177 P5A 0.423077 0.727273
178 WAQ 0.423077 0.794872
179 5F1 0.421687 0.811594
180 ADQ 0.421569 0.779221
181 A3R 0.421569 0.794872
182 8PZ 0.420561 0.701149
183 QQY 0.420455 0.75
184 YLP 0.419643 0.759036
185 OZP 0.419643 0.849315
186 FYA 0.419048 0.789474
187 AFH 0.418182 0.753086
188 GA7 0.418182 0.792208
189 CC5 0.417722 0.907692
190 K2H 0.417476 0.808219
191 00A 0.417476 0.728395
192 OVE 0.41573 0.766234
193 KY5 0.415094 0.9
194 3L1 0.414634 0.882353
195 3D1 0.414634 0.882353
196 MTP 0.414634 0.805556
197 TAD 0.414414 0.775
198 KXW 0.414414 0.875
199 IOT 0.413793 0.75
200 OAD 0.413462 0.75641
201 3UK 0.413462 0.75641
202 9X8 0.413462 0.759494
203 ADP BMA 0.413462 0.779221
204 A2P 0.413043 0.76
205 SO8 0.412371 0.84507
206 9SN 0.411215 0.719512
207 2VA 0.410526 0.857143
208 PR8 0.409524 0.7875
209 B5V 0.409524 0.746835
210 J4G 0.409524 0.782051
211 K2K 0.409524 0.887324
212 QQX 0.409091 0.74026
213 F0P 0.408696 0.849315
214 B5Y 0.407407 0.7375
215 K3K 0.407407 0.859155
216 B5M 0.407407 0.7375
217 FA5 0.407407 0.769231
218 NOC 0.407407 0.820895
219 48N 0.40708 0.740741
220 3OD 0.40566 0.75641
221 9K8 0.40566 0.659341
222 1ZZ 0.40566 0.73494
223 BIS 0.40566 0.75
224 7MD 0.405405 0.756098
225 ARG AMP 0.405405 0.746988
226 SP1 0.404494 0.753247
227 ACK 0.404494 0.767123
228 RP1 0.404494 0.753247
229 PPS 0.40404 0.702381
230 B1U 0.40367 0.645161
231 HY8 0.403509 0.876712
232 PAP 0.402062 0.763158
233 MYR AMP 0.401869 0.73494
234 25L 0.401869 0.766234
235 KH3 0.401786 0.828947
236 N37 0.4 0.833333
237 WSA 0.4 0.709302
238 K3E 0.4 0.847222
Similar Ligands (3D)
Ligand no: 1; Ligand: A7D; Similar ligands found: 0
No: Ligand Similarity coefficient
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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