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: 201
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 ADN 0.614286 0.909091
12 RAB 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 LMS 0.54321 0.722892
21 A 0.54321 0.797297
22 AMP 0.54321 0.797297
23 ZAS 0.52439 0.794521
24 J7C 0.52381 0.847222
25 ABM 0.52381 0.776316
26 6RE 0.518072 0.835616
27 SRA 0.518072 0.779221
28 S4M 0.517647 0.842105
29 AOC 0.511905 0.882353
30 TT8 0.510638 0.9
31 A3N 0.505882 0.869565
32 A2D 0.505882 0.776316
33 SFG 0.505618 0.882353
34 GJV 0.5 0.824324
35 5AD 0.5 0.80303
36 SSA 0.5 0.72093
37 EEM 0.494624 0.826667
38 SA8 0.494505 0.849315
39 ADX 0.494382 0.722892
40 BA3 0.494253 0.776316
41 MAO 0.494253 0.807692
42 A12 0.494253 0.792208
43 AP2 0.494253 0.792208
44 Y3J 0.493506 0.779412
45 5CA 0.489583 0.72093
46 SAI 0.48913 0.885714
47 ADP 0.488636 0.776316
48 B4P 0.488636 0.776316
49 5AS 0.488636 0.701149
50 AP5 0.488636 0.776316
51 A6D 0.484848 0.769231
52 SMM 0.484211 0.818182
53 SAM 0.483871 0.851351
54 SON 0.483146 0.792208
55 AN2 0.483146 0.766234
56 AT4 0.483146 0.769231
57 KAA 0.48 0.735632
58 52H 0.479167 0.681818
59 AU1 0.477778 0.75641
60 M33 0.477778 0.766234
61 CA0 0.477778 0.75641
62 MHZ 0.477778 0.807692
63 NVA LMS 0.474747 0.696629
64 TSB 0.474227 0.697674
65 7D7 0.473684 0.850746
66 A5A 0.473684 0.705882
67 G5A 0.473118 0.72093
68 50T 0.472527 0.766234
69 HEJ 0.472527 0.776316
70 ATP 0.472527 0.776316
71 ACP 0.472527 0.779221
72 K15 0.47 0.815789
73 GEK 0.469388 0.887324
74 8QN 0.469388 0.766234
75 S7M 0.46875 0.851351
76 SRP 0.46875 0.792208
77 APR 0.467391 0.776316
78 APC 0.467391 0.792208
79 PRX 0.467391 0.779221
80 5FA 0.467391 0.776316
81 AR6 0.467391 0.776316
82 AQP 0.467391 0.776316
83 GSU 0.465347 0.72093
84 DSZ 0.464646 0.701149
85 LSS 0.464646 0.685393
86 54H 0.463918 0.689655
87 VMS 0.463918 0.689655
88 5AL 0.463158 0.766234
89 AD9 0.462366 0.75641
90 ADV 0.462366 0.792208
91 RBY 0.462366 0.792208
92 SAP 0.462366 0.759494
93 ADP PO3 0.462366 0.797297
94 AGS 0.462366 0.759494
95 ME8 0.460784 0.777778
96 AHX 0.46 0.7625
97 62X 0.46 0.794872
98 NEC 0.45977 0.8
99 53H 0.459184 0.681818
100 3AM 0.458824 0.783784
101 ACQ 0.452632 0.779221
102 ANP 0.452632 0.75641
103 TAT 0.452632 0.769231
104 T99 0.452632 0.769231
105 GAP 0.452632 0.779221
106 LAD 0.45098 0.797468
107 A3S 0.450549 0.897059
108 NSS 0.45 0.701149
109 0UM 0.45 0.837838
110 PAJ 0.45 0.731707
111 8X1 0.444444 0.715909
112 DAL AMP 0.444444 0.766234
113 A3P 0.444444 0.773333
114 XAH 0.443396 0.777778
115 ADP ALF 0.443299 0.7375
116 ATF 0.443299 0.746835
117 ALF ADP 0.443299 0.7375
118 A3G 0.443182 0.884058
119 36A 0.441441 0.864865
120 LEU LMS 0.441176 0.677778
121 A3T 0.44086 0.882353
122 9ZA 0.44 0.728395
123 25A 0.44 0.776316
124 9ZD 0.44 0.728395
125 ADP VO4 0.438776 0.766234
126 6YZ 0.438776 0.779221
127 VO4 ADP 0.438776 0.766234
128 AMO 0.435644 0.769231
129 A1R 0.435644 0.794872
130 4AD 0.435644 0.759494
131 7D5 0.435294 0.763158
132 NB8 0.432692 0.740741
133 JB6 0.432692 0.794872
134 TXA 0.432692 0.746835
135 PTJ 0.432692 0.719512
136 3AD 0.432099 0.923077
137 NVA 2AD 0.431579 0.861111
138 DLL 0.431373 0.766234
139 2AM 0.430233 0.773333
140 MAP 0.43 0.7375
141 A22 0.43 0.766234
142 YSA 0.429907 0.701149
143 KB1 0.428571 0.837838
144 VRT 0.427083 0.873239
145 AMP DBH 0.425926 0.75641
146 5SV 0.425743 0.7625
147 OOB 0.425743 0.766234
148 WAQ 0.423077 0.794872
149 P5A 0.423077 0.727273
150 5F1 0.421687 0.811594
151 ADQ 0.421569 0.779221
152 A3R 0.421569 0.794872
153 8PZ 0.420561 0.701149
154 QQY 0.420455 0.75
155 YLP 0.419643 0.759036
156 FYA 0.419048 0.789474
157 GA7 0.418182 0.792208
158 AFH 0.418182 0.753086
159 CC5 0.417722 0.907692
160 00A 0.417476 0.728395
161 OVE 0.41573 0.766234
162 MTP 0.414634 0.805556
163 3D1 0.414634 0.882353
164 3L1 0.414634 0.882353
165 TAD 0.414414 0.775
166 IOT 0.413793 0.75
167 OAD 0.413462 0.75641
168 3UK 0.413462 0.75641
169 9X8 0.413462 0.759494
170 ADP BMA 0.413462 0.779221
171 A2P 0.413043 0.76
172 SO8 0.412371 0.84507
173 9SN 0.411215 0.719512
174 2VA 0.410526 0.857143
175 PR8 0.409524 0.7875
176 A A 0.409524 0.776316
177 B5V 0.409524 0.746835
178 QQX 0.409091 0.74026
179 F0P 0.408696 0.849315
180 FA5 0.407407 0.769231
181 NOC 0.407407 0.820895
182 B5M 0.407407 0.7375
183 B5Y 0.407407 0.7375
184 YAP 0.407407 0.759494
185 48N 0.40708 0.740741
186 BIS 0.40566 0.75
187 1ZZ 0.40566 0.73494
188 9K8 0.40566 0.659341
189 3OD 0.40566 0.75641
190 7MD 0.405405 0.756098
191 ARG AMP 0.405405 0.746988
192 SP1 0.404494 0.753247
193 RP1 0.404494 0.753247
194 ACK 0.404494 0.767123
195 PPS 0.40404 0.702381
196 PAP 0.402062 0.763158
197 MYR AMP 0.401869 0.73494
198 25L 0.401869 0.766234
199 KH3 0.401786 0.828947
200 TYR AMP 0.4 0.759494
201 WSA 0.4 0.709302
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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