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: 190
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 ADN 0.614286 0.909091
11 XYA 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 AMP 0.54321 0.797297
21 A 0.54321 0.797297
22 ZAS 0.52439 0.794521
23 ABM 0.52381 0.776316
24 J7C 0.52381 0.847222
25 SRA 0.518072 0.779221
26 6RE 0.518072 0.835616
27 S4M 0.517647 0.842105
28 AMP MG 0.511905 0.776316
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 A12 0.494253 0.792208
41 BA3 0.494253 0.776316
42 MAO 0.494253 0.807692
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 AP5 0.488636 0.776316
50 5AS 0.488636 0.701149
51 A6D 0.484848 0.769231
52 SMM 0.484211 0.818182
53 SAM 0.483871 0.851351
54 AN2 0.483146 0.766234
55 SON 0.483146 0.792208
56 KAA 0.48 0.735632
57 52H 0.479167 0.681818
58 M33 0.477778 0.766234
59 MHZ 0.477778 0.807692
60 ADP MG 0.477778 0.766234
61 CA0 0.477778 0.75641
62 AU1 0.477778 0.75641
63 TSB 0.474227 0.697674
64 7D7 0.473684 0.850746
65 A5A 0.473684 0.705882
66 G5A 0.473118 0.72093
67 ACP 0.472527 0.779221
68 ATP 0.472527 0.776316
69 BEF ADP 0.472527 0.746835
70 50T 0.472527 0.766234
71 ADP BEF 0.472527 0.746835
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 5FA 0.467391 0.776316
78 PRX 0.467391 0.779221
79 APC 0.467391 0.792208
80 APR 0.467391 0.776316
81 AR6 0.467391 0.776316
82 AQP 0.467391 0.776316
83 GSU 0.465347 0.72093
84 LSS 0.464646 0.685393
85 DSZ 0.464646 0.701149
86 VMS 0.463918 0.689655
87 54H 0.463918 0.689655
88 5AL 0.463158 0.766234
89 AD9 0.462366 0.75641
90 ADP PO3 0.462366 0.797297
91 SAP 0.462366 0.759494
92 ADV 0.462366 0.792208
93 AGS 0.462366 0.759494
94 RBY 0.462366 0.792208
95 ME8 0.460784 0.777778
96 AHX 0.46 0.7625
97 62X 0.46 0.794872
98 NVA LMS 0.46 0.685393
99 NEC 0.45977 0.8
100 53H 0.459184 0.681818
101 3AM 0.458824 0.783784
102 ATP MG 0.457447 0.766234
103 ANP 0.452632 0.75641
104 ACQ 0.452632 0.779221
105 TAT 0.452632 0.769231
106 GAP 0.452632 0.779221
107 LAD 0.45098 0.797468
108 A3S 0.450549 0.897059
109 NSS 0.45 0.701149
110 PAJ 0.45 0.731707
111 0UM 0.45 0.837838
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 ALF ADP 0.443299 0.7375
117 ATF 0.443299 0.746835
118 A3G 0.443182 0.884058
119 36A 0.441441 0.864865
120 LEU LMS 0.441176 0.666667
121 A3T 0.44086 0.882353
122 25A 0.44 0.776316
123 VO4 ADP 0.438776 0.766234
124 ADP VO4 0.438776 0.766234
125 ANP MG 0.438776 0.7375
126 A1R 0.435644 0.794872
127 AMO 0.435644 0.769231
128 4AD 0.435644 0.759494
129 7D5 0.435294 0.763158
130 JB6 0.432692 0.794872
131 TXA 0.432692 0.746835
132 PTJ 0.432692 0.719512
133 NB8 0.432692 0.740741
134 3AD 0.432099 0.923077
135 DLL 0.431373 0.766234
136 2AM 0.430233 0.773333
137 MAP 0.43 0.7375
138 A22 0.43 0.766234
139 YSA 0.429907 0.701149
140 KB1 0.428571 0.837838
141 VRT 0.427083 0.873239
142 AMP DBH 0.425926 0.75641
143 OOB 0.425743 0.766234
144 5SV 0.425743 0.7625
145 P5A 0.423077 0.727273
146 WAQ 0.423077 0.794872
147 5F1 0.421687 0.811594
148 ADQ 0.421569 0.779221
149 QQY 0.420455 0.75
150 YLP 0.419643 0.759036
151 FYA 0.419048 0.789474
152 AFH 0.418182 0.753086
153 CC5 0.417722 0.907692
154 00A 0.417476 0.728395
155 TYR AMP 0.416667 0.746835
156 OVE 0.41573 0.766234
157 MTP 0.414634 0.805556
158 3D1 0.414634 0.882353
159 3L1 0.414634 0.882353
160 TAD 0.414414 0.775
161 IOT 0.413793 0.75
162 3UK 0.413462 0.75641
163 ADP BMA 0.413462 0.779221
164 OAD 0.413462 0.75641
165 A2P 0.413043 0.76
166 SO8 0.412371 0.84507
167 9SN 0.411215 0.719512
168 ARG AMP 0.410714 0.746988
169 2VA 0.410526 0.857143
170 PR8 0.409524 0.7875
171 A A 0.409524 0.776316
172 QQX 0.409091 0.74026
173 FA5 0.407407 0.769231
174 NOC 0.407407 0.820895
175 YAP 0.407407 0.759494
176 48N 0.40708 0.740741
177 BIS 0.40566 0.75
178 3OD 0.40566 0.75641
179 1ZZ 0.40566 0.73494
180 7MD 0.405405 0.756098
181 ACK 0.404494 0.767123
182 RP1 0.404494 0.753247
183 SP1 0.404494 0.753247
184 PPS 0.40404 0.702381
185 PAP 0.402062 0.763158
186 NVA 2AD 0.402062 0.819444
187 25L 0.401869 0.766234
188 MYR AMP 0.401869 0.73494
189 KH3 0.401786 0.828947
190 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: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3COW; Ligand: 52H; Similar sites found: 28
This union binding pocket(no: 2) in the query (biounit: 3cow.bio1) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3JRX S1A 0.03478 0.40027 1.66113
2 3ZIU LSS 0.00000576 0.41197 1.99336
3 2PID YSA 0.00001517 0.41256 2.24719
4 1PFY MSP 0.000009007 0.41365 2.32558
5 2YLN CYS 0.03763 0.41859 3.18021
6 3C8Z 5CA 0.00001508 0.55124 3.32226
7 4E2J MOF 0.01038 0.41359 3.6
8 5UFS 1TA 0.02043 0.40034 3.62903
9 1G27 BB1 0.0266 0.40308 4.16667
10 4GQY AMP 0.02535 0.42033 4.24242
11 3R9V DXC 0.002825 0.42978 4.31894
12 1R6T TYM 0.0001066 0.4568 4.65116
13 4J75 TYM 0.000005874 0.43172 4.88998
14 4IZY 1J2 0.02476 0.40178 5.31561
15 1R4W GSH 0.03057 0.41247 5.75221
16 2QTR NXX 0.0001706 0.407 5.82011
17 1S9D AFB 0.03721 0.41143 6.40394
18 2X1L ADN 0.00006608 0.5435 6.97674
19 3ND6 ATP 0.0001626 0.40209 7.30897
20 3HUN ZZ7 0.03785 0.41468 8.30565
21 2XG5 EC5 0.01024 0.45217 8.7156
22 2XG5 EC2 0.01024 0.45217 8.7156
23 5BXV MGP 0.02564 0.42693 9.09091
24 3KFL ME8 0.0000005149 0.44981 9.63455
25 1WS1 BB2 0.03719 0.40174 12.8205
26 3KP6 SAL 0.008535 0.45594 13.245
27 3HL4 CDC 0.001182 0.46333 14.4068
28 1N1D C2G 0.003558 0.42834 17.0543
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