Receptor
PDB id Resolution Class Description Source Keywords
3IOC 2.5 Å EC: 6.3.2.1 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE SYNTHETASE AT 2.50 ANG RESOLUTION IN COMPLEX WITH 5'-DEOXY-( BENZYLDISULFANYL)-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
A5D A:301;
B:302;
Valid;
Valid;
none;
none;
Kd = 210 uM
405.494 C17 H19 N5 O3 S2 c1ccc...
GOL A:701;
A:708;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
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: A5D; Similar ligands found: 224
No: Ligand ECFP6 Tc MDL keys Tc
1 A5D 1 1
2 DTA 0.746479 1
3 A6D 0.696629 0.876712
4 MTA 0.623377 0.867647
5 3DH 0.607595 0.867647
6 5N5 0.586667 0.865672
7 RAB 0.581081 0.865672
8 XYA 0.581081 0.865672
9 ADN 0.581081 0.865672
10 5CD 0.578947 0.878788
11 DSH 0.578313 0.833333
12 A4D 0.558442 0.893939
13 5X8 0.550562 0.855072
14 A7D 0.545455 0.869565
15 EP4 0.5375 0.816901
16 A 0.535714 0.808219
17 AMP 0.535714 0.808219
18 SAH 0.532609 0.857143
19 M2T 0.530864 0.819444
20 DLL 0.530612 0.8
21 SRA 0.529412 0.813333
22 AAT 0.521277 0.810811
23 LMS 0.517647 0.753086
24 FYA 0.514852 0.8
25 FA5 0.514563 0.779221
26 OOB 0.510204 0.8
27 AOC 0.505747 0.84058
28 J7C 0.5 0.783784
29 ZAS 0.5 0.830986
30 A2D 0.5 0.810811
31 45A 0.5 0.786667
32 ABM 0.5 0.786667
33 S8M 0.494949 0.847222
34 SON 0.494505 0.779221
35 6RE 0.494253 0.773333
36 AMP MG 0.494253 0.819444
37 8LE 0.489583 0.746835
38 CA0 0.48913 0.766234
39 ADX 0.48913 0.753086
40 M33 0.48913 0.776316
41 A12 0.488889 0.779221
42 AP2 0.488889 0.779221
43 BA3 0.488889 0.810811
44 3AM 0.488372 0.77027
45 KG4 0.483871 0.766234
46 50T 0.483871 0.776316
47 AP5 0.483516 0.810811
48 ADP 0.483516 0.786667
49 B4P 0.483516 0.810811
50 A3N 0.483146 0.828571
51 NWW 0.481481 0.80303
52 3UK 0.480392 0.789474
53 AR6 0.478723 0.786667
54 APR 0.478723 0.786667
55 AN2 0.478261 0.776316
56 AT4 0.478261 0.802632
57 GJV 0.477778 0.763158
58 S4M 0.477778 0.759494
59 5AD 0.474359 0.815385
60 ADV 0.473684 0.779221
61 RBY 0.473684 0.779221
62 AU1 0.473118 0.766234
63 A3P 0.472527 0.783784
64 MAO 0.472527 0.75
65 SXZ 0.471154 0.789474
66 ATF 0.469388 0.75641
67 SFG 0.468085 0.84058
68 ACP 0.468085 0.766234
69 HEJ 0.468085 0.786667
70 ATP 0.468085 0.786667
71 H1Q 0.468085 0.797297
72 5AS 0.467391 0.709302
73 QXP 0.465347 0.756098
74 8LH 0.464646 0.75641
75 V47 0.464646 0.852941
76 SRP 0.464646 0.75641
77 APC 0.463158 0.779221
78 AQP 0.463158 0.786667
79 5FA 0.463158 0.786667
80 PRX 0.463158 0.766234
81 ADP MG 0.462366 0.808219
82 ADP BEF 0.462366 0.808219
83 B5V 0.461538 0.779221
84 V2G 0.459184 0.728395
85 EEM 0.459184 0.766234
86 5AL 0.459184 0.776316
87 AD9 0.458333 0.766234
88 AGS 0.458333 0.792208
89 SA8 0.458333 0.786667
90 8PZ 0.457944 0.729412
91 MHZ 0.457447 0.75
92 00A 0.456311 0.759494
93 NEC 0.455556 0.785714
94 QA7 0.455446 0.746835
95 8LQ 0.455446 0.75641
96 SAI 0.453608 0.819444
97 G5A 0.453608 0.709302
98 Y3J 0.451219 0.791045
99 8QN 0.45098 0.776316
100 7D7 0.45 0.808824
101 SMM 0.45 0.759494
102 T99 0.44898 0.802632
103 TAT 0.44898 0.802632
104 ACQ 0.44898 0.766234
105 ANP 0.44898 0.766234
106 SAM 0.44898 0.789474
107 GAP 0.44898 0.766234
108 PAJ 0.446602 0.719512
109 52H 0.445545 0.709302
110 APC MG 0.443299 0.810811
111 ATP MG 0.443299 0.808219
112 ADP PO3 0.443299 0.808219
113 2AM 0.443182 0.76
114 KOY 0.442478 0.819444
115 AHX 0.442308 0.728395
116 53H 0.441176 0.709302
117 DAL AMP 0.441176 0.776316
118 A5A 0.44 0.73494
119 A3G 0.43956 0.816901
120 KY5 0.439252 0.833333
121 BEF ADP 0.438776 0.786667
122 QXG 0.438095 0.746988
123 OAD 0.438095 0.766234
124 9ZD 0.436893 0.7375
125 OZV 0.436893 0.786667
126 9ZA 0.436893 0.7375
127 25A 0.436893 0.810811
128 SSA 0.435644 0.709302
129 S7M 0.435644 0.789474
130 6YZ 0.435644 0.766234
131 9SN 0.435185 0.75
132 649 0.434783 0.715909
133 PR8 0.433962 0.731707
134 R2V 0.433962 0.756098
135 WAQ 0.433962 0.759494
136 4AD 0.432692 0.746835
137 AMO 0.432692 0.75641
138 7D5 0.431818 0.75
139 54H 0.431373 0.717647
140 VMS 0.431373 0.717647
141 HQG 0.431373 0.776316
142 B5M 0.431193 0.769231
143 F0P 0.431034 0.810811
144 PPS 0.43 0.731707
145 ME8 0.429907 0.722892
146 PTJ 0.429907 0.728395
147 3OD 0.429907 0.766234
148 1ZZ 0.429907 0.722892
149 U4Y 0.429825 0.847222
150 OZP 0.429825 0.810811
151 OVE 0.428571 0.776316
152 PAP 0.428571 0.773333
153 NVA LMS 0.428571 0.685393
154 B1U 0.427273 0.688889
155 8X1 0.427184 0.685393
156 MAP 0.427184 0.746835
157 KY2 0.427184 0.766234
158 TSB 0.427184 0.72619
159 5CA 0.427184 0.709302
160 A22 0.427184 0.8
161 NWQ 0.426966 0.779412
162 KB1 0.425926 0.8
163 ANP MG 0.425743 0.776316
164 VO4 ADP 0.425743 0.766234
165 ALF ADP 0.425743 0.746835
166 4YB 0.424779 0.712644
167 KXW 0.424779 0.810811
168 N5O 0.423913 0.777778
169 AMP DBH 0.423423 0.789474
170 5SV 0.423077 0.75
171 GEK 0.423077 0.821918
172 KY8 0.420561 0.810811
173 LAD 0.420561 0.740741
174 P5A 0.420561 0.696629
175 KL2 0.420455 0.733333
176 Q2V 0.420168 0.8
177 A3R 0.419048 0.759494
178 NSS 0.419048 0.709302
179 A1R 0.419048 0.759494
180 KYB 0.419048 0.766234
181 0UM 0.419048 0.776316
182 DSZ 0.419048 0.709302
183 ADQ 0.419048 0.789474
184 LSS 0.419048 0.693182
185 B5Y 0.418182 0.769231
186 BIS 0.416667 0.7375
187 A3S 0.416667 0.828571
188 TXA 0.416667 0.75641
189 NB8 0.416667 0.728395
190 9K8 0.416667 0.704545
191 JNT 0.415094 0.766234
192 62X 0.415094 0.7375
193 N5A 0.414894 0.774648
194 XAH 0.414414 0.722892
195 YSA 0.414414 0.729412
196 NVA 2AD 0.414141 0.773333
197 DQV 0.412281 0.8
198 3AD 0.411765 0.850746
199 9X8 0.411215 0.769231
200 K15 0.411215 0.75641
201 LEU LMS 0.411215 0.701149
202 4UV 0.410714 0.769231
203 K3E 0.410714 0.808219
204 A2P 0.410526 0.77027
205 TYM 0.410256 0.779221
206 LAQ 0.408696 0.7875
207 A3T 0.408163 0.84058
208 KAA 0.407407 0.704545
209 GSU 0.407407 0.709302
210 V3L 0.405941 0.786667
211 K3K 0.405405 0.819444
212 JB6 0.40367 0.805195
213 QQY 0.402174 0.76
214 K2H 0.401869 0.819444
215 KYE 0.401786 0.746835
216 K2W 0.401786 0.8
217 NAX 0.401709 0.731707
218 EU9 0.401709 0.756098
219 DND 0.401709 0.779221
220 D3Y 0.4 0.830986
221 MYR AMP 0.4 0.722892
222 25L 0.4 0.8
223 IOT 0.4 0.697674
224 TAD 0.4 0.7625
Similar Ligands (3D)
Ligand no: 1; Ligand: A5D; Similar ligands found: 1
No: Ligand Similarity coefficient
1 GMV 0.8572
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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