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 = 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: A5D; Similar ligands found: 204
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 ADN 0.581081 0.865672
9 XYA 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 AMP 0.535714 0.808219
17 A 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 A2D 0.5 0.810811
29 45A 0.5 0.786667
30 J7C 0.5 0.783784
31 ZAS 0.5 0.830986
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 8LE 0.489583 0.746835
37 M33 0.48913 0.776316
38 CA0 0.48913 0.766234
39 ADX 0.48913 0.753086
40 AP2 0.488889 0.779221
41 A12 0.488889 0.779221
42 BA3 0.488889 0.810811
43 3AM 0.488372 0.77027
44 KG4 0.483871 0.766234
45 50T 0.483871 0.776316
46 ADP 0.483516 0.786667
47 B4P 0.483516 0.810811
48 AP5 0.483516 0.810811
49 A3N 0.483146 0.828571
50 3UK 0.480392 0.789474
51 AR6 0.478723 0.786667
52 APR 0.478723 0.786667
53 AN2 0.478261 0.776316
54 AT4 0.478261 0.802632
55 GJV 0.477778 0.763158
56 S4M 0.477778 0.759494
57 5AD 0.474359 0.815385
58 RBY 0.473684 0.779221
59 ADV 0.473684 0.779221
60 AU1 0.473118 0.766234
61 A3P 0.472527 0.783784
62 MAO 0.472527 0.75
63 SXZ 0.471154 0.789474
64 ATF 0.469388 0.75641
65 ATP 0.468085 0.786667
66 H1Q 0.468085 0.797297
67 SFG 0.468085 0.84058
68 ACP 0.468085 0.766234
69 HEJ 0.468085 0.786667
70 5AS 0.467391 0.709302
71 8LH 0.464646 0.75641
72 SRP 0.464646 0.75641
73 AQP 0.463158 0.786667
74 5FA 0.463158 0.786667
75 PRX 0.463158 0.766234
76 APC 0.463158 0.779221
77 ADP MG 0.462366 0.808219
78 B5V 0.461538 0.779221
79 EEM 0.459184 0.766234
80 5AL 0.459184 0.776316
81 SAP 0.458333 0.792208
82 SA8 0.458333 0.786667
83 AD9 0.458333 0.766234
84 AGS 0.458333 0.792208
85 8PZ 0.457944 0.729412
86 MHZ 0.457447 0.75
87 00A 0.456311 0.759494
88 NEC 0.455556 0.785714
89 8LQ 0.455446 0.75641
90 G5A 0.453608 0.709302
91 SAI 0.453608 0.819444
92 Y3J 0.451219 0.791045
93 8QN 0.45098 0.776316
94 SMM 0.45 0.759494
95 7D7 0.45 0.808824
96 SAM 0.44898 0.789474
97 ACQ 0.44898 0.766234
98 ANP 0.44898 0.766234
99 TAT 0.44898 0.802632
100 GAP 0.44898 0.766234
101 T99 0.44898 0.802632
102 PAJ 0.446602 0.719512
103 52H 0.445545 0.709302
104 YAP 0.444444 0.769231
105 APC MG 0.443299 0.810811
106 ATP MG 0.443299 0.808219
107 ADP PO3 0.443299 0.808219
108 2AM 0.443182 0.76
109 KOY 0.442478 0.819444
110 AHX 0.442308 0.728395
111 53H 0.441176 0.709302
112 DAL AMP 0.441176 0.776316
113 A5A 0.44 0.73494
114 A3G 0.43956 0.816901
115 OAD 0.438095 0.766234
116 9ZA 0.436893 0.7375
117 9ZD 0.436893 0.7375
118 25A 0.436893 0.810811
119 OZV 0.436893 0.786667
120 6YZ 0.435644 0.766234
121 SSA 0.435644 0.709302
122 ADP VO4 0.435644 0.776316
123 S7M 0.435644 0.789474
124 VO4 ADP 0.435644 0.776316
125 9SN 0.435185 0.75
126 649 0.434783 0.715909
127 PR8 0.433962 0.731707
128 WAQ 0.433962 0.759494
129 4AD 0.432692 0.746835
130 AMO 0.432692 0.75641
131 7D5 0.431818 0.75
132 54H 0.431373 0.717647
133 HQG 0.431373 0.776316
134 VMS 0.431373 0.717647
135 B5M 0.431193 0.769231
136 F0P 0.431034 0.810811
137 PPS 0.43 0.731707
138 ME8 0.429907 0.722892
139 3OD 0.429907 0.766234
140 PTJ 0.429907 0.728395
141 1ZZ 0.429907 0.722892
142 OZP 0.429825 0.810811
143 NVA LMS 0.428571 0.685393
144 PAP 0.428571 0.773333
145 OVE 0.428571 0.776316
146 B1U 0.427273 0.688889
147 TSB 0.427184 0.72619
148 8X1 0.427184 0.685393
149 A22 0.427184 0.8
150 5CA 0.427184 0.709302
151 MAP 0.427184 0.746835
152 KB1 0.425926 0.8
153 ADP ALF 0.425743 0.746835
154 ALF ADP 0.425743 0.746835
155 4YB 0.424779 0.712644
156 LEU LMS 0.424528 0.685393
157 N5O 0.423913 0.777778
158 AMP DBH 0.423423 0.789474
159 5SV 0.423077 0.75
160 GEK 0.423077 0.821918
161 P5A 0.420561 0.696629
162 LAD 0.420561 0.740741
163 DSZ 0.419048 0.709302
164 NSS 0.419048 0.709302
165 LSS 0.419048 0.693182
166 ADQ 0.419048 0.789474
167 A3R 0.419048 0.759494
168 0UM 0.419048 0.776316
169 A1R 0.419048 0.759494
170 B5Y 0.418182 0.769231
171 9K8 0.416667 0.704545
172 BIS 0.416667 0.7375
173 A3S 0.416667 0.828571
174 TXA 0.416667 0.75641
175 NB8 0.416667 0.728395
176 62X 0.415094 0.7375
177 N5A 0.414894 0.774648
178 XAH 0.414414 0.722892
179 YSA 0.414414 0.729412
180 NVA 2AD 0.414141 0.773333
181 DQV 0.412281 0.8
182 3AD 0.411765 0.850746
183 9X8 0.411215 0.769231
184 K15 0.411215 0.75641
185 4UV 0.410714 0.769231
186 TYR AMP 0.410714 0.769231
187 A2P 0.410526 0.77027
188 TYM 0.410256 0.779221
189 LAQ 0.408696 0.7875
190 A3T 0.408163 0.84058
191 KAA 0.407407 0.704545
192 GSU 0.407407 0.709302
193 A A 0.407407 0.810811
194 V3L 0.405941 0.786667
195 JB6 0.40367 0.805195
196 QQY 0.402174 0.76
197 NAX 0.401709 0.731707
198 DND 0.401709 0.779221
199 NXX 0.401709 0.779221
200 MYR AMP 0.4 0.722892
201 TAD 0.4 0.7625
202 IOT 0.4 0.697674
203 25L 0.4 0.8
204 D3Y 0.4 0.830986
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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