Receptor
PDB id Resolution Class Description Source Keywords
3IOD 1.75 Å EC: 6.3.2.1 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE SYNTHETASE AT 1.75 ANG RESOLUTION IN COMPLEX WITH 5'-DEOXY-N ITROBENZYL)DISULFANYL)-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
A6D A:302;
B:301;
Valid;
Valid;
none;
none;
Kd = 80 uM
450.492 C17 H18 N6 O5 S2 c1cc(...
EOH A:710;
A:711;
B:712;
Invalid;
Invalid;
Invalid;
none;
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: A6D; Similar ligands found: 161
No: Ligand ECFP6 Tc MDL keys Tc
1 A6D 1 1
2 A5D 0.696629 0.876712
3 DTA 0.646341 0.876712
4 MTA 0.545455 0.766234
5 3DH 0.533333 0.766234
6 5N5 0.511628 0.763158
7 DSH 0.510638 0.740741
8 XYA 0.505882 0.763158
9 ADN 0.505882 0.763158
10 RAB 0.505882 0.763158
11 5CD 0.505747 0.773333
12 5X8 0.50505 0.75641
13 SAH 0.490196 0.759494
14 LMS 0.489362 0.715909
15 AMP 0.489362 0.740741
16 A 0.489362 0.740741
17 A4D 0.488636 0.786667
18 A7D 0.484848 0.769231
19 B1U 0.473684 0.788889
20 EP4 0.472527 0.725
21 V47 0.471698 0.753247
22 SRA 0.46875 0.746988
23 AMP MG 0.46875 0.772152
24 M2T 0.467391 0.75
25 ATF 0.462264 0.697674
26 50T 0.460784 0.714286
27 ADP 0.46 0.722892
28 ABM 0.459184 0.722892
29 45A 0.459184 0.722892
30 A2D 0.459184 0.743902
31 SON 0.455446 0.717647
32 GJV 0.454545 0.722892
33 6RE 0.453608 0.731707
34 AAT 0.45283 0.722892
35 ADX 0.45098 0.696629
36 CA0 0.45098 0.705882
37 M33 0.45098 0.714286
38 AP2 0.45 0.717647
39 BA3 0.45 0.743902
40 A12 0.45 0.717647
41 AOC 0.44898 0.74359
42 KG4 0.446602 0.705882
43 3UK 0.446429 0.72619
44 B4P 0.445545 0.743902
45 AP5 0.445545 0.743902
46 OOB 0.445455 0.73494
47 J7C 0.444444 0.719512
48 ZAS 0.443299 0.828947
49 ADP MG 0.441176 0.7625
50 ADP BEF 0.441176 0.7625
51 AT4 0.441176 0.738095
52 AN2 0.441176 0.73494
53 S4M 0.44 0.701149
54 NWW 0.43956 0.706667
55 8LE 0.439252 0.689655
56 SXZ 0.438596 0.705882
57 APC MG 0.438095 0.765432
58 DLL 0.4375 0.73494
59 AU1 0.436893 0.746988
60 8LQ 0.436364 0.697674
61 A3P 0.435644 0.719512
62 SAI 0.433962 0.728395
63 3AM 0.43299 0.707317
64 ATP 0.432692 0.722892
65 ACP 0.432692 0.705882
66 SFG 0.432692 0.74359
67 H1Q 0.432692 0.753086
68 HEJ 0.432692 0.722892
69 QXP 0.432432 0.719101
70 S8M 0.432432 0.797468
71 5AS 0.431373 0.677419
72 SRP 0.431193 0.697674
73 SMM 0.431193 0.701149
74 A3N 0.43 0.734177
75 SAM 0.429907 0.72619
76 GAP 0.429907 0.72619
77 PR8 0.429825 0.677778
78 R2V 0.429825 0.719101
79 B5V 0.429825 0.717647
80 PRX 0.428571 0.705882
81 PAJ 0.428571 0.666667
82 AQP 0.428571 0.722892
83 APC 0.428571 0.717647
84 AR6 0.428571 0.722892
85 5FA 0.428571 0.722892
86 APR 0.428571 0.722892
87 F0P 0.427419 0.722892
88 KOY 0.42623 0.728395
89 OZP 0.42623 0.722892
90 5AL 0.425926 0.714286
91 EEM 0.425926 0.705882
92 V2G 0.425926 0.693182
93 00A 0.424779 0.701149
94 ATP MG 0.424528 0.7625
95 AD9 0.424528 0.705882
96 SA8 0.424528 0.702381
97 AGS 0.424528 0.729412
98 RBY 0.424528 0.717647
99 ADP PO3 0.424528 0.7625
100 ADV 0.424528 0.717647
101 EU9 0.422764 0.865854
102 MAO 0.421569 0.752941
103 QXG 0.421053 0.711111
104 G5A 0.420561 0.677419
105 BEF ADP 0.420561 0.743902
106 8QN 0.419643 0.714286
107 9SN 0.418803 0.693182
108 8LH 0.418182 0.697674
109 P5A 0.417391 0.666667
110 TAT 0.416667 0.738095
111 ANP 0.416667 0.746988
112 T99 0.416667 0.738095
113 ACQ 0.416667 0.705882
114 5AD 0.41573 0.716216
115 B5M 0.415254 0.709302
116 B5Y 0.415254 0.709302
117 FA5 0.415254 0.717647
118 U4Y 0.414634 0.753086
119 HQG 0.414414 0.714286
120 52H 0.414414 0.677419
121 3OD 0.413793 0.705882
122 FYA 0.413793 0.73494
123 NVA LMS 0.412281 0.673684
124 AHX 0.412281 0.732558
125 PAP 0.411215 0.710843
126 QA7 0.410714 0.689655
127 DAL AMP 0.410714 0.73494
128 53H 0.410714 0.677419
129 8X1 0.410714 0.65625
130 DQV 0.409836 0.73494
131 MHZ 0.409524 0.693182
132 VO4 ADP 0.409091 0.72619
133 A5A 0.409091 0.7
134 ANP MG 0.409091 0.777778
135 ALF ADP 0.409091 0.709302
136 LEU LMS 0.408696 0.706522
137 2AM 0.408163 0.698795
138 25A 0.40708 0.743902
139 9ZD 0.40708 0.701149
140 GEK 0.40708 0.753086
141 9ZA 0.40708 0.701149
142 OZV 0.40708 0.722892
143 A3G 0.405941 0.725
144 NEC 0.405941 0.696203
145 SSA 0.405405 0.677419
146 S7M 0.405405 0.72619
147 6YZ 0.405405 0.705882
148 WAQ 0.405172 0.701149
149 LSS 0.403509 0.663158
150 4AD 0.403509 0.709302
151 AMO 0.403509 0.697674
152 ADQ 0.403509 0.72619
153 VMS 0.401786 0.684783
154 54H 0.401786 0.684783
155 PTJ 0.401709 0.674157
156 9K8 0.401709 0.65625
157 BIS 0.401709 0.681818
158 ME8 0.401709 0.67033
159 1ZZ 0.401709 0.67033
160 A3S 0.4 0.734177
161 PPS 0.4 0.677778
Similar Ligands (3D)
Ligand no: 1; Ligand: A6D; 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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