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 = 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: A6D; Similar ligands found: 152
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 RAB 0.505882 0.763158
9 ADN 0.505882 0.763158
10 XYA 0.505882 0.763158
11 5CD 0.505747 0.773333
12 5X8 0.50505 0.75641
13 SAH 0.490196 0.759494
14 AMP 0.489362 0.740741
15 LMS 0.489362 0.715909
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 SRA 0.46875 0.746988
22 M2T 0.467391 0.75
23 ATF 0.462264 0.697674
24 50T 0.460784 0.714286
25 ADP 0.46 0.722892
26 A2D 0.459184 0.743902
27 45A 0.459184 0.722892
28 ABM 0.459184 0.722892
29 SON 0.455446 0.717647
30 GJV 0.454545 0.722892
31 6RE 0.453608 0.731707
32 AAT 0.45283 0.722892
33 ADX 0.45098 0.696629
34 CA0 0.45098 0.705882
35 M33 0.45098 0.714286
36 A12 0.45 0.717647
37 BA3 0.45 0.743902
38 AP2 0.45 0.717647
39 AOC 0.44898 0.74359
40 KG4 0.446602 0.705882
41 3UK 0.446429 0.72619
42 AP5 0.445545 0.743902
43 B4P 0.445545 0.743902
44 OOB 0.445455 0.73494
45 J7C 0.444444 0.719512
46 ZAS 0.443299 0.828947
47 AT4 0.441176 0.738095
48 ADP MG 0.441176 0.7625
49 AN2 0.441176 0.73494
50 S4M 0.44 0.701149
51 8LE 0.439252 0.689655
52 SXZ 0.438596 0.705882
53 APC MG 0.438095 0.765432
54 DLL 0.4375 0.73494
55 AU1 0.436893 0.746988
56 8LQ 0.436364 0.697674
57 A3P 0.435644 0.719512
58 SAI 0.433962 0.728395
59 3AM 0.43299 0.707317
60 ACP 0.432692 0.705882
61 HEJ 0.432692 0.722892
62 ATP 0.432692 0.722892
63 SFG 0.432692 0.74359
64 H1Q 0.432692 0.753086
65 S8M 0.432432 0.797468
66 5AS 0.431373 0.677419
67 SRP 0.431193 0.697674
68 SMM 0.431193 0.701149
69 A3N 0.43 0.734177
70 GAP 0.429907 0.72619
71 SAM 0.429907 0.72619
72 B5V 0.429825 0.717647
73 PR8 0.429825 0.677778
74 APR 0.428571 0.722892
75 AQP 0.428571 0.722892
76 5FA 0.428571 0.722892
77 AR6 0.428571 0.722892
78 APC 0.428571 0.717647
79 PAJ 0.428571 0.666667
80 PRX 0.428571 0.705882
81 F0P 0.427419 0.722892
82 OZP 0.42623 0.722892
83 KOY 0.42623 0.728395
84 5AL 0.425926 0.714286
85 EEM 0.425926 0.705882
86 00A 0.424779 0.701149
87 ATP MG 0.424528 0.7625
88 SAP 0.424528 0.729412
89 AD9 0.424528 0.705882
90 ADP PO3 0.424528 0.7625
91 RBY 0.424528 0.717647
92 ADV 0.424528 0.717647
93 SA8 0.424528 0.702381
94 AGS 0.424528 0.729412
95 MAO 0.421569 0.752941
96 G5A 0.420561 0.677419
97 8QN 0.419643 0.714286
98 9SN 0.418803 0.693182
99 8LH 0.418182 0.697674
100 VO4 ADP 0.418182 0.73494
101 ADP VO4 0.418182 0.73494
102 P5A 0.417391 0.666667
103 ACQ 0.416667 0.705882
104 TAT 0.416667 0.738095
105 T99 0.416667 0.738095
106 ANP 0.416667 0.746988
107 5AD 0.41573 0.716216
108 FA5 0.415254 0.717647
109 B5Y 0.415254 0.709302
110 B5M 0.415254 0.709302
111 HQG 0.414414 0.714286
112 52H 0.414414 0.677419
113 FYA 0.413793 0.73494
114 3OD 0.413793 0.705882
115 NVA LMS 0.412281 0.673684
116 AHX 0.412281 0.732558
117 PAP 0.411215 0.710843
118 DAL AMP 0.410714 0.73494
119 53H 0.410714 0.677419
120 8X1 0.410714 0.65625
121 DQV 0.409836 0.73494
122 MHZ 0.409524 0.693182
123 A5A 0.409091 0.7
124 ADP ALF 0.409091 0.709302
125 ALF ADP 0.409091 0.709302
126 2AM 0.408163 0.698795
127 9ZD 0.40708 0.701149
128 OZV 0.40708 0.722892
129 9ZA 0.40708 0.701149
130 GEK 0.40708 0.753086
131 25A 0.40708 0.743902
132 A3G 0.405941 0.725
133 NEC 0.405941 0.696203
134 6YZ 0.405405 0.705882
135 S7M 0.405405 0.72619
136 SSA 0.405405 0.677419
137 WAQ 0.405172 0.701149
138 A A 0.405172 0.765432
139 AMO 0.403509 0.697674
140 4AD 0.403509 0.709302
141 LSS 0.403509 0.663158
142 ADQ 0.403509 0.72619
143 YAP 0.403361 0.709302
144 54H 0.401786 0.684783
145 VMS 0.401786 0.684783
146 1ZZ 0.401709 0.67033
147 BIS 0.401709 0.681818
148 PTJ 0.401709 0.674157
149 9K8 0.401709 0.65625
150 ME8 0.401709 0.67033
151 A3S 0.4 0.734177
152 PPS 0.4 0.677778
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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