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: 138
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 XYA 0.505882 0.763158
10 ADN 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 EP4 0.472527 0.725
20 SRA 0.46875 0.746988
21 M2T 0.467391 0.75
22 ATF 0.462264 0.697674
23 50T 0.460784 0.714286
24 ADP 0.46 0.722892
25 ABM 0.459184 0.722892
26 A2D 0.459184 0.743902
27 SON 0.455446 0.717647
28 GJV 0.454545 0.722892
29 6RE 0.453608 0.731707
30 AAT 0.45283 0.722892
31 M33 0.45098 0.714286
32 CA0 0.45098 0.705882
33 ADX 0.45098 0.696629
34 AP2 0.45 0.717647
35 A12 0.45 0.717647
36 BA3 0.45 0.743902
37 AOC 0.44898 0.74359
38 3UK 0.446429 0.72619
39 B4P 0.445545 0.743902
40 AP5 0.445545 0.743902
41 OOB 0.445455 0.73494
42 J7C 0.444444 0.719512
43 ZAS 0.443299 0.828947
44 AT4 0.441176 0.738095
45 AN2 0.441176 0.73494
46 S4M 0.44 0.701149
47 SXZ 0.438596 0.705882
48 DLL 0.4375 0.73494
49 AU1 0.436893 0.746988
50 A3P 0.435644 0.719512
51 SAI 0.433962 0.728395
52 3AM 0.43299 0.707317
53 ACP 0.432692 0.705882
54 ATP 0.432692 0.722892
55 SFG 0.432692 0.74359
56 HEJ 0.432692 0.722892
57 S8M 0.432432 0.797468
58 5AS 0.431373 0.677419
59 SRP 0.431193 0.697674
60 SMM 0.431193 0.701149
61 A3N 0.43 0.734177
62 GAP 0.429907 0.72619
63 SAM 0.429907 0.72619
64 PR8 0.429825 0.677778
65 B5V 0.429825 0.717647
66 PRX 0.428571 0.705882
67 AR6 0.428571 0.722892
68 5FA 0.428571 0.722892
69 APR 0.428571 0.722892
70 AQP 0.428571 0.722892
71 PAJ 0.428571 0.666667
72 APC 0.428571 0.717647
73 F0P 0.427419 0.722892
74 5AL 0.425926 0.714286
75 EEM 0.425926 0.705882
76 00A 0.424779 0.701149
77 SA8 0.424528 0.702381
78 AGS 0.424528 0.729412
79 RBY 0.424528 0.717647
80 SAP 0.424528 0.729412
81 AD9 0.424528 0.705882
82 ADV 0.424528 0.717647
83 ADP PO3 0.424528 0.7625
84 MAO 0.421569 0.752941
85 G5A 0.420561 0.677419
86 8QN 0.419643 0.714286
87 9SN 0.418803 0.693182
88 VO4 ADP 0.418182 0.73494
89 ADP VO4 0.418182 0.73494
90 P5A 0.417391 0.666667
91 ACQ 0.416667 0.705882
92 TAT 0.416667 0.738095
93 ANP 0.416667 0.746988
94 T99 0.416667 0.738095
95 5AD 0.41573 0.716216
96 B5Y 0.415254 0.709302
97 FA5 0.415254 0.717647
98 B5M 0.415254 0.709302
99 52H 0.414414 0.677419
100 FYA 0.413793 0.73494
101 3OD 0.413793 0.705882
102 AHX 0.412281 0.732558
103 NVA LMS 0.412281 0.673684
104 PAP 0.411215 0.710843
105 8X1 0.410714 0.65625
106 DAL AMP 0.410714 0.73494
107 53H 0.410714 0.677419
108 DQV 0.409836 0.73494
109 MHZ 0.409524 0.693182
110 ADP ALF 0.409091 0.709302
111 ALF ADP 0.409091 0.709302
112 A5A 0.409091 0.7
113 2AM 0.408163 0.698795
114 25A 0.40708 0.743902
115 9ZA 0.40708 0.701149
116 9ZD 0.40708 0.701149
117 GEK 0.40708 0.753086
118 A3G 0.405941 0.725
119 NEC 0.405941 0.696203
120 S7M 0.405405 0.72619
121 6YZ 0.405405 0.705882
122 SSA 0.405405 0.677419
123 A A 0.405172 0.765432
124 WAQ 0.405172 0.701149
125 AMO 0.403509 0.697674
126 ADQ 0.403509 0.72619
127 LSS 0.403509 0.663158
128 4AD 0.403509 0.709302
129 YAP 0.403361 0.709302
130 VMS 0.401786 0.684783
131 54H 0.401786 0.684783
132 BIS 0.401709 0.681818
133 ME8 0.401709 0.67033
134 9K8 0.401709 0.65625
135 PTJ 0.401709 0.674157
136 1ZZ 0.401709 0.67033
137 A3S 0.4 0.734177
138 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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